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I have openmpi-4.1.4 installed and python 3.9 on Ubuntu 18.04. When I go to build mpi4py from source, I get this error:

(DL) root@autodl-container-7e5411a952-3306111c:/usr/local/mpi4py/mpi4py-3.1.1# python setup.py build --mpi=openmpi

running build
running build_src
running build_py
running build_clib
MPI configuration: [openmpi] from 'mpi.cfg'
MPI C compiler:    /usr/local/openmpi/openmpi-4.1.4/build/bin/mpicc
MPI C++ compiler:  /usr/local/openmpi/openmpi-4.1.4/build/bin/mpicxx
running build_ext
MPI configuration: [openmpi] from 'mpi.cfg'
MPI C compiler:    /usr/local/openmpi/openmpi-4.1.4/build/bin/mpicc
MPI C++ compiler:  /usr/local/openmpi/openmpi-4.1.4/build/bin/mpicxx
checking for MPI compile and link ...
/usr/local/openmpi/openmpi-4.1.4/build/bin/mpicc -pthread -B /root/miniconda3/envs/DL/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /root/miniconda3/envs/DL/include -I/root/miniconda3/envs/DL/include -fPIC -O2 -isystem /root/miniconda3/envs/DL/include -fPIC -I/root/miniconda3/envs/DL/include/python3.9 -I/usr/local/openmpi/openmpi-4.1.4/build/include -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
/usr/local/openmpi/openmpi-4.1.4/build/bin/mpicc -pthread -B /root/miniconda3/envs/DL/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /root/miniconda3/envs/DL/include -I/root/miniconda3/envs/DL/include -fPIC -O2 -isystem /root/miniconda3/envs/DL/include -fPIC -I/root/miniconda3/envs/DL/include/python3.9 -I/usr/local/openmpi/openmpi-4.1.4/build/include -c _configtest.c -o _configtest.o
/usr/local/openmpi/openmpi-4.1.4/build/bin/mpicc -pthread -B /root/miniconda3/envs/DL/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-39 -L/usr/local/openmpi/openmpi-4.1.4/build/lib -Wl,--enable-new-dtags,-R/usr/local/openmpi/openmpi-4.1.4/build/lib -lmpi -o _configtest
/root/miniconda3/envs/DL/compiler_compat/ld: warning: libm.so.6, needed by /usr/local/openmpi/openmpi-4.1.4/build/lib/libmpi.so, not found (try using -rpath or -rpath-link)
/root/miniconda3/envs/DL/compiler_compat/ld: warning: libz.so.1, needed by /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-rte.so.40, not found (try using -rpath or -rpath-link)
/root/miniconda3/envs/DL/compiler_compat/ld: warning: libdl.so.2, needed by /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-pal.so.40, not found (try using -rpath or -rpath-link)
/root/miniconda3/envs/DL/compiler_compat/ld: warning: libutil.so.1, needed by /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-pal.so.40, not found (try using -rpath or -rpath-link)
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-rte.so.40: undefined reference to `inflate'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libmpi.so: undefined reference to `log@GLIBC_2.29'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-pal.so.40: undefined reference to `dlopen@GLIBC_2.2.5'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-pal.so.40: undefined reference to `dlerror@GLIBC_2.2.5'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libmpi.so: undefined reference to `sqrt@GLIBC_2.2.5'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-rte.so.40: undefined reference to `deflate'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-pal.so.40: undefined reference to `openpty@GLIBC_2.2.5'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-rte.so.40: undefined reference to `deflateInit_'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-rte.so.40: undefined reference to `inflateEnd'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-pal.so.40: undefined reference to `dlclose@GLIBC_2.2.5'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-rte.so.40: undefined reference to `deflateEnd'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-rte.so.40: undefined reference to `deflateBound@ZLIB_1.2.0'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-rte.so.40: undefined reference to `inflateInit_'
/root/miniconda3/envs/DL/compiler_compat/ld: /usr/local/openmpi/openmpi-4.1.4/build/lib/libopen-pal.so.40: undefined reference to `dlsym@GLIBC_2.2.5'
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!

It shows I don't have libmpi.so, but actually I found libmpi.so in that folder. Any ideas as to what's going on?

tripleee
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dairhepon
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  • The warnings earlier in the transcript shows which dependencies it can't find. It finds `libmpi.so` but it can't run it because it can't find `libm.so.6` (sic). There are a few similar warnings on the following lines. – tripleee Apr 12 '23 at 06:55
  • As an aside, Ubuntu 18.04 is long out of support. Probably try to upgrade to a supported platform. – tripleee Apr 12 '23 at 06:56

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