INSTALLATION ERROR

[Raj Choudhary]

Dear Sir

While installation of gmx_MMPBSA, I am getting the following error.

(base) guju@guju-desktop:~$ python -m pip install gmx_MMPBSA

Collecting gmx_MMPBSA
  Downloading gmx_MMPBSA-1.6.2-py3-none-any.whl.metadata (4.1 kB)
Collecting pandas==1.2.2 (from gmx_MMPBSA)
  Downloading pandas-1.2.2.tar.gz (5.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.5/5.5 MB 6.2 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting seaborn<0.12 (from gmx_MMPBSA)
  Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 292.8/292.8 kB 4.6 MB/s eta 0:00:00
Collecting mpi4py>=3.1.3 (from gmx_MMPBSA)
  Downloading mpi4py-3.1.5.tar.gz (2.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.5/2.5 MB 5.3 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting scipy>=1.6.1 (from gmx_MMPBSA)
  Downloading scipy-1.11.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 2.7 MB/s eta 0:00:00
Collecting matplotlib>=3.5.1 (from gmx_MMPBSA)
  Downloading matplotlib-3.8.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Requirement already satisfied: tqdm in ./miniconda3/lib/python3.11/site-packages (from gmx_MMPBSA) (4.65.0)
Collecting python-dateutil>=2.7.3 (from pandas==1.2.2->gmx_MMPBSA)
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 6.7 MB/s eta 0:00:00
Collecting pytz>=2017.3 (from pandas==1.2.2->gmx_MMPBSA)
  Downloading pytz-2023.3.post1-py2.py3-none-any.whl.metadata (22 kB)
Collecting numpy>=1.16.5 (from pandas==1.2.2->gmx_MMPBSA)
  Using cached numpy-1.26.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting contourpy>=1.0.1 (from matplotlib>=3.5.1->gmx_MMPBSA)
  Downloading contourpy-1.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib>=3.5.1->gmx_MMPBSA)
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib>=3.5.1->gmx_MMPBSA)
  Downloading fonttools-4.45.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (154 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.0/155.0 kB 5.0 MB/s eta 0:00:00
Collecting kiwisolver>=1.3.1 (from matplotlib>=3.5.1->gmx_MMPBSA)
  Downloading kiwisolver-1.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB)
Requirement already satisfied: packaging>=20.0 in ./miniconda3/lib/python3.11/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (23.1)
Collecting pillow>=8 (from matplotlib>=3.5.1->gmx_MMPBSA)
  Downloading Pillow-10.1.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (9.5 kB)
Collecting pyparsing>=2.3.1 (from matplotlib>=3.5.1->gmx_MMPBSA)
  Downloading pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB)
Collecting six>=1.5 (from python-dateutil>=2.7.3->pandas==1.2.2->gmx_MMPBSA)
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Downloading gmx_MMPBSA-1.6.2-py3-none-any.whl (6.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 7.5 MB/s eta 0:00:00
Downloading matplotlib-3.8.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 6.9 MB/s eta 0:00:00
Downloading scipy-1.11.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (36.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 36.4/36.4 MB 7.9 MB/s eta 0:00:00
Downloading contourpy-1.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (313 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 313.4/313.4 kB 4.8 MB/s eta 0:00:00
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading fonttools-4.45.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 7.1 MB/s eta 0:00:00
Downloading kiwisolver-1.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 5.3 MB/s eta 0:00:00
Using cached numpy-1.26.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
Downloading Pillow-10.1.0-cp311-cp311-manylinux_2_28_x86_64.whl (3.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 7.5 MB/s eta 0:00:00
Downloading pyparsing-3.1.1-py3-none-any.whl (103 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.1/103.1 kB 9.0 MB/s eta 0:00:00
Downloading pytz-2023.3.post1-py2.py3-none-any.whl (502 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 502.5/502.5 kB 11.1 MB/s eta 0:00:00
Building wheels for collected packages: pandas, mpi4py
  Building wheel for pandas (pyproject.toml) ... done
  Created wheel for pandas: filename=pandas-1.2.2-cp311-cp311-linux_x86_64.whl size=10909803 sha256=9db20caf74290cb8cd183600540bf9d2b811fe99fbd66ff87c3a39039dd513ce
  Stored in directory: /home/guju/.cache/pip/wheels/1b/8d/a5/57fdc048a498f81dedeb10320a2ad884d0e88282263ca61585
  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
  ╰─> [148 lines of output]
      running bdist_wheel
      running build
      running build_src
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-311
      creating build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__init__.py -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__main__.py -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/run.py -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/bench.py -> build/lib.linux-x86_64-cpython-311/mpi4py
      creating build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/__init__.py -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/__main__.py -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_core.py -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      creating build/lib.linux-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/__init__.py -> build/lib.linux-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/dtlib.py -> build/lib.linux-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/pkl5.py -> build/lib.linux-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/py.typed -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/bench.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/MPI.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__main__.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__init__.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/dl.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/run.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__init__.pxd -> build/lib.linux-x86_64-cpython-311/mpi4py
      copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-cpython-311/mpi4py
      creating build/lib.linux-x86_64-cpython-311/mpi4py/include
      creating build/lib.linux-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/futures/__main__.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/pool.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_lib.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/__init__.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/server.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/aplus.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_core.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/util/dtlib.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/__init__.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/pkl5.pyi -> build/lib.linux-x86_64-cpython-311/mpi4py/util
      running build_clib
      MPI configuration: [mpi] from 'mpi.cfg'
      checking for library 'lmpe' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c _configtest.c -o _configtest.o
      /home/guju/miniconda3/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,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include _configtest.o -llmpe -o _configtest
      /home/guju/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llmpe: No such file or directory
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o
      building 'mpe' dylib library
      creating build/temp.linux-x86_64-cpython-311
      creating build/temp.linux-x86_64-cpython-311/src
      creating build/temp.linux-x86_64-cpython-311/src/lib-pmpi
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-cpython-311/src/lib-pmpi/mpe.o
      creating build/lib.linux-x86_64-cpython-311/mpi4py/lib-pmpi
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -shared -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -Wl,--no-as-needed build/temp.linux-x86_64-cpython-311/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-cpython-311/mpi4py/lib-pmpi/libmpe.so
      checking for library 'vt-mpi' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c _configtest.c -o _configtest.o
      /home/guju/miniconda3/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,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include _configtest.o -lvt-mpi -o _configtest
      /home/guju/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt-mpi: No such file or directory
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o
      checking for library 'vt.mpi' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c _configtest.c -o _configtest.o
      /home/guju/miniconda3/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,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include _configtest.o -lvt.mpi -o _configtest
      /home/guju/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt.mpi: No such file or directory
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o
      building 'vt' dylib library
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-cpython-311/src/lib-pmpi/vt.o
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -shared -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -Wl,--no-as-needed build/temp.linux-x86_64-cpython-311/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-cpython-311/mpi4py/lib-pmpi/libvt.so
      checking for library 'vt-mpi' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c _configtest.c -o _configtest.o
      /home/guju/miniconda3/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,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include _configtest.o -lvt-mpi -o _configtest
      /home/guju/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt-mpi: No such file or directory
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o
      checking for library 'vt.mpi' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c _configtest.c -o _configtest.o
      /home/guju/miniconda3/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,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include _configtest.o -lvt.mpi -o _configtest
      /home/guju/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt.mpi: No such file or directory
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o
      building 'vt-mpi' dylib library
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-cpython-311/src/lib-pmpi/vt-mpi.o
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -shared -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -Wl,--no-as-needed build/temp.linux-x86_64-cpython-311/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-cpython-311/mpi4py/lib-pmpi/libvt-mpi.so
      checking for library 'vt-hyb' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c _configtest.c -o _configtest.o
      /home/guju/miniconda3/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,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include _configtest.o -lvt-hyb -o _configtest
      /home/guju/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt-hyb: No such file or directory
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o
      checking for library 'vt.ompi' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c _configtest.c -o _configtest.o
      /home/guju/miniconda3/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,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include _configtest.o -lvt.ompi -o _configtest
      /home/guju/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt.ompi: No such file or directory
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o
      building 'vt-hyb' dylib library
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-cpython-311/src/lib-pmpi/vt-hyb.o
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -shared -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -Wl,--no-as-needed build/temp.linux-x86_64-cpython-311/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-cpython-311/mpi4py/lib-pmpi/libvt-hyb.so
      running build_ext
      MPI configuration: [mpi] from 'mpi.cfg'
      checking for dlopen() availability ...
      checking for header 'dlfcn.h' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -I/home/guju/miniconda3/include/python3.11 -c _configtest.c -o _configtest.o
      success!
      removing: _configtest.c _configtest.o
      success!
      checking for library 'dl' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -I/home/guju/miniconda3/include/python3.11 -c _configtest.c -o _configtest.o
      /home/guju/miniconda3/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,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include _configtest.o -Lbuild/temp.linux-x86_64-cpython-311 -ldl -o _configtest
      success!
      removing: _configtest.c _configtest.o _configtest
      checking for function 'dlopen' ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -I/home/guju/miniconda3/include/python3.11 -c _configtest.c -o _configtest.o
      /home/guju/miniconda3/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,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include _configtest.o -Lbuild/temp.linux-x86_64-cpython-311 -ldl -o _configtest
      success!
      removing: _configtest.c _configtest.o _configtest
      building 'mpi4py.dl' extension
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/guju/miniconda3/include/python3.11 -c src/dynload.c -o build/temp.linux-x86_64-cpython-311/src/dynload.o
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -shared -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/guju/miniconda3/lib -Wl,-rpath-link,/home/guju/miniconda3/lib -L/home/guju/miniconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include build/temp.linux-x86_64-cpython-311/src/dynload.o -Lbuild/temp.linux-x86_64-cpython-311 -ldl -o build/lib.linux-x86_64-cpython-311/mpi4py/dl.cpython-311-x86_64-linux-gnu.so
      checking for MPI compile and link ...
      /home/guju/miniconda3/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/guju/miniconda3/include -fPIC -O2 -isystem /home/guju/miniconda3/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/guju/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/guju/miniconda3/include -fPIC -I/home/guju/miniconda3/include/python3.11 -c _configtest.c -o _configtest.o
      _configtest.c:2:10: fatal error: mpi.h: No such file or directory
          2 | #include <mpi.h>
            |          ^~~~~~~
      compilation terminated.
      failure.
      removing: _configtest.c _configtest.o
      error: Cannot compile MPI programs. Check your configuration!!!
      [end of output]
 
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for mpi4py
Successfully built pandas
Failed to build mpi4py
ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

Kindly help me to solve this issue.

Thank you.

Warm Regards

Raj Choudhary

[gmx_MMPBSA]

Please, trying to install mpi4py from conda before installing gmx_MMPBSA

[Raj Choudhary]

Thank you sir for the suggestion. The problem is solved now.

Warm regards

Raj Choudhary

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