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IBAMR / autoibamr

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"Off the Shelf" IBFE examples won't run #168

Open colegruninger97 opened 1 day ago

colegruninger97 commented 1 day ago

I've been trying to use autoibamr to setup and build IBAMR on my MAC. Using autoibamr "out of the box" with a version of python which has xdrlib needed for older petsc versions, I am able to compile IBAMR, but it appears that IBFE example which uses libmesh throws the following runtime error:

`./main2d input2d [COLE.local:18727] shmem: mmap: an error occurred while determining whether or not /var/folders/_v/14dsbdpn6797b07d66skcvqh0000gn/T//ompi.COLE.501/jf.0/3246718976/sm_segment.COLE.501.c1850000.0 could be created.

IBFEMethod: mesh part 0 is using SECOND order LAGRANGE finite elements.

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD Proc: [[49541,0],0] Errorcode: 1

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

--------------------------------------------------------------------------`

I'll note that I am able to compile and run examples which do not require libmesh. This indicates to me there is an issue with the libmesh installation. I'm attaching the CMakeConfigureLog.yaml file for IBAMR here for reference. I've tried building IBAMR on my own from scratch, but I also run into a variety of errors associated with libmesh. I'm wondering if the compilers I am using are not compatible with libmesh.

Something else to note is that older versions of petsc are not compatible with python versions 3.13.0+ since these newer version of python lack xdrlib. See this relevant discussion from the petsc developers:https://gitlab.com/petsc/petsc/-/merge_requests/7790. Therefore, to use autoibamr "out of the box", one has to be using an older version of python.

CMakeConfigureLog.txt

drwells commented 1 day ago

We do need to fix the PETSc incompatibility but I don't think that's the root cause of your issues. Does your mac now have 3.13? That was only released a month ago.

How did you install python and openmpi?

colegruninger97 commented 1 day ago

@drwells I installed python and openmpi via homebrew. My hunch now is that after updating, apple's command line tools may have updated as well and may be causing these issues. I tried installing an older version of open-mpi and I could not configure it.