Mumps installation with Petsc


(Talal Alotaibi) #1

Hi guys,

I tried to install petsc with mumps but couldn’t using brew. I did install mumps saperatly but when run my code it does not find mumps solver.
to be more specific, I did the following:

  1. brew install petsc --build-from-source
  2. brew install dpo/openblas/mumps

I set the right linking and have no issues when make. but then I run my code it says:


| |--------------------------------------

| | Full-Coupled = 0

| | DOFs :

| | u (Elasticity)

| | v (Fluid)

| | mu (Phase-field)

| |--------------------------------------

|

| N-R Iteration = 1

| sumsqf= 28.024119489256918 relative= 28.024119489256918

[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------

[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html for possible LU and Cholesky solvers

[0]PETSC ERROR: Could not locate solver package mumps. Perhaps you must ./configure with --download-mumps

[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.

[0]PETSC ERROR: Petsc Release Version 3.9.3, Jul, 02, 2018

[0]PETSC ERROR: ./Frac on a named Talals-MacBook-Pro.local by talal1 Wed Oct 31 16:19:10 2018

[0]PETSC ERROR: Configure options --prefix=/usr/local/Cellar/petsc/3.9.3 --with-debugging=0 --with-scalar-type=real --with-x=0

[0]PETSC ERROR: #1 MatGetFactor() line 4326 in /private/tmp/petsc-20181031-59652-1467k83/petsc-3.9.3/src/mat/interface/matrix.c

[0]PETSC ERROR: #2 PCSetUp_LU() line 93 in /private/tmp/petsc-20181031-59652-1467k83/petsc-3.9.3/src/ksp/pc/impls/factor/lu/lu.c

[0]PETSC ERROR: #3 PCSetUp() line 923 in /private/tmp/petsc-20181031-59652-1467k83/petsc-3.9.3/src/ksp/pc/interface/precon.c

[0]PETSC ERROR: #4 KSPSetUp() line 381 in /private/tmp/petsc-20181031-59652-1467k83/petsc-3.9.3/src/ksp/ksp/interface/itfunc.c

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:

#0 0x10a80f1ac

#1 0x10a80e553

#2 0x7fff52040f59

#0 0x1133c61ac

#1 0x1133c5553

#2 0x7fff52040f59


Primary job terminated normally, but 1 process returned

a non-zero exit code. Per user-direction, the job has been aborted.



MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD

with errorcode 59.

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.


[0]PETSC ERROR: ------------------------------------------------------------------------

[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see …

[0]PETSC ERROR: or try […) on GNU/linux and Apple Mac OS X to find memory corruption errors

[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[0]PETSC ERROR: to get more information on the crash.

[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------

[0]PETSC ERROR: Signal received

[0]PETSC ERROR: See … for trouble shooting.

[0]PETSC ERROR: Petsc Release Version 3.9.3, Jul, 02, 2018

[0]PETSC ERROR: ./Frac on a named Talals-MacBook-Pro.local by talal1 Wed Oct 31 16:19:10 2018

[0]PETSC ERROR: Configure options --prefix=/usr/local/Cellar/petsc/3.9.3 --with-debugging=0 --with-scalar-type=real --with-x=0

[0]PETSC ERROR: #5 User provided function() line 0 in unknown file


mpiexec noticed that process rank 1 with PID 0 on node Talals-MacBook-Pro exited on signal 6 (Abort trap: 6).



How can I install petsc with mumps so the linking would be set right? I tried:
brew install petsc --with-mumps
but it doesn’t recognize --with-mumps

Any idea?

Talal


(Claudia) #2

Hey Talal, thanks for reaching out and taking your time for a thorough description.

You’re right, the --with-mumps option was removed from the formula earlier this year as the formula was migrated to our main tap homebrew-core. (There are various reasons for this which have been discussed in sufficient detail elsewhere.)

This means that unfortunately, you’re mostly on your own here. Have you looked at an older revision of petsci, back when it was on the (now defunct) homebrew-science tap? You will find a few hints there on how mumps used to be linked. That may help you craft your own custom version of the petsci formula.

Although we’re not in a position to support such a customization, let me know if this helped!