@adamjhepburn, first off, glad that you have PETSc and ISSM compiled correctly now. To address your questions/comments in one response...
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ISSM_DIR/lib/libISSMCore.so
This should be export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ISSM_DIR/lib
, if anything, but shouldn't be necessary.
I think there is a fundamental issue with your setup though that I didn't notice before: when we use ISSM on a cluster (or any remote solution server), we really need two ISSM installations.
1) a local installation: used for model setup and results parsing in either MATLAB or Python, requires a customized cluster class (see $ISSM_DIR/src/m/classes/clusters
) to handle transfer of I/O files to/from cluster and to trigger actual job, external packages should be installed
2) a remote installation on a solution server or on the head/login node of a cluster: use --with-wrappers=no
option in configuration, no need for external packages to be installed
Cannot send after transport endpoint shutdown
I have never seen this error before. That said, if you have access to a shared location on disk (say, /usr/local/ISSM
) that only a group of users have permission to access, that's how I usually go about this. You should be able to install ISSM to your /home
directory, but if it is not accessible from both the login node and compute nodes, this is not helpful.
Could I use a docker environment?
You could. I personally have not tackled this yet (and I have not used the image that we have on the website) but it is on my long term list of activities. We would welcome you sharing the results (i.e. setup notes, Docker image) if you get something working as it will likely help other users.