Hi,
I am trying both in a computer with Ubuntu 16.04 and another one (older) with Cent OS 6.3. The output from run.cmake can be found below. No errors after running make install appear, although no *.py.MPI programs are compiled:
-- **************************************************************************
-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.19.0
-- 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
-- MPI C Compiler: /usr/bin/mpicc
-- MPI CXX Compiler: /usr/bin/mpicxx
-- MPI Fortran Compiler: /usr/bin/mpif90
-- If these are not the correct MPI wrappers, then set MPI_<language>_COMPILER to the correct wrapper and reconfigure.
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Miniconda is installed in the build directory!
-- 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 20
-- >>> No new updates available for Amber 20
-- Updater done. If you want to install updates, then set the APPLY_UPDATES variable to true.
-- Checking whether to use built-in libraries...
-- Could NOT find Readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY READLINE_IS_LINKABLE)
-- Could NOT find Termcap (missing: TERMCAP_LIBRARY TERMCAP_INCLUDE_DIR)
-- Cannot use internal readline because its dependency (libtermcap/libtinfo/libncurses) was not found.
-- 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-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (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:221 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at /usr/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (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:221 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at /usr/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (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:221 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY)
-- 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 FFTW_LIBRARY_MPI FFTW_INCLUDES_MPI FFTW_MPI_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 xblas. Please set XBLAS_LIBRARY to point to libxblas.a.
-- 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)
CMake Warning (dev) at /usr/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (message):
The package name passed to `find_package_handle_standard_args` (PnetCDF_C)
does not match the name of the calling package (PnetCDF). 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/FindPnetCDF.cmake:273 (find_package_handle_standard_args)
cmake/FindPnetCDF.cmake:396 (find_package_component)
cmake/3rdPartyTools.cmake:339 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find PnetCDF_C (missing: PnetCDF_C_LIBRARY PnetCDF_C_INCLUDE_DIR)
-- 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, 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_MALOC_LIB APBS_WORKS APBS_INCLUDES)
CMake Warning (dev) at /usr/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (message):
The package name passed to `find_package_handle_standard_args` (JNI) does
not match the name of the calling package (JNIFixed). 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/FindJNIFixed.cmake:323 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
cmake/FindPUPIL.cmake:19 (find_package)
cmake/3rdPartyTools.cmake:368 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
-- Could not find the Java development libraries, so PUPIL can't be used. (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB)
-- Could not find lio. If you want to use it, set LIO_HOME to point to a built lio source directory.
-- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5")
-- Checking for Python package mpi4py -- not found
-- 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.
-- 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.
-- 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...
-- FFTW: compiler supports stack alignment: TRUE
-- Found bash: /bin/bash
-- netcdf-fortran: Detected TS29113 support in Fortran compiler
-- Reticulating splines...
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 -O0
-- C Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -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 -O0
-- Fortran Optimized: -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -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
-- mpi4py - MPI support library for MMPBSA.py
-- pnetcdf - used by cpptraj for parallel trajectory output
-- perlmol - chemistry library used by FEW
-- ---using installed: ------------------------------------------------------
-- 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
-- readline - used for the console functionality of cpptraj
-- 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
-- Features:
-- MPI: ON
-- OpenMP: OFF
-- CUDA: OFF
-- NCCL: OFF
-- Build Shared Libraries: ON
-- Build GUI Interfaces: ON
-- Build Python Programs: ON
-- -Python Interpreter: Internal Miniconda (version 3.8)
-- Build Perl Programs: ON
-- Build configuration: RELEASE
-- Target Processor: x86_64
-- Build Documentation: OFF
-- Sander Variants: normal LES API LES-API MPI LES-MPI
-- Install location: /programas/amber20/
-- Installation of Tests: ON
-- Compilers:
-- C: GNU 5.4.0 (/usr/bin/gcc)
-- CXX: GNU 5.4.0 (/usr/bin/g++)
-- Fortran: GNU 5.4.0 (/usr/bin/gfortran)
-- Building Tools:
-- addles amberlite ambpdb antechamber cifparse cphstats cpptraj emil etc few gbnsr6 gem.pmemd leap lib mdgx mm_pbsa mmpbsa_py moft nab ndiff-2.00 nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit parmed pbsa pdb4amber pmemd pymsmt pysander pytraj reduce rism sander saxs sebomd sff sqm xray xtalutil
-- NOT Building Tools:
-- quick - In-development programs are disabled.
-- pymdgx - In-development programs are disabled.
-- 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
-- /programas/amber20//amber.sh file in your shell. Consider adding the line
-- test -f /programas/amber20//amber.sh && source /programas/amber20//amber.sh
-- to your startup file (e.g., ~/.bashrc)
--
-- If you use a C shell (e.g., csh, tcsh), source the
-- /programas/amber20//amber.csh file in your shell. Consider adding the line
-- test -f /programas/amber20//amber.csh && source /programas/amber20//amber.csh
-- to your startup file (e.g., ~/.cshrc)
--
-- Amber will be installed to /programas/amber20/
-- Configuring done
-- Generating done
-- Build files have been written to: /programas/amber20/amber20_src/build
If the cmake build report looks OK, you should now do the following:
make install
source /programas/amber20/amber20/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
Thank you. Best.
> El 4 dic 2020, a las 17:15, David A Case <david.case.rutgers.edu> escribió:
>
> On Tue, Dec 01, 2020, Jose Manuel Granadino Roldán wrote:
>>
>> I have been so far successful installing the MPI versions of some of
>> the programs in the suite. However, I have checked in previous post
>> that mpi4py is needed in order to compile MMPBSA.py.MPI. I have tried
>> to install it with the miniconda downloaded with the installation
>> program, which was straightforward. However, the run.cmake program is
>> not able to find it and thus does not install MMPSA.py.MPI. I am not
>> able to find any flag or option to let run.cmake know where mpi4py
>> is. What am I doing wrong? Any hint?
>
> Can you say what operating system you are using? Could you post the
> exact error messages from run.cmake? I don't remember that anyone else
> has reported this problem, so any guesses you have about how your
> environment might be unique would be appreciated.
>
> ...thanks...dac
>
>
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Received on Sat Dec 05 2020 - 00:00:02 PST
