Dear prj,
Thanks a lot for your rapid response.
I tried both of your solutions and only the second one worked.
The first one using the develop branch, did not even succeed “make petsc-slepc”.
Eventually, I also had the problem with libparmmgtypes.h as in (Freefem installation error on ubuntu 18.04)
In the end, I had to do,
./reconfigure MPIRUN=mpiexec --disable-parmmg
which worked for installation!
However, I faced other problem.
When I run the code with PETSc, errors occur for buildMat.
Other codes in examples/hpddm WITHOUT PETSc work fine as well as block-PETSc.edp, which does not call buildMat.
Is it related to the configuration --disable-parmmg ?
The example errors for diffusion-2d-PETSc.edp using 4 tasks with 12GB memory are
– Square mesh : nb vertices =1681 , nb triangles = 3200 , nb boundary edges 160
— global mesh of 3200 elements (prior to refinement) partitioned with metis --metisESCOA: 4-way Edge-Cut: 3, Balance: 1.01 Nodal=0/Dual 1
(in 4.019976e-03)
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
[2]PETSC ERROR: ------------------------------------------------------------------------
[2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[2]PETSC ERROR: or see https//www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[2]PETSC ERROR: or try http//valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[2]PETSC ERROR: to get more information on the crash.
[2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[2]PETSC ERROR: Signal received
[2]PETSC ERROR: See https//www.mcs.anl.gov/petsc/documentation/faqhtml for trouble shooting.
[2]PETSC ERROR: Petsc Release Version 3.13.0, Mar 29, 2020
[2]PETSC ERROR: /home/yim/FreeFem-sources/src/mpi/FreeFem+±mpi on a named f372 by yim Sat Aug 22 10:34:18 2020
[2]PETSC ERROR: Configure options MAKEFLAGS= --prefix=/home/yim/FreeFem-install/ff-petsc//r --with-debugging=0 COPTFLAGS="-O3 -mtune=native" CXXOPTFLAGS="-O3 -mtune=native" FOPTFLAGS="-O3 -mtune=native" --with-cxx-dialect=C++11 --with-ssl=0 --with-x=0 --with-fortran-bindings=0 --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort --with-scalar-type=real --download-openblas --download-scalapack --download-metis --download-ptscotch --download-mumps --download-hypre --download-parmetis --download-superlu --download-suitesparse --download-tetgen --download-slepc --download-hpddm --download-hpddm-commit=e8639ff PETSC_ARCH=fr
[2]PETSC ERROR: #1 User provided function() line 0 in unknown file
application called MPI_Abort(MPI_COMM_WORLD, 50152059) - process 2
In: PMI_Abort(50152059, application called MPI_Abort(MPI_COMM_WORLD, 50152059) - process 2)
slurmstepd: error: *** STEP 5023601.0 ON f366 CANCELLED AT 2020-08-22T10:34:18 ***
srun: error: f372: task 2: Exited with exit code 123
srun: Terminating job step 5023601.0
srun: error: f366: tasks 0-1: Killed
srun: error: f372: task 3: Killed
Thank you.
Best,
Eunok