Hello I tried to installed dolfinx on a HPC machine using spack, I followed this guide
but changed the version to 0.7.2 since my code is written in this version. (I believe 0.7.2 is one of the safe version in spack.)
spack add fenics-dolfinx@0.7.2+adios2 py-fenics-dolfinx cflags="-O3" fflags="-O3"
But when I tried to compile my codes, I got the error message:
/proj/naiss2024-23-125/local/Work/spack/opt/spack/linux-centos7-broadwell/gcc-13.2.0/petsc-3.22.3-je3j3by35teir4hdfbsimwwa3l3kkls5/lib/libpetsc.so: undefined reference to `MPI_Neighbor_alltoallv_init'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/demo_poisson.dir/build.make:126: demo_poisson] Error 1
make[1]: *** [CMakeFiles/Makefile2:83: CMakeFiles/demo_poisson.dir/all] Error 2
make: *** [Makefile:91: all] Error 2
so it seems there is something wrong with the installation os PETSC. Does anyone has any suggestion or comment regarding my problem?
dokken
February 6, 2025, 3:39pm
2
Seems like it is picking up a wrong/not modern enough mpi version. Could you check what you get with mpirun —version and which mpirun?
Thanks for quick replying, here is the output:
-bash-4.2$ mpirun -version
mpirun (Open MPI) 5.0.6
Report bugs to https://www.open-mpi.org/community/help/
and
-bash-4.2$ which mpirun
/crex/proj/uppstore2017025/local/Work/spack/opt/spack/linux-centos7-broadwell/gcc-13.2.0/openmpi-5.0.6-6nysh7af27lxacxcz24rygtjhb752sb5/bin/mpirun
dokken
February 6, 2025, 4:13pm
4
Hm, that is the latest version of mpich. Seems strange that it doesn’t find
It should be part of your openmpi installation
https://docs.open-mpi.org/en/v5.0.6/man-openmpi/man3/MPI_Neighbor_alltoallv_init.3.html
Could you try pinning the PETSC version to an older version than 3.22?
Hi I tried to install petsc@3.21.0 but still get the same problem, here is the packages I have installed:
-bash-4.2$ spack find petsc
==> In environment fenicsx-env
==> 3 root specs
[+] fenics-dolfinx@0.7.2 +adios2 [+] petsc@3.21.0 [+] py-fenics-dolfinx cflags=-O3 fflags=-O3
-- linux-centos7-broadwell / gcc@13.2.0 -------------------------
petsc@3.21.0
==> 1 installed package
==> 0 concretized packages to be installed (show with `spack find -c`)
Oh, I just cleaned the old cache and configuration, now it works. Thanks!