Hi Pierre, Thanks for your reply. I am now trying to configure PETSc with the same METIS/ParMETIS of my main code.
I get the following error, and I still get it even if I change the option --with-precision=double/--with-precision=single Metis specified is incompatible! IDXTYPEWIDTH=64 metis build appears to be specified for a default 32-bit-indices build of PETSc. Suggest using --download-metis for a compatible metis ******************************************************************************* In the cofigure.log I have: compilation aborted for /tmp/petsc-yxtl_gwd/config.packages.metis/conftest.c (code 2) Source: #include "confdefs.h" #include "conffix.h" #include "metis.h" int main() { #if (IDXTYPEWIDTH != 32) #error incompatible IDXTYPEWIDTH #endif; return 0; } How could I proceed? Thanks, Victoria Il giorno ven 3 nov 2023 alle ore 11:34 Pierre Jolivet <pie...@joliv.et> ha scritto: > > > On 3 Nov 2023, at 7:28 PM, Victoria Rolandi <victoria.roland...@gmail.com> > wrote: > > Pierre, > > Sure, I have now installed PETSc with MUMPS and PT-SCHOTCH, I got some > errors at the beginning but then it worked adding > --COPTFLAGS="-D_POSIX_C_SOURCE=199309L" > to the configuration. > Also, I have compilation errors when I try to use newer versions, so I > kept the 3.17.0 for the moment. > > > You should ask for assistance to get the latest version. > (Par)METIS snapshots may have not changed, but the MUMPS one did, with > performance improvements. > > Now the parallel ordering works with PT-SCOTCH, however, is it normal that > I do not see any difference in the performance compared to sequential > ordering ? > > > Impossible to tell without you providing actual figures (number of nnz, > number of processes, timings with sequential ordering, etc.), but 699k is > not that big of a problem, so that is not extremely surprising. > > Also, could the error using Metis/Parmetis be due to the fact that my main > code (to which I linked PETSc) uses a different ParMetis than the one > separately installed by PETSC during the configuration? > > > Yes. > > Hence should I configure PETSc linking ParMetis to the same library used > by my main code? > > > Yes. > > Thanks, > Pierre > > Thanks, > Victoria > > Il giorno gio 2 nov 2023 alle ore 09:35 Pierre Jolivet <pie...@joliv.et> > ha scritto: > >> >> On 2 Nov 2023, at 5:29 PM, Victoria Rolandi <victoria.roland...@gmail.com> >> wrote: >> >> Pierre, >> Yes, sorry, I'll keep the list in copy. >> Launching with those options (-mat_mumps_icntl_28 2 -mat_mumps_icntl_29 >> 2) I get an error during the analysis step. I also launched increasing the >> memory and I still have the error. >> >> >> Oh, OK, that’s bad. >> Would you be willing to give SCOTCH and/or PT-SCOTCH a try? >> You’d need to reconfigure/recompile with --download-ptscotch (and maybe >> --download-bison depending on your system). >> Then, the option would become either -mat_mumps_icntl_28 2 >> -mat_mumps_icntl_29 2 (PT-SCOTCH) or -mat_mumps_icntl_7 3 (SCOTCH). >> It may be worth updating PETSc as well (you are using 3.17.0, we are at >> 3.20.1), though I’m not sure we updated the METIS/ParMETIS snapshots since >> then, so it may not fix the present issue. >> >> Thanks, >> Pierre >> >> *The calculations stops at :* >> >> Entering CMUMPS 5.4.1 from C interface with JOB, N = 1 699150 >> executing #MPI = 2, without OMP >> >> ================================================= >> MUMPS compiled with option -Dmetis >> MUMPS compiled with option -Dparmetis >> ================================================= >> L U Solver for unsymmetric matrices >> Type of parallelism: Working host >> >> ****** ANALYSIS STEP ******** >> >> ** Maximum transversal (ICNTL(6)) not allowed because matrix is >> distributed >> Using ParMETIS for parallel ordering >> Structural symmetry is: 90% >> >> >> *The error:* >> >> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >> probably memory access out of range >> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind >> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple MacOS >> 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 https://petsc.org/release/faq/ for trouble shooting. >> [0]PETSC ERROR: Petsc Release Version 3.17.0, unknown >> [0]PETSC ERROR: ./charlin.exe on a named n1056 by vrolandi Wed Nov 1 >> 11:38:28 2023 >> [0]PETSC ERROR: Configure options >> --prefix=/u/home/v/vrolandi/CODES/LIBRARY/packages/petsc/installationDir >> --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort CXXOPTFLAGS=-O3 >> --with-scalar-type=complex --with-debugging=0 --with-precision=single >> --download-mumps --download-scalapack --download-parmetis --download-metis >> >> [0]PETSC ERROR: #1 User provided function() at unknown file:0 >> [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is >> causing the crash. >> Abort(59) on node 0 (rank 0 in comm 0): application called >> MPI_Abort(MPI_COMM_WORLD, 59) - process 0 >> >> >> Thanks, >> Victoria >> >> Il giorno mer 1 nov 2023 alle ore 10:33 Pierre Jolivet <pie...@joliv.et> >> ha scritto: >> >>> Victoria, please keep the list in copy. >>> >>> I am not understanding how can I switch to ParMetis if it does not >>> appear in the options of -mat_mumps_icntl_7.In the options I only have >>> Metis and not ParMetis. >>> >>> >>> You need to use -mat_mumps_icntl_28 2 -mat_mumps_icntl_29 2 >>> >>> Barry, I don’t think we can programmatically shut off this warning, it’s >>> guarded by a bunch of KEEP() values, see src/dana_driver.F:4707, which are >>> only settable/gettable by people with access to consortium releases. >>> I’ll ask the MUMPS people for confirmation. >>> Note that this warning is only printed to screen with the option >>> -mat_mumps_icntl_4 2 (or higher), so this won’t show up for standard runs. >>> >>> Thanks, >>> Pierre >>> >>> On 1 Nov 2023, at 5:52 PM, Barry Smith <bsm...@petsc.dev> wrote: >>> >>> >>> Pierre, >>> >>> Could the PETSc MUMPS interface "turn-off" ICNTL(6) in this >>> situation so as to not trigger the confusing warning message from MUMPS? >>> >>> Barry >>> >>> On Nov 1, 2023, at 12:17 PM, Pierre Jolivet <pie...@joliv.et> wrote: >>> >>> >>> >>> On 1 Nov 2023, at 3:33 PM, Zhang, Hong via petsc-users < >>> petsc-users@mcs.anl.gov> wrote: >>> >>> Victoria, >>> "** Maximum transversal (ICNTL(6)) not allowed because matrix is >>> distributed >>> Ordering based on METIS" >>> >>> >>> This warning is benign and appears for every run using a sequential >>> partitioner in MUMPS with a MATMPIAIJ. >>> (I’m not saying switching to ParMETIS will not make the issue go away) >>> >>> Thanks, >>> Pierre >>> >>> $ ../../../../arch-darwin-c-debug-real/bin/mpirun -n 2 ./ex2 -pc_type lu >>> -mat_mumps_icntl_4 2 >>> Entering DMUMPS 5.6.2 from C interface with JOB, N = 1 56 >>> executing #MPI = 2, without OMP >>> >>> ================================================= >>> MUMPS compiled with option -Dmetis >>> MUMPS compiled with option -Dparmetis >>> MUMPS compiled with option -Dpord >>> MUMPS compiled with option -Dptscotch >>> MUMPS compiled with option -Dscotch >>> ================================================= >>> L U Solver for unsymmetric matrices >>> Type of parallelism: Working host >>> >>> ****** ANALYSIS STEP ******** >>> >>> ** Maximum transversal (ICNTL(6)) not allowed because matrix is >>> distributed >>> Processing a graph of size: 56 with 194 edges >>> Ordering based on AMF >>> WARNING: Largest root node of size 26 not selected for parallel >>> execution >>> >>> Leaving analysis phase with ... >>> INFOG(1) = 0 >>> INFOG(2) = 0 >>> […] >>> >>> Try parmetis. >>> Hong >>> ------------------------------ >>> *From:* petsc-users <petsc-users-boun...@mcs.anl.gov> on behalf of >>> Victoria Rolandi <victoria.roland...@gmail.com> >>> *Sent:* Tuesday, October 31, 2023 10:30 PM >>> *To:* petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> >>> *Subject:* [petsc-users] Error using Metis with PETSc installed with >>> MUMPS >>> >>> Hi, >>> >>> I'm solving a large sparse linear system in parallel and I am using >>> PETSc with MUMPS. I am trying to test different options, like the ordering >>> of the matrix. Everything works if I use the *-mat_mumps_icntl_7 2 *or >>> *-mat_mumps_icntl_7 >>> 0 *options (with the first one, AMF, performing better than AMD), >>> however when I test METIS *-mat_mumps_icntl_7** 5 *I get an error >>> (reported at the end of the email). >>> >>> I have configured PETSc with the following options: >>> >>> --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort >>> --with-scalar-type=complex --with-debugging=0 --with-precision=single >>> --download-mumps --download-scalapack --download-parmetis --download-metis >>> >>> and the installation didn't give any problems. >>> >>> Could you help me understand why metis is not working? >>> >>> Thank you in advance, >>> Victoria >>> >>> Error: >>> >>> ****** ANALYSIS STEP ******** >>> ** Maximum transversal (ICNTL(6)) not allowed because matrix is >>> distributed >>> Processing a graph of size: 699150 with 69238690 edges >>> Ordering based on METIS >>> 510522 37081376 [100] [10486 699150] >>> Error! Unknown CType: -1 >>> >>> >>> >>> >>> >> >