Petsc error during execution

1

I am trying to execute on my desktop computer but it gives me the following error message (the same file however works on a colleague’s computer, so I know that the problem is not with the file itself but it is with my fenics installation).

Invalid MIT-MAGIC-COOKIE-1 key[computername:09959] pmix_mca_base_component_repository_open: unable to open mca_preg_compress: /usr/local/lib/pmix/mca_preg_compress.so: undefined symbol: pmix_compress (ignored)
[computername:09958] pmix_mca_base_component_repository_open: unable to open mca_preg_compress: /usr/local/lib/pmix/mca_preg_compress.so: undefined symbol: pmix_compress (ignored)
PETSc Error — Open MPI library version
Open MPI v4.1.1, package: Open MPI user@computername Distribution, ident: 4.1.1, repo rev: v4.1.1, Apr 24, 2021 does not match what PETSc was compiled with 4.0, aborting
PETSc Error — Open MPI library version
Open MPI v4.1.1, package: Open MPI user@computername Distribution, ident: 4.1.1, repo rev: v4.1.1, Apr 24, 2021 does not match what PETSc was compiled with 4.0, aborting
[computername:09958] *** Process received signal ***
[computername:09958] Signal: Segmentation fault (11)
[computername:09958] Signal code: Address not mapped (1)
[computername:09958] Failing at address: (nil)
[computername:09958] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x46210)[0x7f896b4ab210]
[computername:09958] [ 1] /lib/x86_64-linux-gnu/libc.so.6(fputs+0x19)[0x7f896b4eae79]
[computername:09958] [ 2] /lib/x86_64-linux-gnu/libpetsc_real.so.3.12(PetscVFPrintfDefault+0xf4)[0x7f896646f8c4]
[computername:09958] [ 3] /lib/x86_64-linux-gnu/libpetsc_real.so.3.12(PetscFPrintf+0x110)[0x7f8966470660]
[computername:09958] [ 4] /lib/x86_64-linux-gnu/libpetsc_real.so.3.12(PetscErrorPrintfDefault+0xb0)[0x7f896647c440]
[computername:09958] [ 5] /lib/x86_64-linux-gnu/libpetsc_real.so.3.12(PetscTraceBackErrorHandler+0xa3)[0x7f896647c973]
[computername:09958] [ 6] /lib/x86_64-linux-gnu/libpetsc_real.so.3.12(PetscError+0x20b)[0x7f89664794fb]
[computername:09958] [ 7] /lib/x86_64-linux-gnu/libslepc_real.so.3.12(SlepcInitialize+0x286)[0x7f896569cd16]
[computername:09958] [ 8] /lib/x86_64-linux-gnu/libdolfin.so.2019.2(_ZN6dolfin17SubSystemsManager10init_petscEiPPc+0x142)[0x7f8967883e32]
[computername:09958] [ 9] /lib/x86_64-linux-gnu/libdolfin.so.2019.2(_ZN6dolfin11PETScVectorC1EP19ompi_communicator_t+0x5c)[0x7f8967b281ec]
[computername:09958] [10] /lib/x86_64-linux-gnu/libdolfin.so.2019.2(_ZNK6dolfin12PETScFactory13create_vectorEP19ompi_communicator_t+0x4d)[0x7f8967b056fd]
[computername:09958] [11] /lib/x86_64-linux-gnu/libdolfin.so.2019.2(_ZNK6dolfin14DefaultFactory13create_vectorEP19ompi_communicator_t+0x36)[0x7f8967ab6d46]
[computername:09958] [12] /lib/x86_64-linux-gnu/libdolfin.so.2019.2(_ZN6dolfin8Function11init_vectorEv+0x9d2)[0x7f896793a472]
[computername:09958] [13] /lib/x86_64-linux-gnu/libdolfin.so.2019.2(_ZN6dolfin8FunctionC1ESt10shared_ptrIKNS_13FunctionSpaceEE+0x33d)[0x7f896793c49d]
[computername:09958] [14] /usr/lib/petsc/lib/python3/dist-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x1cc8a3)[0x7f8967f0a8a3]
[computername:09958] [15] /usr/lib/petsc/lib/python3/dist-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x245984)[0x7f8967f83984]
[computername:09958] [16] python3(PyCFunction_Call+0x59)[0x5f2fb9]
[computername:09958] [17] python3(_PyObject_MakeTpCall+0x296)[0x5f3446]
[computername:09958] [18] python3[0x50aa2b]
[computername:09958] [19] python3(PyObject_Call+0x1f7)[0x5f2b87]
[computername:09958] [20] python3[0x59bc1c]
[computername:09958] [21] python3[0x5a6867]
[computername:09958] [22] /usr/lib/petsc/lib/python3/dist-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x2451e7)[0x7f8967f831e7]
[computername:09958] [23] python3(_PyObject_MakeTpCall+0x296)[0x5f3446]
[computername:09958] [24] python3(_PyEval_EvalFrameDefault+0x5dc0)[0x56f600]
[computername:09958] [25] python3(_PyEval_EvalCodeWithName+0x26a)[0x56822a]
[computername:09958] [26] python3(_PyFunction_Vectorcall+0x393)[0x5f6033]
[computername:09958] [27] python3[0x59ba6e]
[computername:09958] [28] python3(_PyObject_MakeTpCall+0x1ff)[0x5f33af]
[computername:09958] [29] python3(_PyEval_EvalFrameDefault+0x598a)[0x56f1ca]
[computername:09958] *** End of error message ***
Segmentation fault (core dumped)

2

The execution command is $ python3 filename.py

3

You need to supply more information for anyone to be of any help.

  • Did you install dolfin and PETSc from source?
  • Did you use the apt-get commands?
  • Which version of dolfin are you trying to run?

To me it seems like you have compiled PETSc with another version of openmpi than you have compiled dolfin with.

4

So I found a rather radical solution. The problem originated from the openmpi version that I had installed prior to installing fenics. The installed version was a higher one compared to the one currently supported by fenics (4.0.3) and I couldn’t downgrade mine. So I reinstalled ubuntu and the first thing I installed after was fenics. It runs perfectly fine now.
Thank you for the help.