-- ************************************************************************** -- Starting configuration of Amber version 22.0.0... -- CMake Version: 3.15.4 -- 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 -- CUDA version 11.2 detected -- Configuring for SM3.5, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1, SM7.0, SM7.5 and SM8.0 -- Checking CUDA and GNU versions -- compatible -- Found system Anaconda at /home/21cy91r03/miniconda3. It will be used as a Python interpereter, and for additional shared libraries.To disable this, set -DUSE_CONDA_LIBS=FALSE.To use Amber's internal Minconda instead, set DOWNLOAD_MINICONDA to TRUE. To use a different Anaconda install, activate it, delete the build dir, and rerun CMake. To change the Python interpreter in use to a different one inside Anaconda, set the PYTHON_EXECUTABLE variable to point to it. -- Python version 3.10 -- OK -- Found PythonLibs: /home/21cy91r03/miniconda3/lib/libpython3.10.so (found version "3.10.10") -- Could NOT find X11 (missing: X11_X11_INCLUDE_PATH X11_X11_LIB) Couldn't find the X11 development libraries! To search for them try the command: locate libXt On new Fedora install the libXt-devel libXext-devel libX11-devel libICE-devel libSM-devel packages. On old Fedora install the xorg-x11-devel package. On RedHat install the XFree86-devel package. On Ubuntu install the xorg-dev and xserver-xorg packages. -- 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 23 -- >>> No new updates available for Amber 22 -- 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. -- 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_INCLUDE_DIR) -- Could NOT find XBLAS (missing: XBLAS_LIBRARY XBLAS_C_WORKS XBLAS_FORTRAN_WORKS) -- A library with BLAS API found. -- A library with LAPACK API found. -- 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 JAVA_AWT_INCLUDE_PATH) -- 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") -- Could NOT find Boost (missing: Boost_INCLUDE_DIR thread system program_options iostreams regex timer chrono filesystem graph) -- Could NOT find NCCL (missing: NCCL_INCLUDE_DIR NCCL_LIBRARY) -- 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: mkl -- 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=. -- Alternatively, you can request that Amber link to all libraries it finds using -DTRUST_SYSTEM_LIBS=TRUE. -- Forcing plumed to be sourced externally -- Forcing arpack to be built internally -- KMMD not added to 3RDPARTY_SUBDIRS : -- : fftw-3.3 -- Building the GTI version of pmemd.cuda -- Generating amber source scripts -- Configuring subdirs... -- FFTW: compiler supports stack alignment: TRUE -- Found bash: /usr/bin/bash -- netcdf-fortran: Detected TS29113 support in Fortran compiler -- NLopt version 2.7.1 -- Found PythonLibs: /home/21cy91r03/miniconda3/lib/libpython3.10.so (found suitable exact version "3.10.10") -- Could NOT find Guile (missing: GUILE_EXECUTABLE GUILE_ROOT_DIR GUILE_INCLUDE_DIRS GUILE_LIBRARIES) -- Command "/usr/bin/swig -swiglib" failed with output: -- 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 /home/opt_ohpc_pub/utils/cmake/3.15.4/share/cmake-3.15/Modules/CPack.cmake:358 (message): CPack.cmake has already been included!! Call Stack (most recent call first): AmberTools/src/nlopt/CMakeLists.txt:368 (include) -- Reticulating splines... -- Set CUDA PIC flag --compiler-options -fPIC -- Found C++11 support: cxx_std_11 -- CUDA version 11.2 detected -- Configuring QUICK for SM3.5, SM5.0, SM6.0, SM7.0, SM7.5, SM8.0 and SM8.6 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 -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: ----------------------------------------------------- -- arpack - for fundamental linear algebra calculations -- 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 -- ---using installed: ------------------------------------------------------ -- blas - for fundamental linear algebra calculations -- lapack - for fundamental linear algebra calculations -- ucpp - used as a preprocessor for the NAB compiler -- readline - enables an interactive terminal in cpptraj -- zlib - for various compression and decompression tasks -- libbz2 - for bzip2 compression in cpptraj -- plumed - used as an alternate MD backend for Sander -- libm - for fundamental math routines if they are not contained in the C library -- perlmol - chemistry library used by FEW -- ---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 -- 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 -- nccl - NVIDIA parallel GPU communication library -- Features: -- MPI: OFF -- OpenMP: OFF -- CUDA: ON -- NCCL: OFF -- Build Shared Libraries: ON -- Build GUI Interfaces: OFF -- Build Python Programs: ON -- -Python Interpreter: /home/21cy91r03/miniconda3/bin/python (version 3.10) -- Build Perl Programs: ON -- Build configuration: RELEASE -- Target Processor: x86_64 -- Build Documentation: OFF -- Sander Variants: normal LES API LES-API QUICK-CUDA -- Install location: /home/21cy91r03/amber22/ -- Installation of Tests: ON -- Compilers: --  C: GNU 8.3.0 (/opt/ohpc/pub/compiler/gcc/8.3.0/bin/gcc) --  CXX: GNU 8.3.0 (/opt/ohpc/pub/compiler/gcc/8.3.0/bin/g++) --  Fortran: GNU 8.3.0 (/opt/ohpc/pub/compiler/gcc/8.3.0/bin/gfortran) -- Building Tools: -- addles ambpdb antechamber cew cifparse cphstats cpptraj emil etc fe-toolkit few gbnsr6 gem.pmemd gpu_utils 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 -- ************************************************************************** -- 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/21cy91r03/amber22//amber.sh file in your shell. Consider adding the line -- test -f /home/21cy91r03/amber22//amber.sh && source /home/21cy91r03/amber22//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /home/21cy91r03/amber22//amber.csh file in your shell. Consider adding the line -- test -f /home/21cy91r03/amber22//amber.csh && source /home/21cy91r03/amber22//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /home/21cy91r03/amber22/ -- Configuring done CMake Error at AmberTools/src/sander/CMakeLists.txt:412 (add_library): Target "libsander" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? CMake Error at AmberTools/src/sander/CMakeLists.txt:429 (add_library): Target "libsanderles" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? CMake Error at AmberTools/src/sander/CMakeLists.txt:412 (add_library): Target "libsander" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? CMake Error at AmberTools/src/sander/CMakeLists.txt:429 (add_library): Target "libsanderles" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? CMake Error at AmberTools/src/sander/CMakeLists.txt:381 (add_executable): Target "sander.LES" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? CMake Error at AmberTools/src/sander/CMakeLists.txt:361 (add_executable): Target "sander" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? CMake Error at AmberTools/src/sander/CMakeLists.txt:491 (add_executable): Target "sander.quick.cuda" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? CMake Error at AmberTools/src/cpptraj/src/CMakeLists.txt:130 (add_executable): Target "cpptraj" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? CMake Error at cmake/CopyTarget.cmake:58 (add_executable): Target "cpptraj.cuda" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? Call Stack (most recent call first): AmberTools/src/cpptraj/src/CMakeLists.txt:320 (copy_target) CMake Error at src/pmemd/src/CMakeLists.txt:171 (add_executable): Target "pmemd" links to target "plumed::plumed" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? -- Generating done CMake Generate step failed. Build files cannot be regenerated correctly.