[petsc-users] Error using Metis with PETSc installed with MUMPS
Victoria Rolandi
victoria.rolandi93 at gmail.com
Tue Nov 7 16:27:53 CST 2023
Great! It compiles now and both the commands -mat_mumps_icntl_7 2 and
-mat_mumps_icntl_29 2 work, and perform better compared to the other
ordering types.
Thank you Pierre!
As you suggested, I'll also send a new email concerning the errors I have
with newer PETSc versions.
Best,
Victoria
Il giorno mar 7 nov 2023 alle ore 12:25 Pierre Jolivet <pierre at joliv.et> ha
scritto:
>
>
> On 7 Nov 2023, at 8:47 PM, Victoria Rolandi <victoria.rolandi93 at gmail.com>
> wrote:
>
> 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?
>
>
> I would use --download-metis and then have your code use METIS from PETSc,
> not the other way around.
>
> Thanks,
> Pierre
>
> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20231107/4d998243/attachment-0001.html>
More information about the petsc-users
mailing list