[petsc-users] Error using Metis with PETSc installed with MUMPS
Victoria Rolandi
victoria.rolandi93 at gmail.com
Tue Nov 7 13:47:40 CST 2023
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 <pierre at joliv.et> ha
scritto:
>
>
> On 3 Nov 2023, at 7:28 PM, Victoria Rolandi <victoria.rolandi93 at 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 <pierre at joliv.et>
> ha scritto:
>
>>
>> On 2 Nov 2023, at 5:29 PM, Victoria Rolandi <victoria.rolandi93 at 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 <pierre at 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 <bsmith at 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 <pierre at joliv.et> wrote:
>>>
>>>
>>>
>>> On 1 Nov 2023, at 3:33 PM, Zhang, Hong via petsc-users <
>>> petsc-users at 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-bounces at mcs.anl.gov> on behalf of
>>> Victoria Rolandi <victoria.rolandi93 at gmail.com>
>>> *Sent:* Tuesday, October 31, 2023 10:30 PM
>>> *To:* petsc-users at mcs.anl.gov <petsc-users at 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
>>>
>>>
>>>
>>>
>>>
>>
>
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