Hello,
I've tried to reproduce the problem on an Ubuntu-24.04 container, but
couldn't. Amber was able to build without problem (except for the need to
install the OS boost package).
Checking your log, I wonder if you have some python problem. Several
python/conda environment installations? On your cmake log file, you have
the following line:
> -- Found PythonLibs:
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/
> libpython3.12.so (Required is exact version "3.11.9")
So 3.12 or 3.11.9?
On my side, I have the following line:
> -- Found PythonLibs:
> /app/amber24_src/build/CMakeFiles/miniconda/install/lib/libpython3.12.so
> (found suitable exact version "3.12.7")
This makes better sense.
You may have a 3.11.9 python installation somewhere in your PATH for which
cmake gets confused (imho).
In your install log, I see version conflicts here:
> byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/FES.py to
> FES.cpython-311.pyc
>
> /home/andriy/amber24//miniconda/lib/python3.12/site-packages/conda_build/convert.py
Best,
Gerald.
On Sat, Nov 2, 2024 at 9:34 AM David A Case via AMBER <amber.ambermd.org>
wrote:
> On Fri, Oct 18, 2024, Andriy Kovalenko via AMBER wrote:
> >
> >At present, I have installed Ubuntu 24.04.1 LTS on my Dell Precision Tower
> >5810 desktop from scratch, and have now been installing Amber24 and
> >AmberTools24.
>
> Hi Andriy: sorry to be so slow in replying. I'm hoping that someone with
> access to Ubuntu 24.04 will be able to try to reproduce your problem. I
> have a request out for volunteers, but maybe someon reading this on the
> Amber mailing list will be able to chime in.
>
> ....dac
>
> >Running *./run_cmake* (please see attached) succeeded in part.
> >Running *make Install* (please see attached) ended up with:
> >
> > CMake Error at
> >/home/andriy/amber24_src/cmake/Replace-function.cmake:32 (file):
> > file failed to open for reading (No such file or directory):
> >
> >
>
> >/home/andriy/amber24//miniconda/lib/python3.12/site-packages/conda_build/convert.py
> > Call Stack (most recent call first):
> >
> >/home/andriy/amber24_src/cmake/FixCondaShebang/FixCondaShebang.cmake:48
> >(configuretime_file_replace)
> >
> >Searching in amberarchives produced little.
> >
> >Could you please advise how to resolve this issue?
> >
> >Sincerely,
> >
> >
> >Dr. Andriy Kovalenko
> >
> >Research Assistant
> >Department of Biological Sciences
> >University of Alberta
> >CW 405, Biological Sciences Bldg.
> >Edmonton, Alberta, Canada T6G 2E9
> >
> >Tel: 780-940-7477 (cell)
> >e-mail: andriy.kovalenko.ualberta.ca
>
> >andriy.andriy-Precision-Tower-5810:~/amber24_src/build$ ./run_cmake
> >--
> **************************************************************************
> >-- Starting configuration of Amber version 24.0.0...
> >-- CMake Version: 3.28.3
> >-- For how to use this build system, please read this wiki:
> >-- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
> >-- For a list of important CMake variables, check here:
> >-- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
> >--
> **************************************************************************
> >-- Amber source found, building AmberTools and Amber
> >-- Miniconda is installed in the build directory!
> >CMake Warning (dev) at cmake/PythonBuildConfig.cmake:13 (find_package):
> > Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs
> modules
> > are removed. Run "cmake --help-policy CMP0148" for policy details. Use
> > the cmake_policy command to set the policy and suppress this warning.
> >
> >Call Stack (most recent call first):
> > CMakeLists.txt:121 (include)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >-- Found PythonLibs:
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/
> libpython3.12.so
> >-- Found perl make: /usr/bin/make
> >-- Perl modules well be installed to AMBERHOME/lib/perl
> >-- Running updater...
> >-- >>> Preparing to apply updates... please wait.
> >-- >>> No new updates available for AmberTools 24
> >-- >>> No new updates available for Amber 24
> >-- Updater done. If you want to install updates, then set the
> APPLY_UPDATES variable to true.
> >-- Checking whether to use built-in libraries...
> >-- Unable to locate MKL_HOME for your system. To use MKL, set MKL_HOME
> to point to your MKL installation location.
> >CMake Warning (dev) at
> /usr/share/cmake-3.28/Modules/FindPackageHandleStandardArgs.cmake:438
> (message):
> > The package name passed to `find_package_handle_standard_args`
> (OpenMP_C)
> > does not match the name of the calling package (OpenMPFixed). This can
> > lead to problems in calling code that expects `find_package` result
> > variables (e.g., `_FOUND`) to follow a certain pattern.
> >Call Stack (most recent call first):
> > cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
> (find_package_handle_standard_args)
> > cmake/hanjianwei/FindMKL.cmake:194 (find_package)
> > cmake/3rdPartyTools.cmake:233 (find_package)
> > CMakeLists.txt:218 (include)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >-- Could NOT find OpenMP_C (missing: OpenMP_pthread_LIBRARY)
> >CMake Warning (dev) at
> /usr/share/cmake-3.28/Modules/FindPackageHandleStandardArgs.cmake:438
> (message):
> > The package name passed to `find_package_handle_standard_args`
> (OpenMP_CXX)
> > does not match the name of the calling package (OpenMPFixed). This can
> > lead to problems in calling code that expects `find_package` result
> > variables (e.g., `_FOUND`) to follow a certain pattern.
> >Call Stack (most recent call first):
> > cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
> (find_package_handle_standard_args)
> > cmake/hanjianwei/FindMKL.cmake:194 (find_package)
> > cmake/3rdPartyTools.cmake:233 (find_package)
> > CMakeLists.txt:218 (include)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >-- Could NOT find OpenMP_CXX (missing: OpenMP_pthread_LIBRARY)
> >CMake Warning (dev) at
> /usr/share/cmake-3.28/Modules/FindPackageHandleStandardArgs.cmake:438
> (message):
> > The package name passed to `find_package_handle_standard_args`
> > (OpenMP_Fortran) does not match the name of the calling package
> > (OpenMPFixed). This can lead to problems in calling code that expects
> > `find_package` result variables (e.g., `_FOUND`) to follow a certain
> > pattern.
> >Call Stack (most recent call first):
> > cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
> (find_package_handle_standard_args)
> > cmake/hanjianwei/FindMKL.cmake:194 (find_package)
> > cmake/3rdPartyTools.cmake:233 (find_package)
> > CMakeLists.txt:218 (include)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >-- Could NOT find OpenMP_Fortran (missing: OpenMP_pthread_LIBRARY)
> >-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY
> MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY
> OpenMP_C_FOUND MKL_WORKS MKL_FORTRAN_WORKS)
> >-- hints given to look for KMMD in DIR:
> >-- found KMMD?: KMMD_LIB-NOTFOUND
> >-- found INCLUDES?:
> >-- Did not find an external KMMD library, should be able to use bundled.
> If you have a custom version then set the path with -DKMMD_DIR (missing:
> KMMD_LIB)
> >-- Cannot search for FFTW Fortran headers because the serial headers were
> not found
> >-- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS
> FFTW_INCLUDES_SERIAL FFTW_FORTRAN_WORKS)
> >-- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 =
> NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 =
> NetCDF_LIBRARIES_F77-NOTFOUND)
> >-- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 =
> NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 =
> NetCDF_LIBRARIES_F90-NOTFOUND)
> >-- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES
> NetCDF_INCLUDES)
> >-- Could NOT find Protobuf (missing: Protobuf_LIBRARIES
> Protobuf_INCLUDE_DIR)
> >-- Could NOT find XBLAS (missing: XBLAS_LIBRARY XBLAS_C_WORKS
> XBLAS_FORTRAN_WORKS)
> >-- A library with BLAS API not found. Please specify library location.
> >-- LAPACK requires BLAS
> >-- A library with LAPACK API not found. Please specify library location.
> >-- The ARPACK library was not found. Please set ARPACK_LIBRARY to point
> to it. (missing: ARPACK_LIBRARY ARPACK_WORKS)
> >-- Could not find some or all of the five main APBS libraries. Please set
> APBS_GENERIC_LIB, APBS_ROUTINES_LIB,
> >APBS_PMGC_LIB, APBS_MG_LIB, APBS_MC_LIB, APBS_FEM_LIB, UMFPACK_LIB, and
> APBS_MALOC_LIB to point to the correct libraries (missing: APBS_API_LIB
> APBS_ROUTINES_LIB APBS_MG_LIB APBS_PMGC_LIB APBS_GENERIC_LIB APBS_FEM_LIB
> APBS_MC_LIB UMFPACK_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES)
> >-- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 AWT
> JVM)
> >-- Could NOT find PUPIL (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB
> PUPIL_TIME_LIB JNI_FOUND PUPIL_WORKS)
> >-- Could NOT find LIO (missing: LIO_G2G_LIBRARY LIO_AMBER_LIBRARY
> LIO_WORKS)
> >-- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY
> PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5")
> >-- Checking for perl module Chemistry::Mol
> >-- Checking for perl module Chemistry::Mol - failed
> >-- Failed to find Perl modules: Chemistry::Mol (missing:
> PERLMODULES_CHEMISTRY_MOL_MODULE)
> >-- Could NOT find MBX (missing: MBX_DIR)
> >-- Could not find MBX. To locate it, add its install dir to the prefix
> path.
> >-- Could NOT find tng_io (missing: tng_io_DIR)
> >-- Could not find tng_io. To locate it, add its install dir to the
> prefix path.
> >-- The following libraries were found on your system, but are not being
> used: boost
> >-- This is because the Amber devs have frequently seen broken installs of
> these libraries causing trouble.
> >-- To tell Amber to link to these libraries, you can select individual
> ones using -DFORCE_EXTERNAL_LIBS=<names>.
> >-- Alternatively, you can request that Amber link to all libraries it
> finds using -DTRUST_SYSTEM_LIBS=TRUE.
> >-- KMMD not added to 3RDPARTY_SUBDIRS :
> >-- : ucpp-1.3;fftw-3.3
> >-- Cannot find PLUMED. You will still be able to load it at runtime. If
> you want to link it at build time, set PLUMED_ROOT to where you installed
> it.
> >-- Generating amber source scripts
> >-- Configuring subdirs...
> >CMake Deprecation Warning at AmberTools/src/fftw-3.3/CMakeLists.txt:1
> (cmake_minimum_required):
> > Compatibility with CMake < 3.5 will be removed from a future version of
> > CMake.
> >
> > Update the VERSION argument <min> value or use a ...<max> suffix to tell
> > CMake that the project does not need compatibility with older versions.
> >
> >
> >-- FFTW: compiler supports stack alignment: TRUE
> >CMake Warning (dev) at AmberTools/src/netcdf-4.6.1/CMakeLists.txt:40
> (exec_program):
> > Policy CMP0153 is not set: The exec_program command should not be
> called.
> > Run "cmake --help-policy CMP0153" for policy details. Use the
> cmake_policy
> > command to set the policy and suppress this warning.
> >
> > Use execute_process() instead.
> >Call Stack (most recent call first):
> > AmberTools/src/netcdf-4.6.1/CMakeLists.txt:42 (getuname)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >CMake Warning (dev) at AmberTools/src/netcdf-4.6.1/CMakeLists.txt:40
> (exec_program):
> > Policy CMP0153 is not set: The exec_program command should not be
> called.
> > Run "cmake --help-policy CMP0153" for policy details. Use the
> cmake_policy
> > command to set the policy and suppress this warning.
> >
> > Use execute_process() instead.
> >Call Stack (most recent call first):
> > AmberTools/src/netcdf-4.6.1/CMakeLists.txt:43 (getuname)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >CMake Warning (dev) at AmberTools/src/netcdf-4.6.1/CMakeLists.txt:40
> (exec_program):
> > Policy CMP0153 is not set: The exec_program command should not be
> called.
> > Run "cmake --help-policy CMP0153" for policy details. Use the
> cmake_policy
> > command to set the policy and suppress this warning.
> >
> > Use execute_process() instead.
> >Call Stack (most recent call first):
> > AmberTools/src/netcdf-4.6.1/CMakeLists.txt:44 (getuname)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >-- Found bash: /usr/bin/bash
> >CMake Warning (dev) at
> AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:37 (exec_program):
> > Policy CMP0153 is not set: The exec_program command should not be
> called.
> > Run "cmake --help-policy CMP0153" for policy details. Use the
> cmake_policy
> > command to set the policy and suppress this warning.
> >
> > Use execute_process() instead.
> >Call Stack (most recent call first):
> > AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:39 (getuname)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >CMake Warning (dev) at
> AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:37 (exec_program):
> > Policy CMP0153 is not set: The exec_program command should not be
> called.
> > Run "cmake --help-policy CMP0153" for policy details. Use the
> cmake_policy
> > command to set the policy and suppress this warning.
> >
> > Use execute_process() instead.
> >Call Stack (most recent call first):
> > AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:40 (getuname)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >CMake Warning (dev) at
> AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:37 (exec_program):
> > Policy CMP0153 is not set: The exec_program command should not be
> called.
> > Run "cmake --help-policy CMP0153" for policy details. Use the
> cmake_policy
> > command to set the policy and suppress this warning.
> >
> > Use execute_process() instead.
> >Call Stack (most recent call first):
> > AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:41 (getuname)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >-- netcdf-fortran: Detected TS29113 support in Fortran compiler
> >CMake Deprecation Warning at AmberTools/src/nlopt/CMakeLists.txt:15
> (cmake_minimum_required):
> > Compatibility with CMake < 3.5 will be removed from a future version of
> > CMake.
> >
> > Update the VERSION argument <min> value or use a ...<max> suffix to tell
> > CMake that the project does not need compatibility with older versions.
> >
> >
> >-- NLopt version 2.7.1
> >CMake Warning (dev) at AmberTools/src/nlopt/CMakeLists.txt:314
> (find_package):
> > Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs
> modules
> > are removed. Run "cmake --help-policy CMP0148" for policy details. Use
> > the cmake_policy command to set the policy and suppress this warning.
> >
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >CMake Warning (dev) at AmberTools/src/nlopt/CMakeLists.txt:315
> (find_package):
> > Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs
> modules
> > are removed. Run "cmake --help-policy CMP0148" for policy details. Use
> > the cmake_policy command to set the policy and suppress this warning.
> >
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >-- Found PythonLibs:
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/
> libpython3.12.so (Required is exact version "3.11.9")
> >CMake Warning (dev) at AmberTools/src/nlopt/cmake/FindNumPy.cmake:45
> (find_package):
> > Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs
> modules
> > are removed. Run "cmake --help-policy CMP0148" for policy details. Use
> > the cmake_policy command to set the policy and suppress this warning.
> >
> >Call Stack (most recent call first):
> > AmberTools/src/nlopt/CMakeLists.txt:316 (find_package)
> >This warning is for project developers. Use -Wno-dev to suppress it.
> >
> >-- Could NOT find Guile (missing: GUILE_EXECUTABLE GUILE_ROOT_DIR
> GUILE_INCLUDE_DIRS GUILE_LIBRARIES)
> >-- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR)
> >-- Could NOT find Octave (missing: OCTAVE_EXECUTABLE OCTAVE_ROOT_DIR
> OCTAVE_INCLUDE_DIRS OCTAVE_LIBRARIES)
> >-- Could NOT find Matlab (missing: Matlab_INCLUDE_DIRS Matlab_MEX_LIBRARY
> Matlab_MEX_EXTENSION Matlab_ROOT_DIR Matlab_MX_LIBRARY MX_LIBRARY
> MAIN_PROGRAM) (found version "NOTFOUND")
> >CMake Warning at /usr/share/cmake-3.28/Modules/CPack.cmake:507 (message):
> > CPack.cmake has already been included!!
> >Call Stack (most recent call first):
> > AmberTools/src/nlopt/CMakeLists.txt:368 (include)
> >
> >
> >-- Reticulating splines...
> >CMake Deprecation Warning at AmberTools/src/cpptraj/CMakeLists.txt:1
> (cmake_minimum_required):
> > Compatibility with CMake < 3.5 will be removed from a future version of
> > CMake.
> >
> > Update the VERSION argument <min> value or use a ...<max> suffix to tell
> > CMake that the project does not need compatibility with older versions.
> >
> >
> >-- Found C++11 support: cxx_std_11
> >CMake Deprecation Warning at AmberTools/src/cphstats/CMakeLists.txt:3
> (cmake_minimum_required):
> > Compatibility with CMake < 3.5 will be removed from a future version of
> > CMake.
> >
> > Update the VERSION argument <min> value or use a ...<max> suffix to tell
> > CMake that the project does not need compatibility with older versions.
> >
> >
> >CMake Warning at src/pmemd/src/xray/CMakeLists.txt:25 (message):
> > PMEMD_XRAY_CPU_FFT_BACKEND=NONE disables xray functionality of `pmemd`
> > executable
> >
> >
> >-- KMMD_LIB: kmmd
> >If you can't see the following build report, then you need to turn off
> COLOR_CMAKE_MESSAGES
> >--
> **************************************************************************
> >-- Build Report
> >-- Compiler Flags:
> >-- C No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas
> -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -O0
> >-- C Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas
> -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -O3 -mtune=native
> >--
> >-- CXX No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas
> -Wno-unused-local-typedefs -Wno-unused-variable
> -Wno-unused-but-set-variable -O0
> >-- CXX Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas
> -Wno-unused-local-typedefs -Wno-unused-variable
> -Wno-unused-but-set-variable -O3 -mtune=native
> >--
> >-- Fortran No-Opt: -Wall -Wno-tabs -Wno-unused-function
> -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable
> -fallow-argument-mismatch -fno-inline-arg-packing -O0
> >-- Fortran Optimized: -Wall -Wno-tabs -Wno-unused-function
> -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable
> -fallow-argument-mismatch -fno-inline-arg-packing -O3 -mtune=native
> >--
> >-- 3rd Party Libraries
> >-- ---building bundled:
> -----------------------------------------------------
> >-- blas - for fundamental linear algebra calculations
> >-- lapack - for fundamental linear algebra calculations
> >-- arpack - for fundamental linear algebra calculations
> >-- ucpp - used as a preprocessor for the NAB compiler
> >-- netcdf - for creating trajectory data files
> >-- netcdf-fortran - for creating trajectory data files from Fortran
> >-- fftw - used to do Fourier transforms very quickly
> >-- xblas - used for high-precision linear algebra calculations
> >-- boost - C++ support library
> >-- kmmd - Machine-learning molecular dynamics
> >-- tng_io - enables GROMACS tng trajectory input in cpptraj
> >-- nlopt - used to perform nonlinear optimizations
> >-- perlmol - chemistry library used by FEW
> >-- ---using installed:
> ------------------------------------------------------
> >-- readline - enables an interactive terminal in cpptraj
> >-- zlib - for various compression and decompression tasks
> >-- libbz2 - for bzip2 compression in cpptraj
> >-- libm - for fundamental math routines if they are not contained in the
> C library
> >-- ---disabled: ------------------------------------------------
> >-- c9x-complex - used as a support library on systems that do not have
> C99 complex.h support
> >-- protobuf - protocol buffers library, used for communication with
> external software in QM/MM
> >-- lio - used by Sander to run certain QM routines on the GPU
> >-- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver
> >-- pupil - used by Sander as an alternate user interface
> >-- plumed - used as an alternate MD backend for Sander
> >-- mkl - alternate implementation of lapack and blas that is tuned for
> speed
> >-- mbx - computes energies and forces for pmemd with the MB-pol model
> >-- libtorch - enables libtorch C++ library for tensor computation and
> dynamic neural networks
> >
> >-- Features:
> >-- MPI: OFF
> >-- MVAPICH2-GDR for GPU-GPU comm.: OFF
> >-- OpenMP: OFF
> >-- CUDA: OFF
> >-- Build Shared Libraries: ON
> >-- Build GUI Interfaces: OFF
> >-- Build Python Programs: ON
> >-- -Python Interpreter: Internal Miniconda (version 3.11)
> >-- Build Perl Programs: ON
> >-- Build configuration: RELEASE
> >-- Target Processor: x86_64
> >-- Build Documentation: ON
> >-- Sander Variants: normal LES API LES-API
> >-- Install location: /home/andriy/amber24/
> >-- Installation of Tests: ON
> >
> >-- Compilers:
> >-- C: GNU 13.2.0 (/usr/bin/gcc)
> >-- CXX: GNU 13.2.0 (/usr/bin/g++)
> >-- Fortran: GNU 13.2.0 (/usr/bin/gfortran)
> >
> >-- Building Tools:
> >-- addles ambpdb antechamber cew cifparse cphstats cpptraj emil etc
> fe-toolkit few gbnsr6 gem.pmemd kmmd leap lib mdgx mm_pbsa mmpbsa_py moft
> nabc ndiff-2.00 nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit
> parmed pbsa pdb4amber pmemd pymsmt pysander pytraj quick reduce rism sander
> saxs sebomd sff sqm xray xtalutil
> >
> >-- NOT Building Tools:
> >-- tcpb-cpp - BUILD_TCPB is not enabled
> >-- tcpb-cpp/pytcpb - BUILD_TCPB is not enabled
> >-- reaxff_puremd - BUILD_REAXFF_PUREMD is not enabled
> >-- gpu_utils - Requires CUDA
> >--
> **************************************************************************
> >-- Environment resource files are provided to set the proper environment
> >-- variables to use AMBER and AmberTools. This is required to run any
> Python
> >-- programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
> >--
> >-- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
> >-- /home/andriy/amber24//amber.sh file in your shell. Consider adding the
> line
> >-- test -f /home/andriy/amber24//amber.sh && source
> /home/andriy/amber24//amber.sh
> >-- to your startup file (e.g., ~/.bashrc)
> >--
> >-- If you use a C shell (e.g., csh, tcsh), source the
> >-- /home/andriy/amber24//amber.csh file in your shell. Consider adding
> the line
> >-- test -f /home/andriy/amber24//amber.csh && source
> /home/andriy/amber24//amber.csh
> >-- to your startup file (e.g., ~/.cshrc)
> >--
> >-- Amber will be installed to /home/andriy/amber24/
> >-- Configuring done (5.9s)
> >-- Generating done (0.8s)
> >-- Build files have been written to: /home/andriy/amber24_src/build
> >
> >If errors are reported, search for 'CMake Error' in the cmake.log file.
> >
> >If the cmake build report looks OK, you should now do the following:
> >
> > make install
> > source /home/andriy/amber24/amber.sh
> >
> >Consider adding the last line to your login startup script, e.g. ~/.bashrc
> >
>
> >andriy.andriy-Precision-Tower-5810:~/amber24_src/build$ make install
> >[ 0%] Built target ucpp
> >[ 0%] Built target simd_support
> >[ 2%] Built target fftw_api
> >[ 3%] Built target dft
> >[ 3%] Built target dft_scalar
> >[ 4%] Built target dft_scalar_codelets
> >[ 8%] Built target dft_sse2_codelets
> >[ 8%] Built target rdft
> >[ 8%] Built target rdft_scalar
> >[ 10%] Built target rdft_scalar_r2cb
> >[ 12%] Built target rdft_scalar_r2cf
> >[ 12%] Built target rdft_scalar_r2r
> >[ 13%] Built target rdft_sse2_codelets
> >[ 14%] Built target fftw_kernel
> >[ 14%] Built target reodft
> >[ 14%] Built target fftw
> >[ 15%] Built target libfftw_bench
> >[ 15%] Built target fftw_benchmark_common_obj
> >[ 15%] Built target fftw_benchmark
> >[ 15%] Built target fftw_wisdom
> >[ 15%] Built target dispatch
> >[ 16%] Built target netcdf3
> >[ 16%] Built target netcdf
> >[ 16%] Built target ncgen
> >[ 16%] Built target ncgen3
> >[ 17%] Built target ncdump
> >[ 17%] Built target nccopy
> >[ 17%] Built target netcdff
> >[ 17%] Built target xblas_build
> >[ 19%] Built target blas
> >[ 25%] Built target lapack
> >[ 26%] Built target arpack
> >[ 26%] Built target PerlMol
> >[ 26%] Built target boost_build
> >[ 26%] Built target tng_io
> >[ 26%] Built target generate-cpp
> >[ 26%] Built target generate-fortran
> >[ 27%] Built target nlopt
> >[ 27%] Built target amber_common
> >[ 28%] Built target rism
> >[ 28%] Built target sff_rism_interface
> >[ 28%] Built target sff_lex
> >[ 28%] Built target dsarpack_obj
> >[ 28%] Built target sff
> >[ 29%] Built target gbnsr6
> >[ 29%] Built target cifparse
> >[ 30%] Built target addles
> >[ 30%] Built target libcew
> >[ 31%] Built target sqm_common
> >[ 31%] Built target libsqm
> >[ 32%] Built target libpbsa
> >[ 32%] Built target sff_fortran
> >[ 32%] Built target sander_rism_interface
> >[ 36%] Built target xc
> >[ 36%] Built target octree
> >[ 39%] Built target libquick
> >[ 44%] Built target sander_base_obj
> >[ 46%] Built target sebomd
> >[ 46%] Built target emil
> >[ 46%] Built target kmmd
> >[ 46%] Built target pbsa_sander
> >[ 46%] Built target sander
> >[ 51%] Built target sander.LES
> >[ 51%] Built target ambmask
> >[ 56%] Built target libsander
> >[ 61%] Built target libsanderles
> >[ 61%] Built target makeDIST_RST
> >[ 61%] Built target makeANG_RST
> >[ 61%] Built target nef_to_RST
> >[ 63%] Built target nmode
> >[ 63%] Built target antechamber_eprintf_obj
> >[ 63%] Built target am1bcc
> >[ 63%] Built target atomtype
> >[ 63%] Built target espgen
> >[ 63%] Built target parmcal
> >[ 63%] Built target parmchk2
> >[ 63%] Built target prepgen
> >[ 63%] Built target residuegen
> >[ 63%] Built target respgen
> >[ 63%] Built target match
> >[ 64%] Built target match_atomname
> >[ 64%] Built target antechamber
> >[ 64%] Built target bondtype
> >[ 64%] Built target test-penalties
> >[ 64%] Built target test-int-part
> >[ 65%] Built target test-combination
> >[ 66%] Built target sqm
> >[ 67%] Built target pdb++
> >[ 67%] Built target toolclasses
> >[ 67%] Built target reduce
> >[ 67%] Built target ndiff
> >[ 69%] Built target gem.pmemd
> >[ 69%] Built target add_pdb
> >[ 69%] Built target add_xray
> >[ 79%] Built target cpptraj_common_obj
> >[ 79%] Built target xdrfile
> >[ 80%] Built target cpptraj
> >[ 80%] Built target libcpptraj
> >[ 81%] Built target cpptraj_core
> >[ 81%] Built target cpptraj_file
> >[ 81%] Built target cpptraj_traj
> >[ 82%] Built target cpptraj_parm
> >[ 82%] Built target ambpdb
> >[ 84%] Built target pbsa
> >[ 84%] Built target simplepbsa
> >[ 84%] Built target hcp_getpdb
> >[ 84%] Built target rism3d.snglpnt
> >[ 84%] Built target rism1d
> >[ 84%] Built target elsize
> >[ 85%] Built target resp
> >[ 85%] Built target gwh
> >[ 85%] Built target tinker_to_amber
> >[ 86%] Built target mdgx_common_obj
> >[ 86%] Built target mdgx
> >[ 86%] Built target libmdgx
> >[ 86%] Built target Xtal
> >[ 86%] Built target AddToBox
> >[ 86%] Built target ChBox
> >[ 86%] Built target PropPDB
> >[ 86%] Built target UnitCell
> >[ 86%] Built target saxs_common_obj
> >[ 86%] Built target saxs_rism
> >[ 86%] Built target saxs_md
> >[ 86%] Built target libsaxs_rism
> >[ 86%] Built target libsaxs_md
> >[ 86%] Built target make_crd_hg
> >[ 86%] Built target nabc
> >[ 86%] Built target mm_pbsa_nabnmode
> >[ 87%] Built target paramfit
> >[ 87%] Built target draw_membrane2
> >[ 87%] Built target cphstats
> >[ 87%] Built target cestats
> >[ 88%] Built target quick
> >[ 88%] Built target test-api
> >[ 88%] Built target nfe-umbrella-slice
> >[ 88%] Built target leap_common_obj
> >[ 88%] Built target leap_general_obj
> >[ 89%] Built target leap_hierarchy_obj
> >[ 90%] Built target utilMakeHelp
> >[ 90%] Built target leap_leap_obj
> >[ 90%] Built target leap_terminal_obj
> >[ 90%] Built target teLeap
> >[ 90%] Built target mmpbsa_py_energy
> >[ 90%] Built target mmpbsa_py_nabnmode
> >[ 90%] Building pysander native library
> >Copying sander extension source to sanderles...
> >running build
> >running build_py
> >copying sanderles/__init__.py ->
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles
> >running build_ext
> >building 'sanderles.pysander' extension
> >gcc -pthread -B
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat
> -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC
> -O2 -isystem
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC
> -DLES -I/home/andriy/amber24_src/AmberTools/src/include
> -I/home/andriy/amber24_src/AmberTools/src/sander
> -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11
> -c sanderles/src/pysandermodule.c -o
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o
> >In file included from sanderles/src/pysandermodule.c:16:
> >/home/andriy/amber24_src/AmberTools/src/sander/sander.h: In function
> ‘pysander_setup’:
> >/home/andriy/amber24_src/AmberTools/src/sander/sander.h:342:5: warning:
> ‘__builtin_strncpy’ specified bound 256 equals destination size
> [-Wstringop-truncation]
> > 342 | strncpy(prmtop, prmname, __MAX_FN_LEN);
> > | ^
> >gcc -pthread -B
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat
> -shared
> -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o
> -L/home/andriy/amber24_src/build/AmberTools/src/sander
> -L/home/andriy/amber24_src/build/AmberTools/src/sander -lsanderles -o
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/
> pysander.cpython-311-x86_64-linux-gnu.so
> >[ 90%] Built target pysander
> >[ 90%] Building pytraj native library
> >sys.argv ['setup.py', 'build', '-b',
> '/home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build',
> '--disable-openmp']
> >Original compiler envs
> >CXX = /usr/bin/g++
> >CC = /usr/bin/gcc
> >COMPILER =
> >use_pip = False, cpptraj_home =
> >compile_c_extension = True
> >2.0.6
> >use_prebuilt_cythonized_files = False
> >pytraj is inside AMBERHOME
> >using environment: CC=/usr/bin/gcc, CXX=/usr/bin/g++
> >using CC=/usr/bin/gcc, CXX=/usr/bin/g++
> >Final compiler envs
> >CXX = /usr/bin/g++
> >CC = /usr/bin/gcc
> >COMPILER =
> >install = True
> >set rpath to /home/andriy/amber24_src/build/AmberTools/src/cpptraj/src
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/dist.py:476:
> SetuptoolsDeprecationWarning: Invalid dash-separated options
> >!!
> >
> >
> ********************************************************************************
> > Usage of dash-separated 'description-file' will not be supported
> in future
> > versions. Please use the underscore name 'description_file'
> instead.
> >
> > This deprecation is overdue, please update your project and
> remove deprecated
> > calls to avoid build errors in the future.
> >
> > See
> https://setuptools.pypa.io/en/latest/userguide/declarative_config.html
> for details.
> >
> ********************************************************************************
> >
> >!!
> > opt = self.warn_dash_deprecation(opt, section)
> >running build
> >running build_py
> >copying pytraj/version.py ->
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj
> >running build_ext
> >[ 90%] Built target pytraj
> >[ 90%] Built target memembed
> >[ 91%] Built target packmol
> >[ 91%] Built target immers
> >[ 91%] Built target metatwist
> >[ 92%] Built target edgembar
> >[ 93%] Built target ndfes
> >[ 93%] Built target ndfes-path
> >[ 93%] Built target pmemd_xray_contracts
> >[ 94%] Built target xray_fft_interface
> >[ 94%] Built target pmemd_xray_cpu
> >[ 97%] Built target pmemd
> >[100%] Built target pmemd.decomp
> >Install the project...
> >-- Install configuration: "RELEASE"
> >-- Installing: /home/andriy/amber24/miniconda/bin/xzmore
> >-- Installing: /home/andriy/amber24/miniconda/bin/ipython
> >-- Installing: /home/andriy/amber24/miniconda/bin/mrcfile-validate
> >-- Installing: /home/andriy/amber24/miniconda/bin/xzgrep
> >-- Installing: /home/andriy/amber24/miniconda/bin/pyftsubset
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter
> >-- Installing: /home/andriy/amber24/miniconda/bin/icu-config
> >-- Installing: /home/andriy/amber24/miniconda/bin/pyftmerge
> >-- Installing: /home/andriy/amber24/miniconda/bin/pdb2pqr
> >-- Installing: /home/andriy/amber24/miniconda/bin/send2trash
> >-- Installing: /home/andriy/amber24/miniconda/bin/deactivate
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-env
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-skeleton
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-debug
> >-- Installing: /home/andriy/amber24/miniconda/bin/jlpm
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-events
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-dejavu
> >-- Installing: /home/andriy/amber24/miniconda/bin/2to3-3.11
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-inspect
> >-- Installing: /home/andriy/amber24/miniconda/bin/idle3.11
> >-- Installing: /home/andriy/amber24/miniconda/bin/xzdiff
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-run
> >-- Installing: /home/andriy/amber24/miniconda/bin/httpx
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-kernelspec
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-migrate
> >-- Installing: /home/andriy/amber24/miniconda/bin/cygdb
> >-- Installing: /home/andriy/amber24/miniconda/bin/normalizer
> >-- Installing: /home/andriy/amber24/miniconda/bin/mrcfile-header
> >-- Installing: /home/andriy/amber24/miniconda/bin/ipython3
> >-- Installing: /home/andriy/amber24/miniconda/bin/wsdump
> >-- Installing: /home/andriy/amber24/miniconda/bin/pydoc3.11
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-content-trust
> >-- Installing: /home/andriy/amber24/miniconda/bin/pyjson5
> >-- Installing: /home/andriy/amber24/miniconda/bin/ncursesw6-config
> >-- Installing: /home/andriy/amber24/miniconda/bin/distro
> >-- Installing: /home/andriy/amber24/miniconda/bin/f2py
> >-- Installing: /home/andriy/amber24/miniconda/bin/activate
> >-- Installing: /home/andriy/amber24/miniconda/bin/c_rehash
> >-- Installing: /home/andriy/amber24/miniconda/bin/archspec
> >-- Installing: /home/andriy/amber24/miniconda/bin/sqlite3_analyzer
> >-- Installing: /home/andriy/amber24/miniconda/bin/cython
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-trust
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-develop
> >-- Installing: /home/andriy/amber24/miniconda/bin/jsonpatch
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-nbconvert
> >-- Installing: /home/andriy/amber24/miniconda/bin/fonttools
> >-- Installing: /home/andriy/amber24/miniconda/bin/propka3
> >-- Installing: /home/andriy/amber24/miniconda/bin/pcre2-config
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-server
> >-- Installing: /home/andriy/amber24/miniconda/bin/wheel
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-build
> >-- Installing: /home/andriy/amber24/miniconda/bin/compile_et
> >-- Installing: /home/andriy/amber24/miniconda/bin/dx2cube
> >-- Installing: /home/andriy/amber24/miniconda/bin/curl-config
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-execute
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-labhub
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-troubleshoot
> >-- Installing: /home/andriy/amber24/miniconda/bin/python3.11-config
> >-- Installing: /home/andriy/amber24/miniconda/bin/pkginfo
> >-- Installing: /home/andriy/amber24/miniconda/bin/pdb2pqr30
> >-- Installing: /home/andriy/amber24/miniconda/bin/pygmentize
> >-- Installing: /home/andriy/amber24/miniconda/bin/jsondiff
> >-- Installing: /home/andriy/amber24/miniconda/bin/pybabel
> >-- Installing: /home/andriy/amber24/miniconda/bin/jsonpointer
> >-- Installing: /home/andriy/amber24/miniconda/bin/xml2-config
> >-- Installing: /home/andriy/amber24/miniconda/bin/zstdless
> >-- Installing: /home/andriy/amber24/miniconda/bin/pip3
> >-- Installing: /home/andriy/amber24/miniconda/bin/pytest
> >-- Installing: /home/andriy/amber24/miniconda/bin/pip3.11
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-labextension
> >-- Installing: /home/andriy/amber24/miniconda/bin/bzdiff
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-lab
> >-- Installing: /home/andriy/amber24/miniconda/bin/ttx
> >-- Installing: /home/andriy/amber24/miniconda/bin/bzgrep
> >-- Installing: /home/andriy/amber24/miniconda/bin/krb5-config
> >-- Installing: /home/andriy/amber24/miniconda/bin/zstdgrep
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda
> >-- Installing: /home/andriy/amber24/miniconda/bin/psize
> >-- Installing: /home/andriy/amber24/miniconda/bin/cythonize
> >-- Installing: /home/andriy/amber24/miniconda/bin/cph
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-convert
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-render
> >-- Installing: /home/andriy/amber24/miniconda/bin/tqdm
> >-- Installing: /home/andriy/amber24/miniconda/bin/xzless
> >-- Installing: /home/andriy/amber24/miniconda/bin/jsonschema
> >-- Installing: /home/andriy/amber24/miniconda/bin/pip
> >-- Installing: /home/andriy/amber24/miniconda/bin/f90nml
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-kernel
> >-- Installing: /home/andriy/amber24/miniconda/bin/py.test
> >-- Installing: /home/andriy/amber24/miniconda/bin/conda-metapackage
> >-- Installing: /home/andriy/amber24/miniconda/bin/chardetect
> >-- Installing: /home/andriy/amber24/miniconda/bin/k5srvutil
> >-- Installing: /home/andriy/amber24/miniconda/bin/inputgen
> >-- Installing: /home/andriy/amber24/miniconda/bin/bzmore
> >-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-notebook
> >-- Installing:
> /home/andriy/amber24/miniconda/share/jupyter/kernels/python3/kernel.json
> >-- Installing: /home/andriy/amber24/bin/fftw-wisdom-to-conf
> >-- Installing: /home/andriy/amber24/bin/nc-config
> >-- Installing: /home/andriy/amber24/bin/nf-config
> >-- Installing: /home/andriy/amber24/bin/senergy
> >-- Installing: /home/andriy/amber24/bin/sviol
> >-- Installing: /home/andriy/amber24/bin/sviol2
> >-- Installing: /home/andriy/amber24/bin/makeCHIR_RST
> >-- Installing: /home/andriy/amber24/bin/makeCSA_RST.na
> >-- Installing: /home/andriy/amber24/bin/makeRIGID_RST
> >-- Installing: /home/andriy/amber24/bin/makeDIP_RST.dna
> >-- Installing: /home/andriy/amber24/bin/makeDIP_RST.protein
> >-- Installing: /home/andriy/amber24/bin/am1bcc
> >-- Installing: /home/andriy/amber24/bin/atomtype
> >-- Installing: /home/andriy/amber24/bin/espgen
> >-- Installing: /home/andriy/amber24/bin/parmcal
> >-- Installing: /home/andriy/amber24/bin/parmchk2
> >-- Installing: /home/andriy/amber24/bin/prepgen
> >-- Installing: /home/andriy/amber24/bin/residuegen
> >-- Installing: /home/andriy/amber24/bin/respgen
> >-- Installing: /home/andriy/amber24/bin/match
> >-- Installing: /home/andriy/amber24/bin/match_atomname
> >-- Installing: /home/andriy/amber24/bin/antechamber
> >-- Installing: /home/andriy/amber24/bin/bondtype
> >-- Installing: /home/andriy/amber24/bin/reduce
> >-- Installing: /home/andriy/amber24/bin/XrayPrep
> >-- Installing: /home/andriy/amber24/bin/sgldinfo.sh
> >-- Installing: /home/andriy/amber24/bin/sgldwt.sh
> >-- Installing: /home/andriy/amber24/bin/process_mdout.perl
> >-- Installing: /home/andriy/amber24/bin/process_minout.perl
> >-- Installing: /home/andriy/amber24/bin/mdout2pymbar.pl
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running build
> >running build_py
> >running build_scripts
> >running install_lib
> >copying build/lib/pyrespgen/constant.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen
> >copying build/lib/pyrespgen/prepin.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen
> >copying build/lib/pyrespgen/zmatrix.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen
> >copying build/lib/pyrespgen/constant_radii.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen
> >copying build/lib/mdoutanalyzer/windows.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
> >copying build/lib/mdoutanalyzer/dataset.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
> >copying build/lib/mdoutanalyzer/constants.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
> >copying build/lib/mdoutanalyzer/toplevel_app.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
> >copying build/lib/mdoutanalyzer/menus.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
> >copying build/lib/mdoutanalyzer/graphproperties.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
> >copying build/lib/mdoutanalyzer/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
> >copying build/lib/mdoutanalyzer/mdout.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
> >copying build/lib/mdoutanalyzer/widgets.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/constant.py to
> constant.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/prepin.py to
> prepin.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/zmatrix.py to
> zmatrix.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/constant_radii.py
> to constant_radii.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/windows.py
> to windows.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/dataset.py
> to dataset.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/constants.py
> to constants.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/toplevel_app.py
> to toplevel_app.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/menus.py
> to menus.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/graphproperties.py
> to graphproperties.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/mdout.py
> to mdout.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/widgets.py
> to widgets.cpython-311.pyc
> >running install_egg_info
> >running egg_info
> >writing AmberUtils.egg-info/PKG-INFO
> >writing dependency_links to AmberUtils.egg-info/dependency_links.txt
> >writing top-level names to AmberUtils.egg-info/top_level.txt
> >reading manifest file 'AmberUtils.egg-info/SOURCES.txt'
> >writing manifest file 'AmberUtils.egg-info/SOURCES.txt'
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/AmberUtils-21.0-py3.11.egg-info'
> (and everything under it)
> >Copying AmberUtils.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/AmberUtils-21.0-py3.11.egg-info
> >running install_scripts
> >copying build/scripts-3.11/fitpkaeo.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/mdout_analyzer.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/cpeinutil.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/genremdinputs.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/fixremdcouts.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/charmmlipid2amber.py ->
> /home/andriy/amber24//bin
> >copying build/scripts-3.11/cpinutil.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/softcore_setup.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/ceinutil.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/finddgref.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/pyresp_gen.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/py_resp.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/bar_pbsa.py -> /home/andriy/amber24//bin
> >changing mode of /home/andriy/amber24//bin/fitpkaeo.py to 775
> >changing mode of /home/andriy/amber24//bin/mdout_analyzer.py to 775
> >changing mode of /home/andriy/amber24//bin/cpeinutil.py to 775
> >changing mode of /home/andriy/amber24//bin/genremdinputs.py to 775
> >changing mode of /home/andriy/amber24//bin/fixremdcouts.py to 775
> >changing mode of /home/andriy/amber24//bin/charmmlipid2amber.py to 775
> >changing mode of /home/andriy/amber24//bin/cpinutil.py to 775
> >changing mode of /home/andriy/amber24//bin/softcore_setup.py to 775
> >changing mode of /home/andriy/amber24//bin/ceinutil.py to 775
> >changing mode of /home/andriy/amber24//bin/finddgref.py to 775
> >changing mode of /home/andriy/amber24//bin/pyresp_gen.py to 775
> >changing mode of /home/andriy/amber24//bin/py_resp.py to 775
> >changing mode of /home/andriy/amber24//bin/bar_pbsa.py to 775
> >-- Installing: /home/andriy/amber24/bin/mm_pbsa.pl
> >-- Installing: /home/andriy/amber24/bin/mm_pbsa_statistics.pl
> >-- Installing: /home/andriy/amber24/bin/FEW.pl
> >-- Installing: /home/andriy/amber24/bin/tleap
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running build
> >running build_py
> >UPDATING build/lib.linux-x86_64-cpython-311/parmed/_version.py
> >set build/lib.linux-x86_64-cpython-311/parmed/_version.py to '0+unknown'
> >running build_ext
> >building 'parmed.amber._rdparm' extension
> >gcc -pthread -B
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat
> -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC
> -O2 -isystem
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC
> -I/home/andriy/amber24_src/AmberTools/src/parmed/src
> -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11
> -c src/_rdparm.cpp -o build/temp.linux-x86_64-cpython-311/src/_rdparm.o
> >gcc -pthread -B
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat
> -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC
> -O2 -isystem
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC
> -I/home/andriy/amber24_src/AmberTools/src/parmed/src
> -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11
> -c src/readparm.cpp -o build/temp.linux-x86_64-cpython-311/src/readparm.o
> >src/readparm.cpp: In function ‘ExitStatus readparm(const std::string&,
> std::vector<std::__cxx11::basic_string<char> >&, ParmDataMap&,
> ParmStringMap&, ParmStringMap&, ParmFormatMap&, std::string&)’:
> >src/readparm.cpp:143:28: warning: ‘char* __builtin_strncpy(char*, const
> char*, long unsigned int)’ specified bound 8 equals destination size
> [-Wstringop-truncation]
> > 143 | strncpy(d.c, word.c_str(),
> MAX_HOLLERITH_SIZE);
> > | ^
> >g++ -pthread -B
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat
> -shared
> -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> build/temp.linux-x86_64-cpython-311/src/_rdparm.o
> build/temp.linux-x86_64-cpython-311/src/readparm.o -o
> build/lib.linux-x86_64-cpython-311/parmed/amber/_
> rdparm.cpython-311-x86_64-linux-gnu.so
> >UPDATING build/lib.linux-x86_64-cpython-311/parmed/_version.py
> >set build/lib.linux-x86_64-cpython-311/parmed/_version.py to '0+unknown'
> >running install_lib
> >copying build/lib.linux-x86_64-cpython-311/parmed/rosetta/pose.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta
> >copying build/lib.linux-x86_64-cpython-311/parmed/rosetta/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta
> >copying build/lib.linux-x86_64-cpython-311/parmed/geometry.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/_version.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/openmm/reporters.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/openmm/utils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/openmm/parameters.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/openmm/topsystem.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/openmm/xmlfile.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/openmm/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/constants.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/rdkit/rdkit.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit
> >copying build/lib.linux-x86_64-cpython-311/parmed/rdkit/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit
> >copying build/lib.linux-x86_64-cpython-311/parmed/utils/netcdf.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
> >copying build/lib.linux-x86_64-cpython-311/parmed/utils/pandautils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
> >copying build/lib.linux-x86_64-cpython-311/parmed/utils/decorators.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
> >copying build/lib.linux-x86_64-cpython-311/parmed/utils/timer.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_lexer.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_input.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/FortranRecordWriter.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_misc.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_exceptions.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/FortranRecordReader.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/config.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_output.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_parser.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_edit_descriptors.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/__init__.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
> >copying build/lib.linux-x86_64-cpython-311/parmed/utils/io.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
> >copying build/lib.linux-x86_64-cpython-311/parmed/utils/pairlist.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
> >copying build/lib.linux-x86_64-cpython-311/parmed/utils/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
> >copying build/lib.linux-x86_64-cpython-311/parmed/structure.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/scripts.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/checkvalidity.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/addljtype.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/argumentlist.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/add1264.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/exceptions.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/parmlist.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/tools/simulations/sanderapi.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/tools/simulations/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/tools/simulations/openmm.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/parmed_cmd.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/logos.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/actions.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/tools/changeradii.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
> >copying build/lib.linux-x86_64-cpython-311/parmed/symmetry.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/exceptions.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/_cpp.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
> >copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/gromacstop.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
> >copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/gromacsgro.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
> >copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/_gromacsfile.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
> >copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
> >copying build/lib.linux-x86_64-cpython-311/parmed/topologyobjects.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/parameters.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/formats/pqr.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
> >copying build/lib.linux-x86_64-cpython-311/parmed/formats/psf.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
> >copying build/lib.linux-x86_64-cpython-311/parmed/formats/mol2.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/PdbxContainers.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/PdbxReader.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/PdbxWriter.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx
> >copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdb.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
> >copying build/lib.linux-x86_64-cpython-311/parmed/formats/registry.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
> >copying build/lib.linux-x86_64-cpython-311/parmed/formats/sdf.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
> >copying build/lib.linux-x86_64-cpython-311/parmed/formats/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
> >copying build/lib.linux-x86_64-cpython-311/parmed/tinker/system.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
> >copying build/lib.linux-x86_64-cpython-311/parmed/tinker/tinkerfiles.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/tinker/topologyobjects.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
> >copying build/lib.linux-x86_64-cpython-311/parmed/tinker/parameterfile.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
> >copying build/lib.linux-x86_64-cpython-311/parmed/tinker/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
> >copying build/lib.linux-x86_64-cpython-311/parmed/periodic_table.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/residue.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/vec3.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/namd/namdbinfiles.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd
> >copying build/lib.linux-x86_64-cpython-311/parmed/namd/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/modeller/data/standard_residues.lib
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/data
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/modeller/data/nonstandard_ccd_residue_templates.json.gz
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/data
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/modeller/data/ccd_residue_templates.json
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/data
> >copying build/lib.linux-x86_64-cpython-311/parmed/modeller/residue.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/modeller/standardtemplates.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller
> >copying build/lib.linux-x86_64-cpython-311/parmed/modeller/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller
> >copying build/lib.linux-x86_64-cpython-311/parmed/entos/imports.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos
> >copying build/lib.linux-x86_64-cpython-311/parmed/entos/converters.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos
> >copying build/lib.linux-x86_64-cpython-311/parmed/entos/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos
> >copying build/lib.linux-x86_64-cpython-311/parmed/dlpoly/dlpolyconfig.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly
> >copying build/lib.linux-x86_64-cpython-311/parmed/dlpoly/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly
> >copying build/lib.linux-x86_64-cpython-311/parmed/dlpoly/dlpolyfield.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/amberformat.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/_chamberparm.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/netcdffiles.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/gbnsr6.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/cntrl.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/qmmm.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/pb.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/rism.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/mdin.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/ewald.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/typing.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/parameters.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/_tinkerparm.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/mask.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/amber/titratable_residues.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/readparm.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/_amberparm.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/offlib.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/_
> rdparm.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/asciicrd.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying build/lib.linux-x86_64-cpython-311/parmed/amber/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/unit/unit_definitions.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit_math.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/constants.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/basedimension.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/prefix.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit_operators.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/quantity.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/mymatrix.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying
> build/lib.linux-x86_64-cpython-311/parmed/unit/standard_dimensions.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/baseunit.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/unit/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
> >copying build/lib.linux-x86_64-cpython-311/parmed/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed
> >copying build/lib.linux-x86_64-cpython-311/parmed/charmm/psf.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/charmm/charmmcrds.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/charmm/parameters.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/charmm/_charmmfile.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
> >copying build/lib.linux-x86_64-cpython-311/parmed/charmm/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta/pose.py
> to pose.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/geometry.py to
> geometry.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/_version.py to
> _version.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/reporters.py
> to reporters.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/utils.py
> to utils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/parameters.py
> to parameters.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/topsystem.py
> to topsystem.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/xmlfile.py
> to xmlfile.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/constants.py to
> constants.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit/rdkit.py to
> rdkit.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/netcdf.py
> to netcdf.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/pandautils.py
> to pandautils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/decorators.py
> to decorators.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/timer.py to
> timer.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_lexer.py
> to _lexer.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_input.py
> to _input.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/FortranRecordWriter.py
> to FortranRecordWriter.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_misc.py
> to _misc.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_exceptions.py
> to _exceptions.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/FortranRecordReader.py
> to FortranRecordReader.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/config.py
> to config.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_output.py
> to _output.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_parser.py
> to _parser.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_edit_descriptors.py
> to _edit_descriptors.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/io.py to
> io.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/pairlist.py
> to pairlist.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/structure.py to
> structure.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/scripts.py to
> scripts.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/checkvalidity.py
> to checkvalidity.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/addljtype.py
> to addljtype.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/argumentlist.py
> to argumentlist.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/add1264.py
> to add1264.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/exceptions.py
> to exceptions.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/parmlist.py
> to parmlist.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations/sanderapi.py
> to sanderapi.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations/openmm.py
> to openmm.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/parmed_cmd.py
> to parmed_cmd.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/logos.py to
> logos.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/actions.py
> to actions.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/changeradii.py
> to changeradii.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/symmetry.py to
> symmetry.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/exceptions.py to
> exceptions.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/_cpp.py
> to _cpp.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/gromacstop.py
> to gromacstop.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/gromacsgro.py
> to gromacsgro.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/_gromacsfile.py
> to _gromacsfile.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/topologyobjects.py
> to topologyobjects.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/parameters.py to
> parameters.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pqr.py to
> pqr.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/psf.py to
> psf.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/mol2.py
> to mol2.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/PdbxContainers.py
> to PdbxContainers.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/PdbxReader.py
> to PdbxReader.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/PdbxWriter.py
> to PdbxWriter.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdb.py to
> pdb.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/registry.py
> to registry.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/sdf.py to
> sdf.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/system.py
> to system.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/tinkerfiles.py
> to tinkerfiles.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/topologyobjects.py
> to topologyobjects.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/parameterfile.py
> to parameterfile.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/periodic_table.py
> to periodic_table.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/residue.py to
> residue.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/vec3.py to
> vec3.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd/namdbinfiles.py
> to namdbinfiles.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/residue.py
> to residue.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/standardtemplates.py
> to standardtemplates.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos/imports.py
> to imports.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos/converters.py
> to converters.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly/dlpolyconfig.py
> to dlpolyconfig.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly/dlpolyfield.py
> to dlpolyfield.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/amberformat.py
> to amberformat.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/_chamberparm.py
> to _chamberparm.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/netcdffiles.py
> to netcdffiles.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/gbnsr6.py
> to gbnsr6.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/cntrl.py
> to cntrl.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/qmmm.py
> to qmmm.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/pb.py
> to pb.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/rism.py
> to rism.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/mdin.py
> to mdin.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/ewald.py
> to ewald.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/typing.py
> to typing.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/parameters.py
> to parameters.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/_tinkerparm.py
> to _tinkerparm.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mask.py to
> mask.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/titratable_residues.py
> to titratable_residues.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/readparm.py
> to readparm.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/_amberparm.py
> to _amberparm.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/offlib.py
> to offlib.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/asciicrd.py
> to asciicrd.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit_definitions.py
> to unit_definitions.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit_math.py
> to unit_math.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/constants.py
> to constants.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/basedimension.py
> to basedimension.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/prefix.py to
> prefix.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit_operators.py
> to unit_operators.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/quantity.py
> to quantity.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit.py to
> unit.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/mymatrix.py
> to mymatrix.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/standard_dimensions.py
> to standard_dimensions.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/baseunit.py
> to baseunit.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/__init__.py to
> __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/psf.py to
> psf.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/charmmcrds.py
> to charmmcrds.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/parameters.py
> to parameters.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/_charmmfile.py
> to _charmmfile.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/__init__.py
> to __init__.cpython-311.pyc
> >running install_egg_info
> >running egg_info
> >writing ParmEd.egg-info/PKG-INFO
> >writing dependency_links to ParmEd.egg-info/dependency_links.txt
> >writing entry points to ParmEd.egg-info/entry_points.txt
> >writing top-level names to ParmEd.egg-info/top_level.txt
> >dependency src/CompatabilityMacros.h won't be automatically included in
> the manifest: the path doesn't exist
> >reading manifest file 'ParmEd.egg-info/SOURCES.txt'
> >reading manifest template 'MANIFEST.in'
> >writing manifest file 'ParmEd.egg-info/SOURCES.txt'
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/ParmEd-0+unknown-py3.11.egg-info'
> (and everything under it)
> >Copying ParmEd.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/ParmEd-0+unknown-py3.11.egg-info
> >running install_scripts
> >Installing parmed script to /home/andriy/amber24//bin
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running build
> >running build_py
> >running build_scripts
> >copying and adjusting MMPBSA.py.MPI -> build/scripts-3.11
> >running install_lib
> >copying build/lib/MMPBSA_mods/timer.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/input_parser.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/utils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/output_file.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/API.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/exceptions.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/createinput.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/main.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/infofile.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/findprogs.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/alamdcrd.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/parm_setup.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/commandlineparser.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/fake_mpi.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/calculation.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/make_trajs.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >copying build/lib/MMPBSA_mods/amber_outputs.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/timer.py to
> timer.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/input_parser.py
> to input_parser.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/utils.py to
> utils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/output_file.py
> to output_file.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/API.py to
> API.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/exceptions.py
> to exceptions.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/createinput.py
> to createinput.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/main.py to
> main.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/infofile.py
> to infofile.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/findprogs.py
> to findprogs.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/alamdcrd.py
> to alamdcrd.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/parm_setup.py
> to parm_setup.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/commandlineparser.py
> to commandlineparser.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/fake_mpi.py
> to fake_mpi.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/calculation.py
> to calculation.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/make_trajs.py
> to make_trajs.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/amber_outputs.py
> to amber_outputs.cpython-311.pyc
> >running install_egg_info
> >running egg_info
> >writing MMPBSA.py.egg-info/PKG-INFO
> >writing dependency_links to MMPBSA.py.egg-info/dependency_links.txt
> >writing top-level names to MMPBSA.py.egg-info/top_level.txt
> >reading manifest file 'MMPBSA.py.egg-info/SOURCES.txt'
> >writing manifest file 'MMPBSA.py.egg-info/SOURCES.txt'
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/MMPBSA.py-16.0-py3.11.egg-info'
> (and everything under it)
> >Copying MMPBSA.py.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA.py-16.0-py3.11.egg-info
> >running install_scripts
> >copying build/scripts-3.11/MMPBSA.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/MMPBSA.py.MPI -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/ante-MMPBSA.py -> /home/andriy/amber24//bin
> >changing mode of /home/andriy/amber24//bin/MMPBSA.py to 775
> >changing mode of /home/andriy/amber24//bin/MMPBSA.py.MPI to 775
> >changing mode of /home/andriy/amber24//bin/ante-MMPBSA.py to 775
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running build
> >running build_py
> >running build_scripts
> >running install_lib
> >copying build/lib/pymsmt/mol/mol.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/constants.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/pdbio.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/mol2io.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/element.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/getlist.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/cal.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/itfc_dict_table.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/cario.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/gmsio.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/amb2chm_typ.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/gauio.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/rstio.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/sqmio.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/mol/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
> >copying build/lib/pymsmt/ipmach/calhfe.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach
> >copying build/lib/pymsmt/ipmach/tifiles.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach
> >copying build/lib/pymsmt/ipmach/caliod.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach
> >copying build/lib/pymsmt/ipmach/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach
> >copying build/lib/pymsmt/title.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt
> >copying build/lib/pymsmt/api/AmberParm.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api
> >copying build/lib/pymsmt/api/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api
> >copying build/lib/pymsmt/exp.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt
> >copying build/lib/pymsmt/mcpb/rename_residues.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
> >copying build/lib/pymsmt/mcpb/gene_model_files.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
> >copying build/lib/pymsmt/mcpb/resp_fitting.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
> >copying build/lib/pymsmt/mcpb/amber_modeling.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
> >copying build/lib/pymsmt/mcpb/gene_pre_frcmod_file.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
> >copying build/lib/pymsmt/mcpb/gene_final_frcmod_file.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
> >copying build/lib/pymsmt/mcpb/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
> >copying build/lib/pymsmt/mcpb/fq_model.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
> >copying build/lib/pymsmt/lib.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt
> >copying build/lib/pymsmt/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/mol.py to
> mol.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/constants.py
> to constants.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/pdbio.py to
> pdbio.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/mol2io.py to
> mol2io.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/element.py to
> element.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/getlist.py to
> getlist.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/cal.py to
> cal.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/itfc_dict_table.py
> to itfc_dict_table.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/cario.py to
> cario.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/gmsio.py to
> gmsio.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/amb2chm_typ.py
> to amb2chm_typ.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/gauio.py to
> gauio.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/rstio.py to
> rstio.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/sqmio.py to
> sqmio.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/calhfe.py
> to calhfe.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/tifiles.py
> to tifiles.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/caliod.py
> to caliod.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/title.py to
> title.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api/AmberParm.py
> to AmberParm.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/exp.py to
> exp.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/rename_residues.py
> to rename_residues.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/gene_model_files.py
> to gene_model_files.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/resp_fitting.py
> to resp_fitting.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/amber_modeling.py
> to amber_modeling.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py
> to gene_pre_frcmod_file.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py
> to gene_final_frcmod_file.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/fq_model.py
> to fq_model.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/lib.py to
> lib.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/__init__.py to
> __init__.cpython-311.pyc
> >running install_egg_info
> >running egg_info
> >writing pyMSMT.egg-info/PKG-INFO
> >writing dependency_links to pyMSMT.egg-info/dependency_links.txt
> >writing top-level names to pyMSMT.egg-info/top_level.txt
> >reading manifest file 'pyMSMT.egg-info/SOURCES.txt'
> >writing manifest file 'pyMSMT.egg-info/SOURCES.txt'
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/pyMSMT-22.0-py3.11.egg-info'
> (and everything under it)
> >Copying pyMSMT.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/pyMSMT-22.0-py3.11.egg-info
> >running install_scripts
> >copying build/scripts-3.11/metalpdb2mol2.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/amb2chm_psf_crd.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/espgen.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/PdbSearcher.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/amb2gro_top_gro.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/OptC4.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/mol2rtf.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/car_to_files.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/MCPB.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/amb2chm_par.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/IPMach.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/ProScrs.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/CartHess2FC.py -> /home/andriy/amber24//bin
> >changing mode of /home/andriy/amber24//bin/metalpdb2mol2.py to 775
> >changing mode of /home/andriy/amber24//bin/amb2chm_psf_crd.py to 775
> >changing mode of /home/andriy/amber24//bin/espgen.py to 775
> >changing mode of /home/andriy/amber24//bin/PdbSearcher.py to 775
> >changing mode of /home/andriy/amber24//bin/amb2gro_top_gro.py to 775
> >changing mode of /home/andriy/amber24//bin/OptC4.py to 775
> >changing mode of /home/andriy/amber24//bin/mol2rtf.py to 775
> >changing mode of /home/andriy/amber24//bin/car_to_files.py to 775
> >changing mode of /home/andriy/amber24//bin/MCPB.py to 775
> >changing mode of /home/andriy/amber24//bin/amb2chm_par.py to 775
> >changing mode of /home/andriy/amber24//bin/IPMach.py to 775
> >changing mode of /home/andriy/amber24//bin/ProScrs.py to 775
> >changing mode of /home/andriy/amber24//bin/CartHess2FC.py to 775
> >Copying sander extension source to sanderles...
> >running build
> >running build_py
> >copying sanderles/__init__.py ->
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles
> >running build_ext
> >building 'sanderles.pysander' extension
> >gcc -pthread -B
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat
> -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC
> -O2 -isystem
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC
> -DLES -I/home/andriy/amber24_src/AmberTools/src/include
> -I/home/andriy/amber24_src/AmberTools/src/sander
> -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11
> -c sanderles/src/pysandermodule.c -o
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o
> >In file included from sanderles/src/pysandermodule.c:16:
> >/home/andriy/amber24_src/AmberTools/src/sander/sander.h: In function
> ‘pysander_setup’:
> >/home/andriy/amber24_src/AmberTools/src/sander/sander.h:342:5: warning:
> ‘__builtin_strncpy’ specified bound 256 equals destination size
> [-Wstringop-truncation]
> > 342 | strncpy(prmtop, prmname, __MAX_FN_LEN);
> > | ^
> >gcc -pthread -B
> /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat
> -shared
> -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o
> -L/home/andriy/amber24//lib -lsanderles -o
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/
> pysander.cpython-311-x86_64-linux-gnu.so
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running install_lib
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/
> pysander.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/sanderles
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/sanderles
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sander/
> pysander.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/sander
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sander/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/sander
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/sanderles/__init__.py to
> __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/sander/__init__.py to
> __init__.cpython-311.pyc
> >running install_egg_info
> >running egg_info
> >writing sander.egg-info/PKG-INFO
> >writing dependency_links to sander.egg-info/dependency_links.txt
> >writing top-level names to sander.egg-info/top_level.txt
> >reading manifest file 'sander.egg-info/SOURCES.txt'
> >writing manifest file 'sander.egg-info/SOURCES.txt'
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/sander-22.0-py3.11.egg-info'
> (and everything under it)
> >Copying sander.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/sander-22.0-py3.11.egg-info
> >running install_scripts
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/dist.py:476:
> SetuptoolsDeprecationWarning: Invalid dash-separated options
> >!!
> >
> >
> ********************************************************************************
> > Usage of dash-separated 'description-file' will not be supported
> in future
> > versions. Please use the underscore name 'description_file'
> instead.
> >
> > This deprecation is overdue, please update your project and
> remove deprecated
> > calls to avoid build errors in the future.
> >
> > See
> https://setuptools.pypa.io/en/latest/userguide/declarative_config.html
> for details.
> >
> ********************************************************************************
> >
> >!!
> > opt = self.warn_dash_deprecation(opt, section)
> >sys.argv ['./setup.py', 'build', '-b',
> '/home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build',
> '--disable-openmp', 'install', '-f', '--prefix=/home/andriy/amber24/',
> '--single-version-externally-managed', '--root', '/']
> >Original compiler envs
> >CXX = /usr/bin/g++
> >CC = /usr/bin/gcc
> >COMPILER =
> >use_pip = False, cpptraj_home =
> >compile_c_extension = True
> >2.0.6
> >use_prebuilt_cythonized_files = False
> >pytraj is inside AMBERHOME
> >using environment: CC=/usr/bin/gcc, CXX=/usr/bin/g++
> >using CC=/usr/bin/gcc, CXX=/usr/bin/g++
> >Final compiler envs
> >CXX = /usr/bin/g++
> >CC = /usr/bin/gcc
> >COMPILER =
> >install = True
> >set rpath to /home/andriy/amber24_src/build/AmberTools/src/cpptraj/src
> >running build
> >running build_py
> >copying pytraj/version.py ->
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj
> >running build_ext
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running install_lib
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/externals/wurlitzer.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/externals/magic.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/externals/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/version.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/cython_extra_header/cpp_algorithm.pxd
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cython_extra_header
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/cython_extra_header/cpp_vector.pxd
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cython_extra_header
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/topology_analysis.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/nmr.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/vector.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/c_analysis.pxd
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/analysis_dict.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/
> c_analysis.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/__init__.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/energy_analysis.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/dihedral_analysis.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/dssp_analysis.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/base_holder.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/matrix.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/water.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/c_action.pxd
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/actionlist.pxd
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/
> c_action.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/
> actionlist.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/__init__.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/rmsd.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/hbond_analysis.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/nucleic_acid_analysis.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/decorators.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/Timer.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/convert.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/progress-circle/progress-circle.js
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/progress-circle
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/progress-circle/css/circle.css
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/progress-circle/css
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/context.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/tools.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/get_common_objects.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/misc.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/
> cyutils.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/c_commands.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/progress.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/check_and_assert.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/css/oceans16.css
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/css
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/visualization/view.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/visualization/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/topology/topology.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/topology/
> topology.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/topology/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/coordinfo.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/
> coordinfo.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/
> parameter_types.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/
> c_core.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_core.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/cpp_vector.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/topology_objects.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/
> c_options.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/parameter_types.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_dict.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/
> topology_objects.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/elements.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/
> box.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/box.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/
> c_dict.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/
> cast_dataset.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasetlist.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/
> c_datasetlist.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasets.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/
> c_datasets.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/datasetlist.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/array.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/math/cpp_math.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/math/
> cpp_math.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/math/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/testing/testing.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/testing/run_tests.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/testing/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/cluster/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cluster
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/builder/build.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/builder
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/builder/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/builder
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/all_actions.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/transform.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/qm.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/TrajectoryBaseIterator.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/lazy.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/frame.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/trajectory_iterator.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/stripped_trajectory.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/
> frame.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/frameiter.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/trajectory.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/shared_methods.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/shared_trajectory.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/c_trajout.pxd
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/
> c_trajout.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/c_trajectory.pxd
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/
> c_trajectory.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/__init__.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/io.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/dataset.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/base.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/multiprocess.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/mpi.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/trpcage/trpcage.pdb.gz
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/trpcage
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/trpcage/__init__.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/trpcage
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/ala3/Ala3.crd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/ala3
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/ala3/Ala3.top
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/ala3
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/ala3/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/ala3
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/load_samples.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/
> datafiles.cpython-311-x86_64-linux-gnu.so ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/rna.pdb
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/dpdp/DPDP.nc
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/dpdp
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/dpdp/DPDP.parm7
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/dpdp
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/dpdp/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/dpdp
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/rem.nc.000
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/ala2.parm7
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/rem.nc.002
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/rem.nc.003
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/rem.nc.001
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/__init__.py
> ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/datafiles.pxd
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/tz2.ortho.parm7
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/tz2.parm7
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/
> tz2.ortho.nc ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/
> tz2.nc ->
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/serialize/serialize.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/serialize/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize
> >copying
> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/__init__.py
> -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals/wurlitzer.py
> to wurlitzer.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals/magic.py
> to magic.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/version.py to
> version.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/topology_analysis.py
> to topology_analysis.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/nmr.py
> to nmr.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/vector.py
> to vector.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis/analysis_dict.py
> to analysis_dict.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/energy_analysis.py
> to energy_analysis.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/dihedral_analysis.py
> to dihedral_analysis.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/dssp_analysis.py
> to dssp_analysis.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/base_holder.py
> to base_holder.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/matrix.py
> to matrix.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/water.py
> to water.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/rmsd.py
> to rmsd.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/hbond_analysis.py
> to hbond_analysis.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/nucleic_acid_analysis.py
> to nucleic_acid_analysis.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/decorators.py
> to decorators.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/Timer.py to
> Timer.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/convert.py
> to convert.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/context.py
> to context.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/tools.py to
> tools.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/get_common_objects.py
> to get_common_objects.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/misc.py to
> misc.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/c_commands.py
> to c_commands.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/progress.py
> to progress.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/check_and_assert.py
> to check_and_assert.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization/view.py
> to view.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core/elements.py
> to elements.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets/datasetlist.py
> to datasetlist.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets/array.py
> to array.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing/testing.py
> to testing.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing/run_tests.py
> to run_tests.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cluster/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/builder/build.py
> to build.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/builder/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/all_actions.py to
> all_actions.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/transform.py
> to transform.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/qm.py to
> qm.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/TrajectoryBaseIterator.py
> to TrajectoryBaseIterator.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/lazy.py
> to lazy.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/trajectory_iterator.py
> to trajectory_iterator.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/stripped_trajectory.py
> to stripped_trajectory.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/frameiter.py
> to frameiter.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/trajectory.py
> to trajectory.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/shared_methods.py
> to shared_methods.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/shared_trajectory.py
> to shared_trajectory.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/io.py to
> io.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/dataset.py
> to dataset.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/base.py
> to base.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/multiprocess.py
> to multiprocess.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/mpi.py
> to mpi.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/trpcage/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/ala3/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/load_samples.py
> to load_samples.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/dpdp/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize/serialize.py
> to serialize.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/__init__.py to
> __init__.cpython-311.pyc
> >running install_egg_info
> >running egg_info
> >writing pytraj.egg-info/PKG-INFO
> >writing dependency_links to pytraj.egg-info/dependency_links.txt
> >writing requirements to pytraj.egg-info/requires.txt
> >writing top-level names to pytraj.egg-info/top_level.txt
> >reading manifest file 'pytraj.egg-info/SOURCES.txt'
> >reading manifest template 'MANIFEST.in'
> >writing manifest file 'pytraj.egg-info/SOURCES.txt'
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/pytraj-2.0.6-py3.11.egg-info'
> (and everything under it)
> >Copying pytraj.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/pytraj-2.0.6-py3.11.egg-info
> >running install_scripts
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running build
> >running build_py
> >running install_lib
> >copying build/lib/pdb4amber/utils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
> >copying build/lib/pdb4amber/pdb4amber.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
> >copying build/lib/pdb4amber/leap_runner.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
> >copying build/lib/pdb4amber/residue.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
> >copying build/lib/pdb4amber/template.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
> >copying build/lib/pdb4amber/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/utils.py to
> utils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/pdb4amber.py
> to pdb4amber.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/leap_runner.py
> to leap_runner.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/residue.py to
> residue.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/template.py to
> template.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/__init__.py to
> __init__.cpython-311.pyc
> >running install_egg_info
> >running egg_info
> >writing pdb4amber.egg-info/PKG-INFO
> >writing dependency_links to pdb4amber.egg-info/dependency_links.txt
> >writing entry points to pdb4amber.egg-info/entry_points.txt
> >writing top-level names to pdb4amber.egg-info/top_level.txt
> >reading manifest file 'pdb4amber.egg-info/SOURCES.txt'
> >adding license file 'LICENSE'
> >writing manifest file 'pdb4amber.egg-info/SOURCES.txt'
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/pdb4amber-22.0-py3.11.egg-info'
> (and everything under it)
> >Copying pdb4amber.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber-22.0-py3.11.egg-info
> >running install_scripts
> >Installing pdb4amber script to /home/andriy/amber24//bin
> >Inside Amber CMake build system, skipping build of native executables
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running build
> >running build_py
> >copying packmol_memgen/lib/utils.py -> build/lib/packmol_memgen/lib
> >running egg_info
> >writing packmol_memgen.egg-info/PKG-INFO
> >writing dependency_links to packmol_memgen.egg-info/dependency_links.txt
> >writing requirements to packmol_memgen.egg-info/requires.txt
> >writing top-level names to packmol_memgen.egg-info/top_level.txt
> >reading manifest file 'packmol_memgen.egg-info/SOURCES.txt'
> >reading manifest template 'MANIFEST.in'
> >adding license file 'LICENSE'
> >writing manifest file 'packmol_memgen.egg-info/SOURCES.txt'
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.data' is absent from the `packages`
> configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.data' as an importable
> package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that 'packmol_memgen.data' is
> explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.data' to be distributed and are
> > already explicitly excluding 'packmol_memgen.data' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.example' is absent from the `packages`
> configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.example' as an importable
> package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that 'packmol_memgen.example' is
> explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.example' to be distributed and
> are
> > already explicitly excluding 'packmol_memgen.example' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.memembed' is absent from the
> `packages` configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.memembed' as an importable
> package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that 'packmol_memgen.lib.memembed' is
> explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.memembed' to be distributed
> and are
> > already explicitly excluding 'packmol_memgen.lib.memembed' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.memembed.bin' is absent from the
> `packages` configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.memembed.bin' as an
> importable package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that 'packmol_memgen.lib.memembed.bin'
> is explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.memembed.bin' to be
> distributed and are
> > already explicitly excluding 'packmol_memgen.lib.memembed.bin' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.memembed.examples' is absent from the
> `packages` configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.memembed.examples' as an
> importable package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that
> 'packmol_memgen.lib.memembed.examples' is explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.memembed.examples' to be
> distributed and are
> > already explicitly excluding
> 'packmol_memgen.lib.memembed.examples' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.memembed.scripts' is absent from the
> `packages` configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.memembed.scripts' as an
> importable package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that
> 'packmol_memgen.lib.memembed.scripts' is explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.memembed.scripts' to be
> distributed and are
> > already explicitly excluding
> 'packmol_memgen.lib.memembed.scripts' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.memembed.src' is absent from the
> `packages` configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.memembed.src' as an
> importable package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that 'packmol_memgen.lib.memembed.src'
> is explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.memembed.src' to be
> distributed and are
> > already explicitly excluding 'packmol_memgen.lib.memembed.src' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.packmol' is absent from the
> `packages` configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.packmol' as an importable
> package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that 'packmol_memgen.lib.packmol' is
> explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.packmol' to be distributed
> and are
> > already explicitly excluding 'packmol_memgen.lib.packmol' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.packmol.docs' is absent from the
> `packages` configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.packmol.docs' as an
> importable package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that 'packmol_memgen.lib.packmol.docs'
> is explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.packmol.docs' to be
> distributed and are
> > already explicitly excluding 'packmol_memgen.lib.packmol.docs' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.packmol.docs.imgs' is absent from the
> `packages` configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.packmol.docs.imgs' as an
> importable package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that
> 'packmol_memgen.lib.packmol.docs.imgs' is explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.packmol.docs.imgs' to be
> distributed and are
> > already explicitly excluding
> 'packmol_memgen.lib.packmol.docs.imgs' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.pdbremix.data' is absent from the
> `packages` configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.pdbremix.data' as an
> importable package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that 'packmol_memgen.lib.pdbremix.data'
> is explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.pdbremix.data' to be
> distributed and are
> > already explicitly excluding 'packmol_memgen.lib.pdbremix.data'
> via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207:
> _Warning: Package 'packmol_memgen.lib.ppm3' is absent from the `packages`
> configuration.
> >!!
> >
> >
> ********************************************************************************
> > ############################
> > # Package would be ignored #
> > ############################
> > Python recognizes 'packmol_memgen.lib.ppm3' as an importable
> package[^1],
> > but it is absent from setuptools' `packages` configuration.
> >
> > This leads to an ambiguous overall configuration. If you want to
> distribute this
> > package, please make sure that 'packmol_memgen.lib.ppm3' is
> explicitly added
> > to the `packages` configuration field.
> >
> > Alternatively, you can also rely on setuptools' discovery methods
> > (for example by using
> `find_namespace_packages(...)`/`find_namespace:`
> > instead of `find_packages(...)`/`find:`).
> >
> > You can read more about "package discovery" on setuptools
> documentation page:
> >
> > -
> https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
> >
> > If you don't want 'packmol_memgen.lib.ppm3' to be distributed and
> are
> > already explicitly excluding 'packmol_memgen.lib.ppm3' via
> > `find_namespace_packages(...)/find_namespace` or
> `find_packages(...)/find`,
> > you can try to use `exclude_package_data`, or
> `include-package-data=False` in
> > combination with a more fine grained `package-data` configuration.
> >
> > You can read more about "package data files" on setuptools
> documentation page:
> >
> > - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
> >
> >
> > [^1]: For Python, any directory (with suitable naming) can be
> imported,
> > even if it does not contain any `.py` files.
> > On the other hand, currently there is no concept of package
> data
> > directory, all directories are treated like packages.
> >
> ********************************************************************************
> >
> >!!
> > check.warn(importable)
> >copying packmol_memgen/lib/memembed/bin/memembed ->
> build/lib/packmol_memgen/lib/memembed/bin
> >running build_scripts
> >running install_lib
> >copying build/lib/packmol_memgen/data/memgen.parm ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
> >copying build/lib/packmol_memgen/data/leaprc.lipid_ext ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
> >copying build/lib/packmol_memgen/data/solvent.parm ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
> >copying build/lib/packmol_memgen/data/pdbs.tar.gz ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
> >copying build/lib/packmol_memgen/data/lipid_ext.lib ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
> >copying build/lib/packmol_memgen/data/frcmod.lipid_ext ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
> >copying build/lib/packmol_memgen/data/leaprc.extra_solvents ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
> >copying build/lib/packmol_memgen/data/extra_solvents.lib ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
> >copying build/lib/packmol_memgen/data/frcmod.solvents ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
> >copying build/lib/packmol_memgen/example/example.sh ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/example
> >copying build/lib/packmol_memgen/main.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen
> >copying build/lib/packmol_memgen/__version__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen
> >copying build/lib/packmol_memgen/Makefile ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen
> >copying build/lib/packmol_memgen/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen
> >copying build/lib/packmol_memgen/lib/utils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib
> >copying build/lib/packmol_memgen/lib/memembed/examples/2x2v.pdb ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples
> >copying build/lib/packmol_memgen/lib/memembed/examples/2iahA.pdb ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples
> >copying build/lib/packmol_memgen/lib/memembed/examples/2iahA.pot ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples
> >copying build/lib/packmol_memgen/lib/memembed/examples/3o7qA.pdb ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples
> >copying
> build/lib/packmol_memgen/lib/memembed/scripts/pymol_membrane_image.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts
> >copying build/lib/packmol_memgen/lib/memembed/scripts/pymol_rotate.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts
> >copying build/lib/packmol_memgen/lib/memembed/bin/memembed ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/bin
> >copying build/lib/packmol_memgen/lib/memembed/bin/.gitignore ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/bin
> >copying build/lib/packmol_memgen/lib/memembed/CMakeLists.txt ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed
> >copying build/lib/packmol_memgen/lib/memembed/LICENSE ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed
> >copying build/lib/packmol_memgen/lib/memembed/Makefile ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed
> >copying build/lib/packmol_memgen/lib/memembed/src/pdb.cpp ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
> >copying build/lib/packmol_memgen/lib/memembed/src/pdb.hpp ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
> >copying build/lib/packmol_memgen/lib/memembed/src/direct.cpp ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
> >copying build/lib/packmol_memgen/lib/memembed/src/grid.cpp ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
> >copying build/lib/packmol_memgen/lib/memembed/src/main.cpp ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
> >copying build/lib/packmol_memgen/lib/memembed/src/direct.hpp ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
> >copying build/lib/packmol_memgen/lib/memembed/src/ga.hpp ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
> >copying build/lib/packmol_memgen/lib/memembed/src/grid.hpp ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
> >copying build/lib/packmol_memgen/lib/memembed/src/ga.cpp ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
> >copying build/lib/packmol_memgen/lib/memembed/README ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed
> >copying
> build/lib/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber
> >copying
> build/lib/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.csv ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber
> >copying build/lib/packmol_memgen/lib/charmmlipid2amber/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber
> >copying build/lib/packmol_memgen/lib/packmol/title.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/data_types.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/gparc.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/computef.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/gencan.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/restmol.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/comprest.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/comparegrad.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/flashmod.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/fparc.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/setijk.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/release.sh ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/swaptype.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/README.md ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/configure ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/CMakeLists.txt ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/usegencan.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/ahestetic.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/sizes.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/LICENSE ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/output.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/writesuccess.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/strlength.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/compute_data.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/heuristics.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/tobar.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/swaptypemod.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/header ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/jacobi.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/cenmass.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/Makefile ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying
> build/lib/packmol_memgen/lib/packmol/gencan_ieee_signal_routines.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/packmol.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/flashsort.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/resetboxes.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/docs/README.md ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs
> >copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img37.png ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
> >copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img38.png ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
> >copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img36.png ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
> >copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img39.png ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
> >copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img31.png ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
> >copying build/lib/packmol_memgen/lib/packmol/docs/imgs/pbc.jpg ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
> >copying build/lib/packmol_memgen/lib/packmol/docs/_config.yml ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs
> >copying build/lib/packmol_memgen/lib/packmol/AUTHORS ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/setsizes.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/gwalls.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/compile_cmake.sh ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/computeg.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/polartocart.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/input.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/exit_codes.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/getinp.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/setibox.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/pgencan.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/initial.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/random.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/checkpoint.f90 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/packmol/solvate.tcl ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
> >copying build/lib/packmol_memgen/lib/ppm3/min.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/rmsd.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/watface.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/locate.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/tilting.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/opm.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/orient.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/CMakeLists.txt ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/ppm3_instructions.docx ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/hbcor.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/deftm.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/Makefile ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/res.lib ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/solva.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/license.txt ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/readpdb.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/read_small.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/profile.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/ppm3/find_segm.f ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
> >copying build/lib/packmol_memgen/lib/amber.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib
> >copying build/lib/packmol_memgen/lib/pdbremix/data/opls.parameter ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/charmm22.parameter ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/phd.frcmod ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/phd.prepin ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/color_b.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/opls.topology ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/binaries.json ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/aminoacid.pdb ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/template.pdb ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/znb.leaprc ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/hin.lib ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/znb.frcmod ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/hydroxide.lib ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/charmm22.topology ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/phd.leaprc ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/znb.lib ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/data/make_chi.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
> >copying build/lib/packmol_memgen/lib/pdbremix/namd.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/pdbatoms.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/spacehash.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/_version.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/data.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/fetch.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/v3.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/force.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/gromacs.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/asa.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/util.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/simulate.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/LICENSE ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/trajectory.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/pymol.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/v3array.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/pdbtext.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/amber.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/rmsd.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/protein.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/v3numpy.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/volume.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
> >copying build/lib/packmol_memgen/lib/pdbremix/lib/docopt.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib
> >copying build/lib/packmol_memgen/lib/pdbremix/lib/pyqcprot.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib
> >copying build/lib/packmol_memgen/lib/pdbremix/lib/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib
> >copying build/lib/packmol_memgen/lib/tqdm/rich.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/std.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/version.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/dask.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/utils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/_tqdm_gui.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/_utils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/notebook.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/tk.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/asyncio.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/gui.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/auto.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/autonotebook.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/__main__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/_tqdm_pandas.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/_monitor.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/_main.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/_tqdm.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/_tqdm_notebook.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/cli.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/tqdm/tqdm.1 ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
> >copying build/lib/packmol_memgen/lib/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/main.py
> to main.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/__version__.py
> to __version__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/utils.py
> to utils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts/pymol_membrane_image.py
> to pymol_membrane_image.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts/pymol_rotate.py
> to pymol_rotate.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py
> to charmmlipid2amber.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/amber.py
> to amber.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data/color_b.py
> to color_b.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data/make_chi.py
> to make_chi.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/namd.py
> to namd.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py
> to pdbatoms.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/spacehash.py
> to spacehash.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/_version.py
> to _version.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data.py
> to data.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/fetch.py
> to fetch.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/v3.py
> to v3.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/force.py
> to force.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/gromacs.py
> to gromacs.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/asa.py
> to asa.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/util.py
> to util.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/simulate.py
> to simulate.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/trajectory.py
> to trajectory.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pymol.py
> to pymol.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/v3array.py
> to v3array.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pdbtext.py
> to pdbtext.cpython-311.pyc
> >home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pdbtext.py:30:
> SyntaxWarning: "is" with a literal. Did you mean "=="?
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/amber.py
> to amber.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/rmsd.py
> to rmsd.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/protein.py
> to protein.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/v3numpy.py
> to v3numpy.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/volume.py
> to volume.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib/docopt.py
> to docopt.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib/pyqcprot.py
> to pyqcprot.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/rich.py
> to rich.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/std.py
> to std.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/version.py
> to version.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/dask.py
> to dask.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/utils.py
> to utils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm_gui.py
> to _tqdm_gui.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_utils.py
> to _utils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/notebook.py
> to notebook.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/tk.py
> to tk.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/asyncio.py
> to asyncio.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/gui.py
> to gui.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/auto.py
> to auto.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/autonotebook.py
> to autonotebook.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/__main__.py
> to __main__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm_pandas.py
> to _tqdm_pandas.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_monitor.py
> to _monitor.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_main.py
> to _main.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm.py
> to _tqdm.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm_notebook.py
> to _tqdm_notebook.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/cli.py
> to cli.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/__init__.py
> to __init__.cpython-311.pyc
> >running install_egg_info
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen-2024.3.27-py3.11.egg-info'
> (and everything under it)
> >Copying packmol_memgen.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen-2024.3.27-py3.11.egg-info
> >running install_scripts
> >copying build/scripts-3.11/packmol-memgen -> /home/andriy/amber24//bin
> >changing mode of /home/andriy/amber24//bin/packmol-memgen to 775
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running build
> >running build_py
> >running egg_info
> >writing edgembar.egg-info/PKG-INFO
> >writing dependency_links to edgembar.egg-info/dependency_links.txt
> >writing requirements to edgembar.egg-info/requires.txt
> >writing top-level names to edgembar.egg-info/top_level.txt
> >reading manifest file 'edgembar.egg-info/SOURCES.txt'
> >writing manifest file 'edgembar.egg-info/SOURCES.txt'
> >running build_scripts
> >running install_lib
> >copying build/lib/edgembar/Splines.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/Stage.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/OptUtils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/Results.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/DiscoverEdges.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/AutoEquil.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/TimeSeriesAnalysis.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/CenteredCubic.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/pkgdata/selerow.js ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
> >copying build/lib/edgembar/pkgdata/sorttable.js ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
> >copying build/lib/edgembar/pkgdata/edge.css ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
> >copying build/lib/edgembar/pkgdata/graph.css ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
> >copying build/lib/edgembar/pkgdata/tschart.js ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
> >copying build/lib/edgembar/pkgdata/vis-iface.js ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
> >copying build/lib/edgembar/pkgdata/vis-network.min.js ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
> >copying build/lib/edgembar/pkgdata/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
> >copying build/lib/edgembar/Trial.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/Edge.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/ImportEdge.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/HtmlUtils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/Env.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/Graph.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/GraphSearch.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/Names.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/Cli.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >copying build/lib/edgembar/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Splines.py to
> Splines.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Stage.py to
> Stage.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/OptUtils.py to
> OptUtils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Results.py to
> Results.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/DiscoverEdges.py
> to DiscoverEdges.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/AutoEquil.py to
> AutoEquil.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/TimeSeriesAnalysis.py
> to TimeSeriesAnalysis.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/CenteredCubic.py
> to CenteredCubic.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Trial.py to
> Trial.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Edge.py to
> Edge.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/ImportEdge.py
> to ImportEdge.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/HtmlUtils.py to
> HtmlUtils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Env.py to
> Env.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Graph.py to
> Graph.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/GraphSearch.py
> to GraphSearch.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Names.py to
> Names.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Cli.py to
> Cli.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/__init__.py to
> __init__.cpython-311.pyc
> >running install_egg_info
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/edgembar-3.0-py3.11.egg-info'
> (and everything under it)
> >Copying edgembar.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/edgembar-3.0-py3.11.egg-info
> >running install_scripts
> >copying build/scripts-3.11/edgembar-WriteGraphHtml.py ->
> /home/andriy/amber24//bin
> >copying build/scripts-3.11/edgembar-amber2dats.py ->
> /home/andriy/amber24//bin
> >changing mode of /home/andriy/amber24//bin/edgembar-WriteGraphHtml.py to
> 775
> >changing mode of /home/andriy/amber24//bin/edgembar-amber2dats.py to 775
> >running install
> >/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> >!!
> >
> >
> ********************************************************************************
> > Please avoid running ``setup.py`` directly.
> > Instead, use pypa/build, pypa/installer or other
> > standards-based tools.
> >
> > See
> https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for
> details.
> >
> ********************************************************************************
> >
> >!!
> > self.initialize_options()
> >running build
> >running build_py
> >running egg_info
> >writing ndfes.egg-info/PKG-INFO
> >writing dependency_links to ndfes.egg-info/dependency_links.txt
> >writing requirements to ndfes.egg-info/requires.txt
> >writing top-level names to ndfes.egg-info/top_level.txt
> >reading manifest file 'ndfes.egg-info/SOURCES.txt'
> >writing manifest file 'ndfes.egg-info/SOURCES.txt'
> >running build_scripts
> >running install_lib
> >copying build/lib/ndfes/vFEP.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/gaussian/GaussianOutput.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian
> >copying build/lib/ndfes/gaussian/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian
> >copying build/lib/ndfes/SpatialBin.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/MBAR.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/PCV.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/PathData.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/normalmode/normalmode.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode
> >copying build/lib/ndfes/normalmode/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode
> >copying build/lib/ndfes/normalmode/kie.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode
> >copying build/lib/ndfes/EvalT.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/PlotUtils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/AutoEquil.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/WAVG.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/GridUtils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/SpatialDim.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/Trajectory.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/ReadCheckpoint.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/Bspline.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/Metafile.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/VirtualGrid.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/deprecated/OptUtils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated
> >copying build/lib/ndfes/deprecated/DensityEst.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated
> >copying build/lib/ndfes/deprecated/DensityString.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated
> >copying build/lib/ndfes/deprecated/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated
> >copying build/lib/ndfes/constants/Conversions.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants
> >copying build/lib/ndfes/constants/PeriodicTable.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants
> >copying build/lib/ndfes/constants/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants
> >copying build/lib/ndfes/amber/Restraint.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
> >copying build/lib/ndfes/amber/Reader.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
> >copying build/lib/ndfes/amber/Geometry.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
> >copying build/lib/ndfes/amber/Disang.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
> >copying build/lib/ndfes/amber/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
> >copying build/lib/ndfes/SmoothCurve.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/ScriptUtils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/PathUtils.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/FTSM.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/__init__.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/RBF.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/GPR.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >copying build/lib/ndfes/FES.py ->
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/vFEP.py to
> vFEP.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian/GaussianOutput.py
> to GaussianOutput.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/SpatialBin.py to
> SpatialBin.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/MBAR.py to
> MBAR.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PCV.py to
> PCV.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PathData.py to
> PathData.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode/normalmode.py
> to normalmode.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode/kie.py
> to kie.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/EvalT.py to
> EvalT.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PlotUtils.py to
> PlotUtils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/AutoEquil.py to
> AutoEquil.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/WAVG.py to
> WAVG.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/GridUtils.py to
> GridUtils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/SpatialDim.py to
> SpatialDim.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/Trajectory.py to
> Trajectory.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/ReadCheckpoint.py
> to ReadCheckpoint.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/Bspline.py to
> Bspline.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/Metafile.py to
> Metafile.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/VirtualGrid.py to
> VirtualGrid.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/OptUtils.py
> to OptUtils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/DensityEst.py
> to DensityEst.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/DensityString.py
> to DensityString.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants/Conversions.py
> to Conversions.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants/PeriodicTable.py
> to PeriodicTable.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Restraint.py
> to Restraint.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Reader.py to
> Reader.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Geometry.py
> to Geometry.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Disang.py to
> Disang.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/__init__.py
> to __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/SmoothCurve.py to
> SmoothCurve.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/ScriptUtils.py to
> ScriptUtils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PathUtils.py to
> PathUtils.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/FTSM.py to
> FTSM.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/__init__.py to
> __init__.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/RBF.py to
> RBF.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/GPR.py to
> GPR.cpython-311.pyc
> >byte-compiling
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/FES.py to
> FES.cpython-311.pyc
> >running install_egg_info
> >removing
> '/home/andriy/amber24//lib/python3.11/site-packages/ndfes-3.0-py3.11.egg-info'
> (and everything under it)
> >Copying ndfes.egg-info to
> /home/andriy/amber24//lib/python3.11/site-packages/ndfes-3.0-py3.11.egg-info
> >running install_scripts
> >copying build/scripts-3.11/ndfes-AvgFESs.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/ndfes-path-analyzesims.py ->
> /home/andriy/amber24//bin
> >copying build/scripts-3.11/ndfes-path-prepguess.py ->
> /home/andriy/amber24//bin
> >copying build/scripts-3.11/ndfes-CombineMetafiles.py ->
> /home/andriy/amber24//bin
> >copying build/scripts-3.11/ndfes-PrepareAmberData.py ->
> /home/andriy/amber24//bin
> >copying build/scripts-3.11/ndfes-PrintFES.py -> /home/andriy/amber24//bin
> >copying build/scripts-3.11/ndfes-CheckEquil.py ->
> /home/andriy/amber24//bin
> >changing mode of /home/andriy/amber24//bin/ndfes-AvgFESs.py to 775
> >changing mode of /home/andriy/amber24//bin/ndfes-path-analyzesims.py to
> 775
> >changing mode of /home/andriy/amber24//bin/ndfes-path-prepguess.py to 775
> >changing mode of /home/andriy/amber24//bin/ndfes-CombineMetafiles.py to
> 775
> >changing mode of /home/andriy/amber24//bin/ndfes-PrepareAmberData.py to
> 775
> >changing mode of /home/andriy/amber24//bin/ndfes-PrintFES.py to 775
> >changing mode of /home/andriy/amber24//bin/ndfes-CheckEquil.py to 775
> >-- Fixing Miniconda script shebangs
> >CMake Error at /home/andriy/amber24_src/cmake/Replace-function.cmake:32
> (file):
> > file failed to open for reading (No such file or directory):
> >
> >
> /home/andriy/amber24//miniconda/lib/python3.12/site-packages/conda_build/convert.py
> >Call Stack (most recent call first):
> > /home/andriy/amber24_src/cmake/FixCondaShebang/FixCondaShebang.cmake:48
> (configuretime_file_replace)
> >
> >
> >
> >
> >
>
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
> --
>
> ====================================================================
> David A. Case | dacase1.gmail.com
> Dept. of Chemistry & Chemical Biology |
> Rutgers University | skype: dacase
> PO Box 937 | cell: +1-609-751-8668
> Arroyo Seco, NM 87514 USA | web: casegroup.rutgers.edu
> ====================================================================
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Nov 05 2024 - 08:00:02 PST
