mpi4py issue in gmx_MMPBSA installation #163

Atulsingh17 · 2022-02-24T12:54:24Z

Hii
I was installing gmx_mmpbsa and ran into this problem.
Kindly help.

sudo pip3 install gmx-MMPBSA
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see pypa/pip#5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
WARNING: The directory '/home/shashank/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
Collecting gmx-MMPBSA
Downloading gmx_MMPBSA-1.5.0.1-py3-none-any.whl (1.7 MB)
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Collecting h5py
Downloading h5py-3.6.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.1 MB)
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Collecting scipy>=1.6.1
Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
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Collecting matplotlib
Downloading matplotlib-3.5.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
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Collecting mpi4py>=3.1.3
Downloading mpi4py-3.1.3.tar.gz (2.5 MB)
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Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting pandas>=1.2.2
Downloading pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
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Collecting seaborn>=0.11.1
Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)
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Requirement already satisfied: pytz>=2017.3 in /usr/lib/python3/dist-packages (from pandas>=1.2.2->gmx-MMPBSA) (2018.3)
Collecting python-dateutil>=2.7.3
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
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Collecting numpy>=1.17.3
Downloading numpy-1.21.5-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
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Collecting pyparsing>=2.2.1
Downloading pyparsing-3.0.7-py3-none-any.whl (98 kB)
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Collecting packaging>=20.0
Downloading packaging-21.3-py3-none-any.whl (40 kB)
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Collecting fonttools>=4.22.0
Downloading fonttools-4.29.1-py3-none-any.whl (895 kB)
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Collecting cycler>=0.10
Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.3.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 1.9 MB/s eta 0:00:00
Collecting pillow>=6.2.0
Downloading Pillow-9.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.3/4.3 MB 1.9 MB/s eta 0:00:00
Collecting cached-property
Downloading cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB)
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.7.3->pandas>=1.2.2->gmx-MMPBSA) (1.11.0)
Building wheels for collected packages: mpi4py
Building wheel for mpi4py (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for mpi4py (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [227 lines of output]
running bdist_wheel
running build
running build_src
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/bench.py -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/init.py -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/run.py -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/main.py -> build/lib.linux-x86_64-3.7/mpi4py
creating build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/_core.py -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/init.py -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/main.py -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-3.7/mpi4py/futures
creating build/lib.linux-x86_64-3.7/mpi4py/util
copying src/mpi4py/util/pkl5.py -> build/lib.linux-x86_64-3.7/mpi4py/util
copying src/mpi4py/util/init.py -> build/lib.linux-x86_64-3.7/mpi4py/util
copying src/mpi4py/util/dtlib.py -> build/lib.linux-x86_64-3.7/mpi4py/util
copying src/mpi4py/py.typed -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/main.pyi -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/run.pyi -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/MPI.pyi -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/bench.pyi -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/init.pyi -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/dl.pyi -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/init.pxd -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-3.7/mpi4py
copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-3.7/mpi4py
creating build/lib.linux-x86_64-3.7/mpi4py/include
creating build/lib.linux-x86_64-3.7/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-3.7/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-3.7/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-3.7/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-3.7/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-3.7/mpi4py/include/mpi4py
copying src/mpi4py/futures/main.pyi -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/pool.pyi -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/init.pyi -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/_lib.pyi -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/server.pyi -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/_core.pyi -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/futures/aplus.pyi -> build/lib.linux-x86_64-3.7/mpi4py/futures
copying src/mpi4py/util/init.pyi -> build/lib.linux-x86_64-3.7/mpi4py/util
copying src/mpi4py/util/dtlib.pyi -> build/lib.linux-x86_64-3.7/mpi4py/util
copying src/mpi4py/util/pkl5.pyi -> build/lib.linux-x86_64-3.7/mpi4py/util
running build_clib
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /usr/bin/mpicc
MPI C++ compiler: /usr/bin/mpicxx
MPI F compiler: /usr/bin/mpifort
MPI F90 compiler: /usr/bin/mpif90
MPI F77 compiler: /usr/bin/mpif77
checking for library 'lmpe' ...
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -llmpe -o _configtest
/usr/bin/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_64-3.7
creating build/temp.linux-x86_64-3.7/src
creating build/temp.linux-x86_64-3.7/src/lib-pmpi
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-3.7/src/lib-pmpi/mpe.o
creating build/lib.linux-x86_64-3.7/mpi4py/lib-pmpi
/usr/bin/mpicc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--no-as-needed build/temp.linux-x86_64-3.7/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-3.7/mpi4py/lib-pmpi/libmpe.so
checking for library 'vt-mpi' ...
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt-mpi -o _configtest
/usr/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt.mpi -o _configtest
/usr/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt' dylib library
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-3.7/src/lib-pmpi/vt.o
/usr/bin/mpicc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--no-as-needed build/temp.linux-x86_64-3.7/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-3.7/mpi4py/lib-pmpi/libvt.so
checking for library 'vt-mpi' ...
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt-mpi -o _configtest
/usr/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt.mpi -o _configtest
/usr/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-mpi' dylib library
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-3.7/src/lib-pmpi/vt-mpi.o
/usr/bin/mpicc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--no-as-needed build/temp.linux-x86_64-3.7/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-3.7/mpi4py/lib-pmpi/libvt-mpi.so
checking for library 'vt-hyb' ...
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt-hyb -o _configtest
/usr/bin/ld: cannot find -lvt-hyb
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.ompi' ...
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt.ompi -o _configtest
/usr/bin/ld: cannot find -lvt.ompi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-hyb' dylib library
/usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-3.7/src/lib-pmpi/vt-hyb.o
/usr/bin/mpicc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--no-as-needed build/temp.linux-x86_64-3.7/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-3.7/mpi4py/lib-pmpi/libvt-hyb.so
running build_ext
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /usr/bin/mpicc
MPI C++ compiler: /usr/bin/mpicxx
MPI F compiler: /usr/bin/mpifort
MPI F90 compiler: /usr/bin/mpif90
MPI F77 compiler: /usr/bin/mpif77
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
x86_64-linux-gnu-gcc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
x86_64-linux-gnu-gcc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.dl' extension
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/usr/include/python3.7m -c src/dynload.c -o build/temp.linux-x86_64-3.7/src/dynload.o
src/dynload.c:5:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
warning: build_ext: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1

  warning: build_ext: building optional extension "mpi4py.dl" failed
  
  checking for MPI compile and link ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  success!
  removing: _configtest.c _configtest.o
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  checking for missing MPI functions/symbols ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  success!
  removing: _configtest.c _configtest.o
  checking for function 'MPI_Type_create_f90_integer' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  checking for function 'MPI_Type_create_f90_real' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  checking for function 'MPI_Type_create_f90_complex' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  checking for function 'MPI_Status_c2f' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  checking for function 'MPI_Status_f2c' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  checking for symbol 'MPI_LB' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  checking for symbol 'MPI_UB' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  checking for dlopen() availability ...
  checking for header 'dlfcn.h' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  success!
  removing: _configtest.c _configtest.o
  success!
  checking for library 'dl' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -ldl -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  checking for function 'dlopen' ...
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.7m -c _configtest.c -o _configtest.o
  /usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.7 -ldl -o _configtest
  success!
  removing: _configtest.c _configtest.o _configtest
  building 'mpi4py.MPI' extension
  /usr/bin/mpicc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/usr/include/python3.7m -c src/MPI.c -o build/temp.linux-x86_64-3.7/src/MPI.o
  In file included from src/MPI.c:4:0:
  src/mpi4py.MPI.c:6:10: fatal error: Python.h: No such file or directory
   #include "Python.h"
            ^~~~~~~~~~
  compilation terminated.
  error: command '/usr/bin/mpicc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for mpi4py
Failed to build mpi4py
ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

The text was updated successfully, but these errors were encountered:

marioernestovaldes · 2022-02-24T14:59:30Z

I see you are running sudo pip3 install gmx-MMPBSA I don't recall seeing that in the installation instructions... A similar issue was already reported and solved... Please, follow carefully the installation instructions to avoid this kind of problem... let us know is the problem still persists after following the installation instructions...

cheers!

Atulsingh17 · 2022-02-25T07:10:59Z

Hii
Thanks for your response.
I followed the installation instruction on given link.
Everything worked fine till these commands.

conda update conda

conda create -n gmxMMPBSA python=3.9 -y -q

conda activate gmxMMPBSA

conda install -c conda-forge mpi4py ambertools compilers -y -q

python -m pip install git+https://github.com/ParmEd/ParmEd.git@16fb236

python -m pip install pyqt5

But when I run this command

python -m pip install gmx_MMPBSA

I got this error.

Terminal Output

(gmxMMPBSA) shashank@shashank:~$ python -m pip install gmx_MMPBSA
Collecting gmx_MMPBSA
Using cached gmx_MMPBSA-1.5.0.2-py3-none-any.whl (1.7 MB)
Requirement already satisfied: pandas>=1.2.2 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from gmx_MMPBSA) (1.3.1)
Collecting seaborn>=0.11.1
Using cached seaborn-0.11.2-py3-none-any.whl (292 kB)
Requirement already satisfied: scipy>=1.6.1 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from gmx_MMPBSA) (1.7.0)
Collecting h5py
Using cached h5py-3.6.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB)
Collecting mpi4py>=3.1.3
Using cached mpi4py-3.1.3.tar.gz (2.5 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
Requirement already satisfied: matplotlib in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from gmx_MMPBSA) (3.4.2)
Requirement already satisfied: numpy>=1.17.3 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (1.21.1)
Requirement already satisfied: python-dateutil>=2.7.3 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (2.8.2)
Requirement already satisfied: pytz>=2017.3 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (2021.3)
Requirement already satisfied: six>=1.5 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from python-dateutil>=2.7.3->pandas>=1.2.2->gmx_MMPBSA) (1.16.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib->gmx_MMPBSA) (1.3.1)
Requirement already satisfied: pillow>=6.2.0 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib->gmx_MMPBSA) (8.2.0)
Requirement already satisfied: cycler>=0.10 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib->gmx_MMPBSA) (0.11.0)
Requirement already satisfied: pyparsing>=2.2.1 in ./anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib->gmx_MMPBSA) (3.0.7)
Building wheels for collected packages: mpi4py
Building wheel for mpi4py (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/python /home/shashank/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpvga81eg8
cwd: /tmp/pip-install-85y4a2_a/mpi4py_70c57c0fa6c94f28ade7d104c62e25d5
Complete output (160 lines):
running bdist_wheel
running build
running build_src
running build_py
creating build
creating build/lib.linux-x86_64-3.9
creating build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/bench.py -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/init.py -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/run.py -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/main.py -> build/lib.linux-x86_64-3.9/mpi4py
creating build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/_core.py -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/init.py -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/main.py -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-3.9/mpi4py/futures
creating build/lib.linux-x86_64-3.9/mpi4py/util
copying src/mpi4py/util/pkl5.py -> build/lib.linux-x86_64-3.9/mpi4py/util
copying src/mpi4py/util/init.py -> build/lib.linux-x86_64-3.9/mpi4py/util
copying src/mpi4py/util/dtlib.py -> build/lib.linux-x86_64-3.9/mpi4py/util
copying src/mpi4py/py.typed -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/main.pyi -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/run.pyi -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/MPI.pyi -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/bench.pyi -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/init.pyi -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/dl.pyi -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/init.pxd -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-3.9/mpi4py
creating build/lib.linux-x86_64-3.9/mpi4py/include
creating build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/futures/main.pyi -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/pool.pyi -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/init.pyi -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/_lib.pyi -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/server.pyi -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/_core.pyi -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/aplus.pyi -> build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/util/init.pyi -> build/lib.linux-x86_64-3.9/mpi4py/util
copying src/mpi4py/util/dtlib.pyi -> build/lib.linux-x86_64-3.9/mpi4py/util
copying src/mpi4py/util/pkl5.pyi -> build/lib.linux-x86_64-3.9/mpi4py/util
running build_clib
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc
MPI C++ compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicxx
MPI F compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpifort
MPI F90 compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpif90
MPI F77 compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpif77
checking for library 'lmpe' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -llmpe -o _configtest
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/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_64-3.9
creating build/temp.linux-x86_64-3.9/src
creating build/temp.linux-x86_64-3.9/src/lib-pmpi
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-3.9/src/lib-pmpi/mpe.o
creating build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -shared -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -Wl,--no-as-needed build/temp.linux-x86_64-3.9/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi/libmpe.so
checking for library 'vt-mpi' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -lvt-mpi -o _configtest
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -lvt.mpi -o _configtest
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt' dylib library
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-3.9/src/lib-pmpi/vt.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -shared -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -Wl,--no-as-needed build/temp.linux-x86_64-3.9/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi/libvt.so
checking for library 'vt-mpi' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -lvt-mpi -o _configtest
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -lvt.mpi -o _configtest
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-mpi' dylib library
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-mpi.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -shared -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -Wl,--no-as-needed build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi/libvt-mpi.so
checking for library 'vt-hyb' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -lvt-hyb -o _configtest
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt-hyb
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.ompi' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -lvt.ompi -o _configtest
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt.ompi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-hyb' dylib library
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-hyb.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -shared -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -Wl,--no-as-needed build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi/libvt-hyb.so
running build_ext
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc
MPI C++ compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicxx
MPI F compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpifort
MPI F90 compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpif90
MPI F77 compiler: /home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpif77
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -I/home/shashank/anaconda3/envs/gmxMMPBSA/include/python3.9 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -I/home/shashank/anaconda3/envs/gmxMMPBSA/include/python3.9 -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -Lbuild/temp.linux-x86_64-3.9 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -I/home/shashank/anaconda3/envs/gmxMMPBSA/include/python3.9 -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -Lbuild/temp.linux-x86_64-3.9 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.dl' extension
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/shashank/anaconda3/envs/gmxMMPBSA/include/python3.9 -c src/dynload.c -o build/temp.linux-x86_64-3.9/src/dynload.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -shared -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include build/temp.linux-x86_64-3.9/src/dynload.o -Lbuild/temp.linux-x86_64-3.9 -ldl -o build/lib.linux-x86_64-3.9/mpi4py/dl.cpython-39-x86_64-linux-gnu.so
checking for MPI compile and link ...
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -I/home/shashank/anaconda3/envs/gmxMMPBSA/include/python3.9 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -I/home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -fPIC -I/home/shashank/anaconda3/envs/gmxMMPBSA/include/python3.9 -c _configtest.c -o _configtest.o
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -Wl,-rpath-link,/home/shashank/anaconda3/envs/gmxMMPBSA/lib -L/home/shashank/anaconda3/envs/gmxMMPBSA/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/shashank/anaconda3/envs/gmxMMPBSA/include _configtest.o -Lbuild/temp.linux-x86_64-3.9 -o _configtest
/home/shashank/anaconda3/envs/gmxMMPBSA/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/shashank/anaconda3/envs/gmxMMPBSA/lib/libz.so.1: undefined reference to `memcpy@GLIBC_2.14'
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!

ERROR: Failed building wheel for mpi4py
Failed to build mpi4py
ERROR: Could not build wheels for mpi4py which use PEP 517 and cannot be installed directly

Atulsingh17 · 2022-02-25T07:38:24Z

Hii again
I think I have successfully installed gmx_mmpbsa by using these commands given by you in response to a researchgate question.

conda create --name AmberTools21
conda activate AmberTools21
conda install -c conda-forge mpi4py ambertools=21 compilers
python -m pip install PyQt5 gmx_MMPBSA

Now when I run the test command
gmx_MMPBSA_test -h in same environment its working normally as below.

(AmberTools21) shashank@shashank:~$ gmx_MMPBSA_test -h
usage: gmx_MMPBSA_test [-h] [-v] [-t [{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,101} ...]] [-f FOLDER] [-r] [-ng] [-n NUM_PROCESSORS]

This program is part of gmx_MMPBSA and will allow you to run various gmx_MMPBSA examples easily.

optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit

Test options:
-t [{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,101} ...]
The level the test is going to be run at. Multiple systems and analysis can be run at the same time.
Nr. of Sys
* 0 16 All -- Run all examples (Can take a long time!!!)
* 1 13 Minimal -- Does a minimal test with a set of systems and analyzes
that show that gmx_MMPBSA runs correctly. Only exclude 3drism, nmode
protein-ligand MT because take a long time or are redundant
* 2 9 Fast -- Only the calculations that take a short time are run (Default)
[Systems]:
Slow Frames
* 3 . | 10 Protein-Ligand (Single trajectory approximation)
* 4 . | 10 Protein-Protein
* 5 . | 10 Protein-DNA
* 6 x | 4 Protein-Membrane
* 7 . | 10 Protein-Glycan
* 8 x | 4 Metalloprotein-Peptide
* 9 . | 10 Protein-DNA-RNA-IONs-Ligand
* 10 x | 4 Protein-Ligand (CHARMM force field)
* 11 x | 4 Protein-ligand complex in membrane with CHARMMff
[Analysis]:
Slow Frames
* 12 . | 10 Alanine Scanning
* 13 . | 10 Stability calculation
* 14 . | 10 Decomposition Analysis
* 15 . | 16 Interaction Entropy approximation
* 16 . | 10 Protein-Ligand (Multiple trajectory approximation)
* 17 x | 4 Entropy calculation using Normal Mode approximation
* 18 x | 4 Calculations using 3D-RISM approximation
-f FOLDER, --folder FOLDER
Defines the folder to store all data
-r, --reuse Defines the existing test forlder will be reuse
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-n NUM_PROCESSORS, --num_processors NUM_PROCESSORS
Defines the number of processor cores you want to use with MPI per calculation. If the number of frames is less than the number of cpus defined, the calculation will be performed withthe number of processors = number of frames

gmx_MMPBSA is an effort to implement the GB/PB and others calculations in GROMACS.
Based on MMPBSA.py (version 16.0) and AmberTools20

But when I leave the environment I am getting this error.

shashank@shashank:~$ gmx_MMPBSA_test -h
Traceback (most recent call last):
File "/home/shashank/.local/bin/gmx_MMPBSA_test", line 5, in
from GMXMMPBSA.app import gmxmmpbsa_test
File "/home/shashank/.local/lib/python3.7/site-packages/GMXMMPBSA/app.py", line 26, in
from GMXMMPBSA.infofile import InfoFile
File "/home/shashank/.local/lib/python3.7/site-packages/GMXMMPBSA/infofile.py", line 120
if rematch := inputre.match(line):
^
SyntaxError: invalid syntax

Valdes-Tresanco-MS · 2022-02-25T07:39:49Z

I don't understand why if you are doing the procedure from scratch, you have installed packages like pandas, matplotlib, etc as gmx_MMPBSA dependencies. Although it is tedious, it is best to carry out everything from the beginning. Please follow these instructions as-is:

Deactivate the gmxMMPBSA environment if it is active
conda deactivate
Remove this env
conda env remove -n gmxMMPBSA
Follow the standard installation instructions

conda create -n gmxMMPBSA python=3.9 -y -q 
conda activate gmxMMPBSA 
conda install -c conda-forge mpi4py ambertools compilers -y -q 
python -m pip install git+https://github.com/ParmEd/ParmEd.git@16fb236 
python -m pip install pyqt5
python -m pip install gmx_MMPBSA

If this does not work, please try to install gmx_MMPBSA from conda follow these instructions:

Deactivate the gmxMMPBSA environment if it is active
conda deactivate
Remove this env
conda env remove -n gmxMMPBSA

conda create -n gmxMMPBSA python=3.9 -y -q        
conda activate gmxMMPBSA                                                     
conda install -c conda-forge gmx_mmpbsa
python -m pip install git+https://github.com/ParmEd/ParmEd.git@16fb236
python -m pip install pyqt5

Valdes-Tresanco-MS · 2022-02-25T07:47:28Z

Excellent... 👍

But when I leave the environment I am getting this error.

Since gmx_MMPBSA is installed in a conda environment so you don't have compatibility issues with other packages or conflicts with environment variables, once you exit this environment, all configuration stops working. To make your work easier, you can create an alias that activates the environment in the following way...
add this line to your .bashrc
alias condammpbsa="conda activate gmxMMPBSA"

Note that the alias name must not be gmx_MMPBSA (executable) to avoid execution conflicts.

I will close this issue as it is solved. Feel free to open a new one if you require

Sincerely.
Mario S

Valdes-Tresanco-MS · 2022-02-25T07:53:26Z

shashank@shashank:~$ gmx_MMPBSA_test -h Traceback (most recent call last): File "/home/shashank/.local/bin/gmx_MMPBSA_test", line 5, in from GMXMMPBSA.app import gmxmmpbsa_test File "/home/shashank/.local/lib/python3.7/site-packages/GMXMMPBSA/app.py", line 26, in from GMXMMPBSA.infofile import InfoFile File "/home/shashank/.local/lib/python3.7/site-packages/GMXMMPBSA/infofile.py", line 120 if rematch := inputre.match(line): ^ SyntaxError: invalid syntax

Now that I'm aware of it, please remove installations of gmx_MMPBSA that are not in an environment. Since it is bound to the python system, it may take precedence in execution, or conflict with its installation in the conda environment if the PYTHONPATH variable is set.

You can remove it using pip if you installed it with it or manually if necessary. Make sure you are not in the conda environment.
which pip should be something like /usr/bin/pip
pip uninstall gmx_MMPBSA

Atulsingh17 · 2022-02-25T08:06:11Z

Thanks a lot. I appreciate your help.

AjitKrSingh08 · 2024-07-06T08:13:00Z

@Valdes-Tresanco-MS I installed gmx_MMPBSA using the commands you shared:
conda create -n gmxMMPBSA python=3.9 -y -q
conda activate gmxMMPBSA
conda install -c conda-forge gmx_mmpbsa
python -m pip install git+https://github.com/ParmEd/ParmEd.git@16fb236
python -m pip install pyqt5

everything looks fine, and I was able to do MMPBSA/MMGBSA analysis for my system, although when I tried calculating Interaction Entropy it shows error:
Traceback (most recent call last):
File "/home/anupam/.local/bin/gmx_MMPBSA_ana", line 8, in
sys.exit(gmxmmpbsa_ana())
File "/home/anupam/.local/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 129, in gmxmmpbsa_ana
from GMXMMPBSA.analyzer.gui import GMX_MMPBSA_ANA
File "/home/anupam/.local/lib/python3.8/site-packages/GMXMMPBSA/analyzer/gui.py", line 32, in
from GMXMMPBSA.analyzer.plots import Tables
File "/home/anupam/.local/lib/python3.8/site-packages/GMXMMPBSA/analyzer/plots.py", line 36, in
import seaborn as sns
File "/home/anupam/.local/lib/python3.8/site-packages/seaborn/init.py", line 2, in
from .rcmod import * # noqa: F401,F403
File "/home/anupam/.local/lib/python3.8/site-packages/seaborn/rcmod.py", line 7, in
from . import palettes
File "/home/anupam/.local/lib/python3.8/site-packages/seaborn/palettes.py", line 9, in
from .utils import desaturate, get_color_cycle
File "/home/anupam/.local/lib/python3.8/site-packages/seaborn/utils.py", line 10, in
from scipy import stats
ModuleNotFoundError: No module named 'scipy'
[ERROR ] Unable to start gmx_MMPBSA_ana...
[INFO ] Finalized...

If anyone can guide me on this.

Valdes-Tresanco-MS · 2024-07-06T08:17:35Z

@AjitKrSingh08 Please, open a new issue since this one was solved a time ago

marioernestovaldes added the third-party package Represents a bug or limitation of a third-party package label Feb 24, 2022

Valdes-Tresanco-MS added python version Using an incompatible Python version or installing in a wrong environment and removed third-party package Represents a bug or limitation of a third-party package labels Feb 24, 2022

Valdes-Tresanco-MS closed this as completed Feb 25, 2022

Repository owner locked as resolved and limited conversation to collaborators Jul 6, 2024

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mpi4py issue in gmx_MMPBSA installation #163

mpi4py issue in gmx_MMPBSA installation #163

Atulsingh17 commented Feb 24, 2022

marioernestovaldes commented Feb 24, 2022

Atulsingh17 commented Feb 25, 2022 •

edited by Valdes-Tresanco-MS

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mpi4py issue in gmx_MMPBSA installation #163

mpi4py issue in gmx_MMPBSA installation #163

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Atulsingh17 commented Feb 24, 2022

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Valdes-Tresanco-MS commented Jul 6, 2024

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edited by Valdes-Tresanco-MS

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