I have created an conda environment and I am trying to install mpi4py using pip. I am getting following error when I do that:
Collecting mpi4py
Using cached mpi4py-3.1.3.tar.gz (2.5 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
Building wheels for collected packages: mpi4py
Building wheel for mpi4py (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /home/pavan/miniconda3/envs/codelab/bin/python /home/pavan/miniconda3/envs/codelab/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmppevhrinu
cwd: /tmp/pip-install-gxgbr0vg/mpi4py_2f4b2eeacbc0465493035e6fe3c8dbdd
Complete output (170 lines):
running bdist_wheel
running build
running build_src
running build_py
creating build
creating build/lib.linux-x86_64-cpython-39
creating build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/bench.py -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/__main__.py -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/run.py -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/__init__.py -> build/lib.linux-x86_64-cpython-39/mpi4py
creating build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/__main__.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/__init__.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/_core.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
creating build/lib.linux-x86_64-cpython-39/mpi4py/util
copying src/mpi4py/util/pkl5.py -> build/lib.linux-x86_64-cpython-39/mpi4py/util
copying src/mpi4py/util/dtlib.py -> build/lib.linux-x86_64-cpython-39/mpi4py/util
copying src/mpi4py/util/__init__.py -> build/lib.linux-x86_64-cpython-39/mpi4py/util
copying src/mpi4py/py.typed -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/dl.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/__main__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/run.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/__init__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/MPI.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/bench.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/__init__.pxd -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-cpython-39/mpi4py
copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-cpython-39/mpi4py
creating build/lib.linux-x86_64-cpython-39/mpi4py/include
creating build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py
copying src/mpi4py/futures/__main__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/server.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/__init__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/_core.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/aplus.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/_lib.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/futures/pool.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures
copying src/mpi4py/util/dtlib.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/util
copying src/mpi4py/util/__init__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/util
copying src/mpi4py/util/pkl5.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/util
running build_clib
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc
MPI C++ compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicxx
MPI F compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpifort
MPI F90 compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpif90
MPI F77 compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpif77
checking for library 'lmpe' ...
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c _configtest.c -o _configtest.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -llmpe -o _configtest
/home/pavan/miniconda3/envs/codelab/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-39
creating build/temp.linux-x86_64-cpython-39/src
creating build/temp.linux-x86_64-cpython-39/src/lib-pmpi
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-cpython-39/src/lib-pmpi/mpe.o
creating build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -shared -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-39/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi/libmpe.so
checking for library 'vt-mpi' ...
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c _configtest.c -o _configtest.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -lvt-mpi -o _configtest
/home/pavan/miniconda3/envs/codelab/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' ...
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c _configtest.c -o _configtest.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -lvt.mpi -o _configtest
/home/pavan/miniconda3/envs/codelab/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
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-cpython-39/src/lib-pmpi/vt.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -shared -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-39/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi/libvt.so
checking for library 'vt-mpi' ...
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c _configtest.c -o _configtest.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -lvt-mpi -o _configtest
/home/pavan/miniconda3/envs/codelab/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' ...
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c _configtest.c -o _configtest.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -lvt.mpi -o _configtest
/home/pavan/miniconda3/envs/codelab/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-mpi' dylib library
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-cpython-39/src/lib-pmpi/vt-mpi.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -shared -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-39/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi/libvt-mpi.so
checking for library 'vt-hyb' ...
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c _configtest.c -o _configtest.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -lvt-hyb -o _configtest
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: cannot find -lvt-hyb: No such file or directory
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.ompi' ...
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c _configtest.c -o _configtest.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -lvt.ompi -o _configtest
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: cannot find -lvt.ompi: No such file or directory
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-hyb' dylib library
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-cpython-39/src/lib-pmpi/vt-hyb.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -shared -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-39/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi/libvt-hyb.so
running build_ext
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc
MPI C++ compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicxx
MPI F compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpifort
MPI F90 compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpif90
MPI F77 compiler: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpif77
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
gcc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -I/home/pavan/miniconda3/envs/codelab/include/python3.9 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
gcc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -I/home/pavan/miniconda3/envs/codelab/include/python3.9 -c _configtest.c -o _configtest.o
gcc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-39 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
gcc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -I/home/pavan/miniconda3/envs/codelab/include/python3.9 -c _configtest.c -o _configtest.o
gcc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-39 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.dl' extension
gcc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/pavan/miniconda3/envs/codelab/include/python3.9 -c src/dynload.c -o build/temp.linux-x86_64-cpython-39/src/dynload.o
gcc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -shared -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath,/home/pavan/miniconda3/envs/codelab/lib -Wl,-rpath-link,/home/pavan/miniconda3/envs/codelab/lib -L/home/pavan/miniconda3/envs/codelab/lib build/temp.linux-x86_64-cpython-39/src/dynload.o -Lbuild/temp.linux-x86_64-cpython-39 -ldl -o build/lib.linux-x86_64-cpython-39/mpi4py/dl.cpython-39-x86_64-linux-gnu.so
checking for MPI compile and link ...
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -I/home/pavan/miniconda3/envs/codelab/include/python3.9 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -I/home/pavan/miniconda3/envs/codelab/include -fPIC -O2 -isystem /home/pavan/miniconda3/envs/codelab/include -fPIC -I/home/pavan/miniconda3/envs/codelab/include/python3.9 -c _configtest.c -o _configtest.o
/home/pavan/packages/openmpi-4.0.7/opt-gfortran/bin/mpicc -pthread -B /home/pavan/miniconda3/envs/codelab/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-39 -o _configtest
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: warning: libm.so.6, needed by /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libmpi.so, not found (try using -rpath or -rpath-link)
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: warning: libz.so.1, needed by /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libopen-rte.so.40, not found (try using -rpath or -rpath-link)
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libopen-rte.so.40: undefined reference to `inflate'
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libmpi.so: undefined reference to `log@GLIBC_2.29'
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libmpi.so: undefined reference to `sqrt@GLIBC_2.2.5'
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libopen-rte.so.40: undefined reference to `deflate'
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libopen-rte.so.40: undefined reference to `deflateInit_'
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libopen-rte.so.40: undefined reference to `inflateEnd'
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libopen-rte.so.40: undefined reference to `deflateEnd'
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libopen-rte.so.40: undefined reference to `deflateBound@ZLIB_1.2.0'
/home/pavan/miniconda3/envs/codelab/compiler_compat/ld: /home/pavan/packages/openmpi-4.0.7/opt-gfortran/lib/libopen-rte.so.40: undefined reference to `inflateInit_'
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!
----------------------------------------
ERROR: Failed building wheel for mpi4py
Failed to build mpi4py
ERROR: Could not build wheels for mpi4py which use PEP 517 and cannot be installed directly
As mentioned in the last part of error, I tried to find if libm.so.6 and libz.so.1 are present or not using find. I found that libm.so.6 was not there, but libz.so.1 is there, still it is saying it didn't find it. Any help to debug this will be much appreciated. Following details might be useful:
It was related to python provided by conda.
the flag "-B /home/pavan/miniconda3/envs/codelab/compiler_compat" will ask the complier to pick up ld from that path. but the ld provided by conda will cause some issue when you are using different compiler toolchains.
step to fix it:
cd /home/pavan/miniconda3/envs/codelab/compiler_compat
rm -f ld
ln -s /usr/bin/ld ld
and try to build mpi4py again.
after that, revoke that change:
cd /home/pavan/miniconda3/envs/codelab/compiler_compat
rm -f ld
ln -s ../bin/x86_64-conda-linux-gnu-ld ld