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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 fordlopen() 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 forfunction'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 mpi4pyFailed to build mpi4pyERROR: 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
The text was updated successfully, but these errors were encountered:
Bug summary
Unable to install using amber.python command. return issue associated with mpi4py. mpich and open mpi installed in my system
Terminal output
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
The text was updated successfully, but these errors were encountered: