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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
226 stars 65 forks source link

[Bug-gmx_MMPBSA_ana]: #491

Open snehachem opened 6 months ago

snehachem commented 6 months ago

Bug summary

Unable to install using amber.python command. return issue associated with mpi4py. mpich and open mpi installed in my system

Terminal output

(base) sneha@sneha:~/Desktop$ amber.python -m pip install gmx_MMPBSA
Collecting gmx_MMPBSA
  Using cached gmx_MMPBSA-1.6.3-py3-none-any.whl.metadata (4.5 kB)
Collecting pandas==1.2.2 (from gmx_MMPBSA)
  Using cached pandas-1.2.2-cp312-cp312-linux_x86_64.whl
Collecting seaborn<0.12 (from gmx_MMPBSA)
  Using cached seaborn-0.11.2-py3-none-any.whl.metadata (2.3 kB)
Collecting mpi4py<=3.1.5 (from gmx_MMPBSA)
  Using cached mpi4py-3.1.5.tar.gz (2.5 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: scipy>=1.6.1 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from gmx_MMPBSA) (1.12.0)
Collecting matplotlib==3.5.2 (from gmx_MMPBSA)
  Using cached matplotlib-3.5.2-cp312-cp312-linux_x86_64.whl
Requirement already satisfied: tqdm in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from gmx_MMPBSA) (4.65.0)
Collecting parmed>=4.2.2 (from gmx_MMPBSA)
  Using cached ParmEd-4.2.2-cp312-cp312-linux_x86_64.whl
Requirement already satisfied: cycler>=0.10 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from matplotlib==3.5.2->gmx_MMPBSA) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from matplotlib==3.5.2->gmx_MMPBSA) (4.51.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from matplotlib==3.5.2->gmx_MMPBSA) (1.4.5)
Requirement already satisfied: numpy>=1.17 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from matplotlib==3.5.2->gmx_MMPBSA) (1.26.4)
Requirement already satisfied: packaging>=20.0 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from matplotlib==3.5.2->gmx_MMPBSA) (23.2)
Requirement already satisfied: pillow>=6.2.0 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from matplotlib==3.5.2->gmx_MMPBSA) (10.3.0)
Requirement already satisfied: pyparsing>=2.2.1 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from matplotlib==3.5.2->gmx_MMPBSA) (3.1.2)
Requirement already satisfied: python-dateutil>=2.7 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from matplotlib==3.5.2->gmx_MMPBSA) (2.8.2)
Requirement already satisfied: pytz>=2017.3 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from pandas==1.2.2->gmx_MMPBSA) (2024.1)
Requirement already satisfied: six>=1.5 in /home/sneha/amber22/miniconda/lib/python3.12/site-packages (from python-dateutil>=2.7->matplotlib==3.5.2->gmx_MMPBSA) (1.16.0)
Using cached gmx_MMPBSA-1.6.3-py3-none-any.whl (6.4 MB)
Using cached seaborn-0.11.2-py3-none-any.whl (292 kB)
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
  ╰─> [404 lines of output]
      running bdist_wheel
      running build
      running build_src
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-312
      creating build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/bench.py -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/__init__.py -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/run.py -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/__main__.py -> build/lib.linux-x86_64-cpython-312/mpi4py
      creating build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/__init__.py -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/_core.py -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/__main__.py -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      creating build/lib.linux-x86_64-cpython-312/mpi4py/util
      copying src/mpi4py/util/dtlib.py -> build/lib.linux-x86_64-cpython-312/mpi4py/util
      copying src/mpi4py/util/__init__.py -> build/lib.linux-x86_64-cpython-312/mpi4py/util
      copying src/mpi4py/util/pkl5.py -> build/lib.linux-x86_64-cpython-312/mpi4py/util
      copying src/mpi4py/bench.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/MPI.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/__main__.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/run.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/__init__.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/dl.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/py.typed -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-cpython-312/mpi4py
      copying src/mpi4py/__init__.pxd -> build/lib.linux-x86_64-cpython-312/mpi4py
      creating build/lib.linux-x86_64-cpython-312/mpi4py/include
      creating build/lib.linux-x86_64-cpython-312/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-cpython-312/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-cpython-312/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-cpython-312/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-cpython-312/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-cpython-312/mpi4py/include/mpi4py
      copying src/mpi4py/futures/_core.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/server.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/__main__.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/__init__.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/aplus.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/_lib.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/futures/pool.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py/futures
      copying src/mpi4py/util/pkl5.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py/util
      copying src/mpi4py/util/__init__.pyi -> build/lib.linux-x86_64-cpython-312/mpi4py/util
      copying src/mpi4py/util/dtlib.pyi -> build/lib.linux-x86_64-cpython-312/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 -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -c _configtest.c -o _configtest.o
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat _configtest.o -llmpe -o _configtest
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/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-312
      creating build/temp.linux-x86_64-cpython-312/src
      creating build/temp.linux-x86_64-cpython-312/src/lib-pmpi
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-cpython-312/src/lib-pmpi/mpe.o
      creating build/lib.linux-x86_64-cpython-312/mpi4py/lib-pmpi
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -L/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -L/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-312/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-cpython-312/mpi4py/lib-pmpi/libmpe.so
      checking for library 'vt-mpi' ...
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -c _configtest.c -o _configtest.o
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat _configtest.o -lvt-mpi -o _configtest
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/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' ...
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -c _configtest.c -o _configtest.o
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat _configtest.o -lvt.mpi -o _configtest
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/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
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-cpython-312/src/lib-pmpi/vt.o
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-cpython-312/src/lib-pmpi/vt-hyb.o
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -L/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -L/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-312/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-cpython-312/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' ...
      gcc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -I/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include/python3.12 -c _configtest.c -o _configtest.o
      success!
      removing: _configtest.c _configtest.o
      success!
      checking for library 'dl' ...
      gcc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -I/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include/python3.12 -c _configtest.c -o _configtest.o
      gcc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-312 -ldl -o _configtest
      success!
      removing: _configtest.c _configtest.o _configtest
      checking for function 'dlopen' ...
      gcc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -I/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include/python3.12 -c _configtest.c -o _configtest.o
      gcc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-312 -ldl -o _configtest
      success!
      removing: _configtest.c _configtest.o _configtest
      building 'mpi4py.dl' extension
      gcc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include/python3.12 -c src/dynload.c -o build/temp.linux-x86_64-cpython-312/src/dynload.o
      gcc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -L/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib -L/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/lib build/temp.linux-x86_64-cpython-312/src/dynload.o -Lbuild/temp.linux-x86_64-cpython-312 -ldl -o build/lib.linux-x86_64-cpython-312/mpi4py/dl.cpython-312-x86_64-linux-gnu.so
      checking for MPI compile and link ...
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -I/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include/python3.12 -c _configtest.c -o _configtest.o
      success!
      removing: _configtest.c _configtest.o
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -I/home/sneha/amber22_src/build/CMakeFiles/miniconda/install/include/python3.12 -c _configtest.c -o _configtest.o
      /usr/bin/mpicc -pthread -B /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-312 -o _configtest
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: warning: libopen-rte.so.40, needed by /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so, not found (try using -rpath or -rpath-link)
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: warning: libopen-pal.so.40, needed by /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so, not found (try using -rpath or -rpath-link)
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: warning: libm.so.6, needed by /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so, not found (try using -rpath or -rpath-link)
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: warning: libhwloc.so.15, needed by /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so, not found (try using -rpath or -rpath-link)
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_framework_components_close'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_list_sort'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_get_element_count'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convertor_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_namelist_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_dump'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_install_dirs'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_set_value_ptr'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_rand'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `hwloc_bitmap_alloc'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `hwloc_get_obj_by_depth'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_delay_abort'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convertor_raw'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `hwloc_bitmap_free'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_get'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_local_arch'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_list_item_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_backtrace_print'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pmix_collect_all_data'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_component_close'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_get_value_ptr'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_data_server_uri'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_str_to_bool'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_register'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_register_framework_params'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_is_monotonic'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `hwloc_bitmap_iszero'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hwloc_base_cset2mapstr'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_proc_local_set'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_unsetenv'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `hwloc_bitmap_isincluded'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_dump_data_flags'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hwloc_topology'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convertor_pack'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_output_stream_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_out'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pmix_base_exchange'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_get_valuelen'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_timer_base_get_cycles'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_allocator_base_framework'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_argv_join'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pmix_base_async_modex'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_set_element_count'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_handle_reset'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_argv_free'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_init'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_process_info'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_path_nfs'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_get'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convertor_clone'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_backtrace_buffer'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hwloc_compute_relative_locality'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_btl_base_framework'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pmix_app_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_progress_set_event_poll_rate'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pointer_array_test_and_set_item'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_thread_get_self'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pointer_array_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_get_nthkey'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_copy_content_same_ddt'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pmix_verbose_output'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `log@GLIBC_2.29'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_components_close'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pointer_array_init'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_infosubscribe_subscribe'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_info_show_orte_version'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_init'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_select'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_argv_append_unique_nosize'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_handle_read_value'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_timer_base_get_freq'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_finalize'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_session_dir_finalize'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_process_name_print'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_handle_alloc'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `hwloc_get_type_depth'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_buffer_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convert_process_name_to_string'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_free_list_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_output'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `sqrt@GLIBC_2.2.5'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_find_by_name'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_get'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_progress'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hwloc_base_single_cpu'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_compare_proc'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `ompi_sync_wait_mt'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_free_list_item_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_contain_basic_datatypes'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_framework_is_open'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_cr_output'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convertor_prepare_for_recv'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `hwloc_bitmap_compare'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_dss'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_value_unload'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_get_value_enum'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_built_with_cuda_support'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_set_value'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_progress_register'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_register_project_frameworks'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_get_bool'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_get_next_key_uint32'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pointer_array_add'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_util_compare_name_fields'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_argv_count'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_finalize_util'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_output_close'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_progress_event_users_increment'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pointer_array_set_item'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_in_parallel_debugger'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convertor_prepare_for_send'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_remove_value_uint32'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_mpool_base_framework'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_ess'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_value_load'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_enum_create_flag'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_bitmap_set_bit'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_compute_ptypes'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_close_components'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_output_verbose'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_dup'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_process_info'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_argv_append_nosize'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `hwloc_get_cpubind'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_class_init_epoch'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_register'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pmix_pdata_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_cr_reg_coord_callback'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_handle_free'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_info_close_components'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_proc_applied_binding'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_proc_local_get'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_component_var_register'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_proc_is_bound'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_name_wildcard'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_get_value'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_rcache_base_framework'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_find'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_output_set_verbosity'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_handle_write_value'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hwloc_base_cset2str'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convertor_compute_remote_size'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_dup_mpistandard'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_crs_base_state_str'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_mpool_base_alloc'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_init_util'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convertor_create'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_output_open'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_thread_self_compare'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_free_list_grow_st'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_condition_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_delete'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_show_help'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_predefined_elem_desc'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_cuda_support'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_clone'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_odls'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_mpool_base_free'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_progress_set_event_flag'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convertor_unpack'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_register_synonym'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_get_value_uint32'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_group_find_by_name'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_argv_split'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_strerror'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_group_get_stamp'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_session_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_pmix'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_srand'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_initialized'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_arch_set_fortran_logical_size'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_object_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_util_convert_process_name_to_string'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_get_count'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_mpool_base_tree_print'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_class_initialize'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_progress_set_yield_when_idle'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_bitmap_is_set_bit'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_get_count'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_find_by_name'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_proc_for_name'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_framework_close'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_bitmap_init'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_framework_components_open'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_standalone_operation'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_uses_threads'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_util_convert_string_to_process_name'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_proc_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_set'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_argv_append'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_mutex_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_component_to_string'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_util_print_name_args'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_allocator_component_lookup'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_handle_stop'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_init'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_set_value_uint32'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_abort_print_stack'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_get_value_uint64'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_group_get'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_convert_string_to_process_name'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_commit'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_bitmap_find_and_set_first_unset_bit'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_show_help'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_getcwd'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_errmgr'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_dump_data_desc'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_enum_create'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_component_repository_release'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_value_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_free_list_init'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_bitmap_set_max_size'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_make_version_str'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_progress_unregister'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_pvar_handle_start'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_infosubscriber_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_create_desc'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_setenv'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_progress_event_users_decrement'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_remove_value_ptr'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_finalize'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_bitmap_clear_bit'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_bitmap_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_set_value_enum'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_get_first_key_uint32'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_component_list_item_t_class'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_infosubscribe_change_info'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_info_register_framework_params'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_framework_open'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `orte_session_dir_cleanup'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_info_show_opal_version'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_add'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_class_finalize'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `mca_base_var_group_get_count'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_datatype_resize'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_hash_table_set_value_uint64'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `MPIR_being_debugged'
      /home/sneha/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so: undefined reference to `opal_list_t_class'
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o
      error: Cannot link 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
Failed to build mpi4py
ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

Actual outcome

error: Cannot link 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 Failed to build mpi4py ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based

Expected outcome

Installed

Additional information

using Gromacs 2024.1

Operating system

Linuxmint 21.3

gmx_MMPBSA_ana Version

v 1.6

Python version

Python 3.12.1

Installation

None

Valdes-Tresanco-MS commented 6 months ago

mpi4py installation from pip is complicated. You may want to install it using amber.conda install -c conda-forge mpi4py