All these complications are due to a --questionnable-- design choice of
our cluster. Nodes are diskless: they receive their root filesystem as a
squashfs that they store in memory. To keep it squashfs small,
scientific programs used in the cluster are installed manually in /opt,
which is NFS shared.
Adding gomp under 'libraries' worked. I also had to add metis which I
forgot earlier. I'm now missing symbol zscal_ from libzmumps. The rabbit
whole looks bottomless...
Etienne
On 17/01/2022 21:54, Christoph Groth wrote:
Etienne Fayen a écrit :
Mumps and scotch were compiled manually in /opt, following
instructions in the readmes.
I’m curious, why are you building mumps yourself?
It is caused by the following import error:
/opt/python3-venv/lib/python3.8/site-packages/kwant-1.4.2-py3.8-linux-x86_64.egg/kwant/linalg/_mumps.cpython-38-x86_64-linux-gnu.so:
undefined symbol: GOMP_loop_nonmonotonic_dynamic_start
This points again to my hand-built Mumps, so again not a kwant issue
per se.
GOMP refers to GNU OpenMP. OpenMP is used for example by OpenBLAS that
you are most likely using through Mumps. Perhaps you have to link your
Mumps (or some other component) with OpenMP by using the linker flag
'-lgomp' or '-fopenmp'. You can also try adding 'gomp' to Kwant’s
build.conf under 'libraries'.
Christoph
