Closed kimlabSchatterjee closed 3 years ago
Valdes-Tresanco-MS
commented
3 years ago Please try installing/reinstalling the OpenMPI library like this:
sudo apt install openmpi-bin libopenmpi-dev openssh-clientor this way
sudo apt install --reinstall openmpi-bin libopenmpi-dev openssh-clientBest!
kimlabSchatterjee
commented
3 years ago I think that trick works, thank you...I am able to install it...Unfortunately unable to execute it . mu .bashrc settings given bellow source /usr/local/gromacs/bin/GMXRC source /home/kimlab/Downloads/amber20/amber.sh export CUDAROOT=/usr/local/cuda/bin/ export CUDA_HOME=/usr/local/cuda export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib:$CUDA_HOME/lib64 export LD_LIBRARY_PATH="/usr/local/cuda/lib:${LD_LIBRARY_PATH}" export GPU_INCLUDE_PATH=/usr/local/cuda/include export GPU_LIBRARY_PATH=/usr/local/cuda/lib64 export PATH="/home/kimlab/Downloads/amber20/bin:$PATH"
I updated gmxMMMPASA still it is not working
please help
(base) kimlab@kimlab:~/Desktop$ amber.python -m pip install gmx_MMPBSA --upgrade
WARNING: Value for scheme.headers does not match. Please report this to https://github.com/pypa/pip/issues/9617 distutils: /home/kimlab/Downloads/amber20/miniconda/include/python3.8/UNKNOWN sysconfig: /home/kimlab/Downloads/amber20/miniconda/include/python3.8 WARNING: Additional context: user = False home = None root = None prefix = None Requirement already satisfied: gmx_MMPBSA in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (1.4.2) Requirement already satisfied: seaborn>=0.11.1 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from gmx_MMPBSA) (0.11.1) Requirement already satisfied: mpi4py>=3.0.3 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from gmx_MMPBSA) (3.0.3) Requirement already satisfied: pandas>=1.2.2 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from gmx_MMPBSA) (1.2.4) Requirement already satisfied: pytz>=2017.3 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (2021.1) Requirement already satisfied: numpy>=1.16.5 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (1.20.1) Requirement already satisfied: python-dateutil>=2.7.3 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (2.8.1) Requirement already satisfied: six>=1.5 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from python-dateutil>=2.7.3->pandas>=1.2.2->gmx_MMPBSA) (1.15.0) Requirement already satisfied: matplotlib>=2.2 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from seaborn>=0.11.1->gmx_MMPBSA) (3.4.1) Requirement already satisfied: scipy>=1.0 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from seaborn>=0.11.1->gmx_MMPBSA) (1.6.2) Requirement already satisfied: pyparsing>=2.2.1 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from matplotlib>=2.2->seaborn>=0.11.1->gmx_MMPBSA) (2.4.7) Requirement already satisfied: cycler>=0.10 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from matplotlib>=2.2->seaborn>=0.11.1->gmx_MMPBSA) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from matplotlib>=2.2->seaborn>=0.11.1->gmx_MMPBSA) (1.3.1) Requirement already satisfied: pillow>=6.2.0 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from matplotlib>=2.2->seaborn>=0.11.1->gmx_MMPBSA) (8.2.0) WARNING: Value for scheme.headers does not match. Please report this to https://github.com/pypa/pip/issues/9617 distutils: /home/kimlab/Downloads/amber20/miniconda/include/python3.8/UNKNOWN sysconfig: /home/kimlab/Downloads/amber20/miniconda/include/python3.8 WARNING: Additional context: user = False home = None root = None prefix = None (base) kimlab@kimlab:~/Desktop$ gmx_MMPBSA gmx_MMPBSA: command not found (base) kimlab@kimlab:~/Desktop$ gmx_MMPBSA_test gmx_MMPBSA_test: command not found (base) kimlab@kimlab:~/Desktop$
**
Valdes-Tresanco-MS
commented
3 years ago The gmx_MMPBSA executables (gmx_MMPBSA, gmx_MMPBSA_ana, and gmx_MMPBSA_test) are created in the bin folder in the Amber miniconda environment (/home/kimlab/Downloads/amber20/miniconda/bin in your case). Please, check this section and tell us if you were able to solve the problem
Valdes-Tresanco-MS
commented
3 years ago Hi @kimlabSchatterjee Were you able to solve the problem?
kimlabSchatterjee
commented
3 years ago Hello sir, Thank you. I have compiled it successfully. Now, I am studying the manual in order to set up VS.
On Thu, May 13, 2021 at 10:25 AM Mario Sergio Valdés Tresanco < @.***> wrote:
Hi @kimlabSchatterjee https://github.com/kimlabSchatterjee Were you able to solve the problem?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/36#issuecomment-840216745, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARJCTISJDGOE3A5AWWXU7XTTNMS7RANCNFSM433H2WZA .
Valdes-Tresanco-MS
commented
3 years ago
i installed amber tools. it working nicely. during installation of gmx_MMPBSA tool encountered by following error
(base) kimlab@kimlab:~/Desktop$ amber.python -m pip install gmx_MMPBSA WARNING: Value for scheme.headers does not match. Please report this to https://github.com/pypa/pip/issues/9617 distutils: /home/kimlab/Downloads/amber20/miniconda/include/python3.8/UNKNOWN sysconfig: /home/kimlab/Downloads/amber20/miniconda/include/python3.8 WARNING: Additional context: user = False home = None root = None prefix = None Collecting gmx_MMPBSA Using cached gmx_MMPBSA-1.4.1-py3-none-any.whl (566 kB) Collecting mpi4py>=3.0.3 Using cached mpi4py-3.0.3.tar.gz (1.4 MB) Requirement already satisfied: seaborn>=0.11.1 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from gmx_MMPBSA) (0.11.1) Requirement already satisfied: pandas>=1.2.2 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from gmx_MMPBSA) (1.2.4) Requirement already satisfied: pytz>=2017.3 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (2021.1) Requirement already satisfied: python-dateutil>=2.7.3 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (2.8.1) Requirement already satisfied: numpy>=1.16.5 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (1.20.1) Requirement already satisfied: six>=1.5 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from python-dateutil>=2.7.3->pandas>=1.2.2->gmx_MMPBSA) (1.15.0) Requirement already satisfied: scipy>=1.0 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from seaborn>=0.11.1->gmx_MMPBSA) (1.6.2) Requirement already satisfied: matplotlib>=2.2 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from seaborn>=0.11.1->gmx_MMPBSA) (3.4.1) Requirement already satisfied: pillow>=6.2.0 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from matplotlib>=2.2->seaborn>=0.11.1->gmx_MMPBSA) (8.2.0) Requirement already satisfied: pyparsing>=2.2.1 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from matplotlib>=2.2->seaborn>=0.11.1->gmx_MMPBSA) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from matplotlib>=2.2->seaborn>=0.11.1->gmx_MMPBSA) (1.3.1) Requirement already satisfied: cycler>=0.10 in /home/kimlab/Downloads/amber20/miniconda/lib/python3.8/site-packages (from matplotlib>=2.2->seaborn>=0.11.1->gmxMMPBSA) (0.10.0) Building wheels for collected packages: mpi4py Building wheel for mpi4py (setup.py) ... error ERROR: Command errored out with exit status 1: command: /home/kimlab/Downloads/amber20/bin/amber.python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-30ys9i7/mpi4py0b0ebb9a6b924999bb908103e40053b8/setup.py'"'"'; file='"'"'/tmp/pip-install-30ys9i7/mpi4py_0b0ebb9a6b924999bb908103e40053b8/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdistwheel -d /tmp/pip-wheel-fhpwgooj cwd: /tmp/pip-install-30ys9i7/mpi4py_0b0ebb9a6b924999bb908103e40053b8/ Complete output (126 lines): running bdist_wheel running build running build_src running build_py creating build creating build/lib.linux-x86_64-3.8 creating build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/init.py -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/run.py -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/bench.py -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/main.py -> build/lib.linux-x86_64-3.8/mpi4py creating build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/init.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/main.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/init.pxd -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-3.8/mpi4py creating build/lib.linux-x86_64-3.8/mpi4py/include creating build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py running build_clib MPI configuration: [mpi] from 'mpi.cfg' checking for library 'lmpe' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -llmpe -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -llmpe collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'mpe' dylib library creating build/temp.linux-x86_64-3.8 creating build/temp.linux-x86_64-3.8/src creating build/temp.linux-x86_64-3.8/src/lib-pmpi gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/mpe.o creating build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libmpe.so checking for library 'vt-mpi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt-mpi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt-mpi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o checking for library 'vt.mpi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt.mpi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt.mpi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'vt' dylib library gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/vt.o gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libvt.so checking for library 'vt-mpi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt-mpi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt-mpi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o checking for library 'vt.mpi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt.mpi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt.mpi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'vt-mpi' dylib library gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-mpi.o gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libvt-mpi.so checking for library 'vt-hyb' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt-hyb -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt-hyb collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o checking for library 'vt.ompi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt.ompi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt.ompi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'vt-hyb' dylib library gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-hyb.o gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libvt-hyb.so running build_ext MPI configuration: [mpi] from 'mpi.cfg' checking for dlopen() availability ... checking for header 'dlfcn.h' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c _configtest.c -o _configtest.o success! removing: _configtest.c _configtest.o success! checking for library 'dl' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o _configtest success! removing: _configtest.c _configtest.o _configtest checking for function 'dlopen' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o _configtest success! removing: _configtest.c _configtest.o _configtest building 'mpi4py.dl' extension gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c src/dynload.c -o build/temp.linux-x86_64-3.8/src/dynload.o gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.8/src/dynload.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o build/lib.linux-x86_64-3.8/mpi4py/dl.cpython-38-x86_64-linux-gnu.so checking for MPI compile and link ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c _configtest.c -o _configtest.o _configtest.c:2:10: fatal error: mpi.h: No such file or directory
include
compilation terminated. failure. removing: _configtest.c _configtest.o error: Cannot compile MPI programs. Check your configuration!!!
ERROR: Failed building wheel for mpi4py Running setup.py clean for mpi4py Failed to build mpi4py Installing collected packages: mpi4py, gmx-MMPBSA Running setup.py install for mpi4py ... error ERROR: Command errored out with exit status 1: command: /home/kimlab/Downloads/amber20/bin/amber.python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-30ys9i7_/mpi4py0b0ebb9a6b924999bb908103e40053b8/setup.py'"'"'; file='"'"'/tmp/pip-install-30ys9i7/mpi4py0b0ebb9a6b924999bb908103e40053b8/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-l0vfp8zd/install-record.txt --single-version-externally-managed --compile --install-headers /home/kimlab/Downloads/amber20/miniconda/include/python3.8/mpi4py cwd: /tmp/pip-install-30ys9i7/mpi4py_0b0ebb9a6b924999bb908103e40053b8/ Complete output (126 lines): running install running build running build_src running build_py creating build creating build/lib.linux-x86_64-3.8 creating build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/init.py -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/run.py -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/bench.py -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/main.py -> build/lib.linux-x86_64-3.8/mpi4py creating build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/init.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/main.py -> build/lib.linux-x86_64-3.8/mpi4py/futures copying src/mpi4py/init.pxd -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-3.8/mpi4py copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-3.8/mpi4py creating build/lib.linux-x86_64-3.8/mpi4py/include creating build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py running build_clib MPI configuration: [mpi] from 'mpi.cfg' checking for library 'lmpe' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -llmpe -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -llmpe collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'mpe' dylib library creating build/temp.linux-x86_64-3.8 creating build/temp.linux-x86_64-3.8/src creating build/temp.linux-x86_64-3.8/src/lib-pmpi gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/mpe.o creating build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libmpe.so checking for library 'vt-mpi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt-mpi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt-mpi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o checking for library 'vt.mpi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt.mpi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt.mpi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'vt' dylib library gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/vt.o gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libvt.so checking for library 'vt-mpi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt-mpi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt-mpi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o checking for library 'vt.mpi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt.mpi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt.mpi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'vt-mpi' dylib library gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-mpi.o gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libvt-mpi.so checking for library 'vt-hyb' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt-hyb -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt-hyb collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o checking for library 'vt.ompi' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt.ompi -o _configtest /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt.ompi collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'vt-hyb' dylib library gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-hyb.o gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libvt-hyb.so running build_ext MPI configuration: [mpi] from 'mpi.cfg' checking for dlopen() availability ... checking for header 'dlfcn.h' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c _configtest.c -o _configtest.o success! removing: _configtest.c _configtest.o success! checking for library 'dl' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o _configtest success! removing: _configtest.c _configtest.o _configtest checking for function 'dlopen' ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c _configtest.c -o _configtest.o gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ _configtest.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o _configtest success! removing: _configtest.c _configtest.o _configtest building 'mpi4py.dl' extension gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c src/dynload.c -o build/temp.linux-x86_64-3.8/src/dynload.o gcc -pthread -shared -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -L/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath=/home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.8/src/dynload.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o build/lib.linux-x86_64-3.8/mpi4py/dl.cpython-38-x86_64-linux-gnu.so checking for MPI compile and link ... gcc -pthread -B /home/kimlab/Downloads/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kimlab/Downloads/amber20/miniconda/include/python3.8 -c _configtest.c -o _configtest.o _configtest.c:2:10: fatal error: mpi.h: No such file or directory
include
ERROR: Command errored out with exit status 1: /home/kimlab/Downloads/amber20/bin/amber.python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-30ys9i7_/mpi4py0b0ebb9a6b924999bb908103e40053b8/setup.py'"'"'; file='"'"'/tmp/pip-install-30ys9i7/mpi4py_0b0ebb9a6b924999bb908103e40053b8/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-l0vfp8zd/install-record.txt --single-version-externally-managed --compile --install-headers /home/kimlab/Downloads/amber20/miniconda/include/python3.8/mpi4py Check the logs for full command output.