When installing NEST 2.18 with:
cmake \
-Dwith-mpi=/usr/lib/x86_64-linux-gnu/openmpi \
-Dwith-python=3 \
-DPYTHON_EXECUTABLE=/home/robin/.pyenv/versions/3.8.6/bin/python \
-DPYTHON_LIBRARY=/home/robin/.pyenv/versions/3.8.6/lib/libpython3.8.so \
-DPYTHON_INCLUDE_DIR=/home/robin/.pyenv/versions/3.8.6/include/python3.8/ \
-DCMAKE_INSTALL_PREFIX=/home/robin/nest-install \
..
It seems that NEST 2.18 tries to look for libmpi_cxx.so.20 even though it doesn't exist and isn't part of the installed mpi lib
$ ldd nest-install/lib/python3.8/site-packages/nest/pynestkernel.so
linux-vdso.so.1 (0x00007fff3bb37000)
libpython3.8.so.1.0 => /home/robin/.pyenv/versions/3.8.6/lib/libpython3.8.so.1.0 (0x00007feaa1401000)
libnest.so => /nest/2.18/lib/libnest.so (0x00007feaa11c1000)
libmodels.so => /nest/2.18/lib/libmodels.so (0x00007feaa0930000)
libtopology.so => /nest/2.18/lib/libtopology.so (0x00007feaa0691000)
libnestkernel.so => /nest/2.18/lib/libnestkernel.so (0x00007feaa0335000)
librandom.so => /nest/2.18/lib/librandom.so (0x00007feaa00e9000)
libsli.so => /nest/2.18/lib/libsli.so (0x00007fea9fd9a000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fea9fba1000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fea9fb86000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fea9f994000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fea9f971000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fea9f969000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007fea9f964000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fea9f815000)
libprecise.so => /nest/2.18/lib/libprecise.so (0x00007fea9f592000)
libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007fea9f587000)
libmpi_cxx.so.20 => /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so.20 (0x00007fea9f567000)
libmpi.so.20 => not found
libnestutil.so => /nest/2.18/lib/libnestutil.so (0x00007fea9f363000)
libgsl.so.23 => /usr/lib/x86_64-linux-gnu/libgsl.so.23 (0x00007fea9f0e7000)
libgslcblas.so.0 => /usr/lib/x86_64-linux-gnu/libgslcblas.so.0 (0x00007fea9f0a5000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fea9f063000)
/lib64/ld-linux-x86-64.so.2 (0x00007feaa180a000)
libmpi.so.20 => not found
libmpi.so.20 => not found
libmpi.so.20 => not found
libmpi.so.20 => not found
libmpi.so.40 => /usr/local/lib/libmpi.so.40 (0x00007fea9ed39000)
libopen-rte.so.40 => /usr/local/lib/libopen-rte.so.40 (0x00007fea9ea83000)
libopen-pal.so.40 => /usr/local/lib/libopen-pal.so.40 (0x00007fea9e76b000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fea9e760000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fea9e744000)
I've tried to change all of the cmake variables using ccmake but I can't get it to link to libmpi_cxx.so.40.
Even without MPI support it includes this link, seems like a bug?
robin@robin-ZenBook-UX533FN:~$ ldd nest-install/lib/python3.8/site-packages/nest/pynestkernel.so
linux-vdso.so.1 (0x00007ffe63518000)
libpython3.8.so.1.0 => /home/robin/.pyenv/versions/3.8.6/lib/libpython3.8.so.1.0 (0x00007fa1e3c37000)
libnest.so => /nest/2.18/lib/libnest.so (0x00007fa1e39f7000)
libmodels.so => /nest/2.18/lib/libmodels.so (0x00007fa1e3166000)
libtopology.so => /nest/2.18/lib/libtopology.so (0x00007fa1e2ec7000)
libnestkernel.so => /nest/2.18/lib/libnestkernel.so (0x00007fa1e2b6b000)
librandom.so => /nest/2.18/lib/librandom.so (0x00007fa1e291f000)
libsli.so => /nest/2.18/lib/libsli.so (0x00007fa1e25d0000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fa1e23d7000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fa1e23bc000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa1e21ca000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa1e21a7000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fa1e219f000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007fa1e219a000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fa1e204b000)
libprecise.so => /nest/2.18/lib/libprecise.so (0x00007fa1e1dc8000)
libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007fa1e1dbd000)
libmpi_cxx.so.20 => not found
libmpi.so.20 => not found
libnestutil.so => /nest/2.18/lib/libnestutil.so (0x00007fa1e1bb7000)
libgsl.so.23 => /usr/lib/x86_64-linux-gnu/libgsl.so.23 (0x00007fa1e193b000)
libgslcblas.so.0 => /usr/lib/x86_64-linux-gnu/libgslcblas.so.0 (0x00007fa1e18f9000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fa1e18b7000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa1e4040000)
libmpi_cxx.so.20 => not found
libmpi.so.20 => not found
libmpi_cxx.so.20 => not found
libmpi.so.20 => not found
libmpi_cxx.so.20 => not found
libmpi.so.20 => not found
libmpi_cxx.so.20 => not found
libmpi.so.20 => not found
The full error when importing it is:
>>> import nest
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/robin/nest-install/lib/python3.8/site-packages/nest/__init__.py", line 26, in <module>
from . import ll_api # noqa
File "/home/robin/nest-install/lib/python3.8/site-packages/nest/ll_api.py", line 72, in <module>
from . import pynestkernel as kernel # noqa
ImportError: libmpi_cxx.so.20: cannot open shared object file: No such file or directory
