[petsc-users] MPI_Iprobe Error with MUMPS Solver on Multi-Nodes

Tue May 23 04:59:36 CDT 2023

On Mon, May 22, 2023 at 10:42 PM Zongze Yang <yangzongze at gmail.com> wrote:

> On Tue, 23 May 2023 at 05:31, Stefano Zampini <stefano.zampini at gmail.com>
> wrote:
>
>> If I may add to the discussion, it may be that you are going OOM since
>> you are trying to factorize a 3 million dofs problem, this problem goes
>> undetected and then fails at a later stage
>>
>
> Thank you for your comment. I ran the problem with 90 processes
> distributed across three nodes, each equipped with 500G of memory. If this
> amount of memory is sufficient for solving the matrix with approximately 3
> million degrees of freedom?
>

It really depends on the fill. Suppose that you get 1% fill, then

  (3e6)^2 * 0.01 * 8 = 1e12 B

and you have 1.5e12 B, so I could easily see running out of memory.

  Thanks,

     Matt

> Thanks!
> Zongze
>
> Il giorno lun 22 mag 2023 alle ore 20:03 Zongze Yang <yangzongze at gmail.com>
>> ha scritto:
>>
>>> Thanks!
>>>
>>> Zongze
>>>
>>> Matthew Knepley <knepley at gmail.com>于2023年5月23日 周二00:09写道：
>>>
>>>> On Mon, May 22, 2023 at 11:07 AM Zongze Yang <yangzongze at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I hope this letter finds you well. I am writing to seek guidance
>>>>> regarding an error I encountered while solving a matrix using MUMPS on
>>>>> multiple nodes:
>>>>>
>>>>
>>>> Iprobe is buggy on several MPI implementations. PETSc has an option for
>>>> shutting it off for this reason.
>>>> I do not know how to shut it off inside MUMPS however. I would mail
>>>> their mailing list to see.
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>>
>>>>> ```bash
>>>>> Abort(1681039) on node 60 (rank 60 in comm 240): Fatal error in
>>>>> PMPI_Iprobe: Other MPI error, error stack:
>>>>> PMPI_Iprobe(124)..............: MPI_Iprobe(src=MPI_ANY_SOURCE,
>>>>> tag=MPI_ANY_TAG, comm=0xc4000026, flag=0x7ffc130f9c4c,
>>>>> status=0x7ffc130f9e80) failed
>>>>> MPID_Iprobe(240)..............:
>>>>> MPIDI_iprobe_safe(108)........:
>>>>> MPIDI_iprobe_unsafe(35).......:
>>>>> MPIDI_OFI_do_iprobe(69).......:
>>>>> MPIDI_OFI_handle_cq_error(949): OFI poll failed
>>>>> (ofi_events.c:951:MPIDI_OFI_handle_cq_error:Input/output error)
>>>>> Assertion failed in file src/mpid/ch4/netmod/ofi/ofi_events.c at line
>>>>> 125: 0
>>>>> ```
>>>>>
>>>>> The matrix in question has a degree of freedom (dof) of 3.86e+06.
>>>>> Interestingly, when solving smaller-scale problems, everything functions
>>>>> perfectly without any issues. However, when attempting to solve the larger
>>>>> matrix on multiple nodes, I encounter the aforementioned error.
>>>>>
>>>>> The complete error message I received is as follows:
>>>>> ```bash
>>>>> Abort(1681039) on node 60 (rank 60 in comm 240): Fatal error in
>>>>> PMPI_Iprobe: Other MPI error, error stack:
>>>>> PMPI_Iprobe(124)..............: MPI_Iprobe(src=MPI_ANY_SOURCE,
>>>>> tag=MPI_ANY_TAG, comm=0xc4000026, flag=0x7ffc130f9c4c,
>>>>> status=0x7ffc130f9e80) failed
>>>>> MPID_Iprobe(240)..............:
>>>>> MPIDI_iprobe_safe(108)........:
>>>>> MPIDI_iprobe_unsafe(35).......:
>>>>> MPIDI_OFI_do_iprobe(69).......:
>>>>> MPIDI_OFI_handle_cq_error(949): OFI poll failed
>>>>> (ofi_events.c:951:MPIDI_OFI_handle_cq_error:Input/output error)
>>>>> Assertion failed in file src/mpid/ch4/netmod/ofi/ofi_events.c at line
>>>>> 125: 0
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(MPL_backtrace_show+0x26)
>>>>> [0x7f6076063f2c]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x41dc24)
>>>>> [0x7f6075fc5c24]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x49cc51)
>>>>> [0x7f6076044c51]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x49f799)
>>>>> [0x7f6076047799]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x451e18)
>>>>> [0x7f6075ff9e18]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x452272)
>>>>> [0x7f6075ffa272]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x2ce836)
>>>>> [0x7f6075e76836]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x2ce90d)
>>>>> [0x7f6075e7690d]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x48137b)
>>>>> [0x7f607602937b]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x44d471)
>>>>> [0x7f6075ff5471]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(+0x407acd)
>>>>> [0x7f6075fafacd]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(MPIR_Err_return_comm+0x10a)
>>>>> [0x7f6075fafbea]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpi.so.12(MPI_Iprobe+0x312)
>>>>> [0x7f6075ddd542]
>>>>> /nfs/opt/cascadelake/linux-centos7-cascadelake/gcc-9.4.0/mpich-3.4.2-qgtz76gekvjzuacy7wq5a26rqlewoxfc/lib/libmpifort.so.12(pmpi_iprobe+0x2f)
>>>>> [0x7f606e08f19f]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/mumps-5.5.1-gb7wlwxwbalf5rw5vkp6gtkhfkdqpntz/lib/libzmumps.so(__zmumps_load_MOD_zmumps_load_recv_msgs+0x142)
>>>>> [0x7f60737b194d]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/mumps-5.5.1-gb7wlwxwbalf5rw5vkp6gtkhfkdqpntz/lib/libzmumps.so(zmumps_try_recvtreat_+0x34)
>>>>> [0x7f60738ab735]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/mumps-5.5.1-gb7wlwxwbalf5rw5vkp6gtkhfkdqpntz/lib/libzmumps.so(__zmumps_fac_par_m_MOD_zmumps_fac_par+0x991)
>>>>> [0x7f607378bcc8]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/mumps-5.5.1-gb7wlwxwbalf5rw5vkp6gtkhfkdqpntz/lib/libzmumps.so(zmumps_fac_par_i_+0x240)
>>>>> [0x7f6073881d36]
>>>>> Abort(805938831) on node 51 (rank 51 in comm 240): Fatal error in
>>>>> PMPI_Iprobe: Other MPI error, error stack:
>>>>> PMPI_Iprobe(124)..............: MPI_Iprobe(src=MPI_ANY_SOURCE,
>>>>> tag=MPI_ANY_TAG, comm=0xc4000017, flag=0x7ffe20e1402c,
>>>>> status=0x7ffe20e14260) failed
>>>>> MPID_Iprobe(244)..............:
>>>>> progress_test(100)............:
>>>>> MPIDI_OFI_handle_cq_error(949): OFI poll failed
>>>>> (ofi_events.c:951:MPIDI_OFI_handle_cq_error:Input/output error)
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/mumps-5.5.1-gb7wlwxwbalf5rw5vkp6gtkhfkdqpntz/lib/libzmumps.so(zmumps_fac_b_+0x1463)
>>>>> [0x7f60738831a1]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/mumps-5.5.1-gb7wlwxwbalf5rw5vkp6gtkhfkdqpntz/lib/libzmumps.so(zmumps_fac_driver_+0x6969)
>>>>> [0x7f60738446c9]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/mumps-5.5.1-gb7wlwxwbalf5rw5vkp6gtkhfkdqpntz/lib/libzmumps.so(zmumps_+0x2d83)
>>>>> [0x7f60738bf9cf]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/mumps-5.5.1-gb7wlwxwbalf5rw5vkp6gtkhfkdqpntz/lib/libzmumps.so(zmumps_f77_+0x178c)
>>>>> [0x7f60738c33bc]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/mumps-5.5.1-gb7wlwxwbalf5rw5vkp6gtkhfkdqpntz/lib/libzmumps.so(zmumps_c+0x8f8)
>>>>> [0x7f60738baacb]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/petsc-develop-5wrc3y6lyelr3iyrlm3sr2jlh2wxif3k/lib/libpetsc.so.3.019(+0x894560)
>>>>> [0x7f6077297560]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/petsc-develop-5wrc3y6lyelr3iyrlm3sr2jlh2wxif3k/lib/libpetsc.so.3.019(MatLUFactorNumeric+0x32e)
>>>>> [0x7f60773bb1e6]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/petsc-develop-5wrc3y6lyelr3iyrlm3sr2jlh2wxif3k/lib/libpetsc.so.3.019(+0xf51665)
>>>>> [0x7f6077954665]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/petsc-develop-5wrc3y6lyelr3iyrlm3sr2jlh2wxif3k/lib/libpetsc.so.3.019(PCSetUp+0x64b)
>>>>> [0x7f60779c77e0]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/petsc-develop-5wrc3y6lyelr3iyrlm3sr2jlh2wxif3k/lib/libpetsc.so.3.019(KSPSetUp+0xfb6)
>>>>> [0x7f6077ac2d53]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/petsc-develop-5wrc3y6lyelr3iyrlm3sr2jlh2wxif3k/lib/libpetsc.so.3.019(+0x10c1c28)
>>>>> [0x7f6077ac4c28]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/petsc-develop-5wrc3y6lyelr3iyrlm3sr2jlh2wxif3k/lib/libpetsc.so.3.019(KSPSolve+0x13)
>>>>> [0x7f6077ac8070]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/petsc-develop-5wrc3y6lyelr3iyrlm3sr2jlh2wxif3k/lib/libpetsc.so.3.019(+0x11249df)
>>>>> [0x7f6077b279df]
>>>>> /nfs/home/zzyang/opt/software/linux-centos7-cascadelake/gcc-9.4.0/petsc-develop-5wrc3y6lyelr3iyrlm3sr2jlh2wxif3k/lib/libpetsc.so.3.019(SNESSolve+0x10df)
>>>>> [0x7f6077b676c6]
>>>>> Abort(1) on node 60: Internal error
>>>>> Abort(1007265423) on node 65 (rank 65 in comm 240): Fatal error in
>>>>> PMPI_Iprobe: Other MPI error, error stack:
>>>>> PMPI_Iprobe(124)..............: MPI_Iprobe(src=MPI_ANY_SOURCE,
>>>>> tag=MPI_ANY_TAG, comm=0xc4000017, flag=0x7fff4d82827c,
>>>>> status=0x7fff4d8284b0) failed
>>>>> MPID_Iprobe(244)..............:
>>>>> progress_test(100)............:
>>>>> MPIDI_OFI_handle_cq_error(949): OFI poll failed
>>>>> (ofi_events.c:951:MPIDI_OFI_handle_cq_error:Input/output error)
>>>>> Abort(941205135) on node 32 (rank 32 in comm 240): Fatal error in
>>>>> PMPI_Iprobe: Other MPI error, error stack:
>>>>> PMPI_Iprobe(124)..............: MPI_Iprobe(src=MPI_ANY_SOURCE,
>>>>> tag=MPI_ANY_TAG, comm=0xc4000017, flag=0x7fff715ba3fc,
>>>>> status=0x7fff715ba630) failed
>>>>> MPID_Iprobe(240)..............:
>>>>> MPIDI_iprobe_safe(108)........:
>>>>> MPIDI_iprobe_unsafe(35).......:
>>>>> MPIDI_OFI_do_iprobe(69).......:
>>>>> MPIDI_OFI_handle_cq_error(949): OFI poll failed
>>>>> (ofi_events.c:951:MPIDI_OFI_handle_cq_error:Input/output error)
>>>>> Abort(470941839) on node 75 (rank 75 in comm 0): Fatal error in
>>>>> PMPI_Test: Other MPI error, error stack:
>>>>> PMPI_Test(188)................: MPI_Test(request=0x7efe31e03014,
>>>>> flag=0x7ffea65d673c, status=0x7ffea65d6760) failed
>>>>> MPIR_Test(73).................:
>>>>> MPIR_Test_state(33)...........:
>>>>> progress_test(100)............:
>>>>> MPIDI_OFI_handle_cq_error(949): OFI poll failed
>>>>> (ofi_events.c:951:MPIDI_OFI_handle_cq_error:Input/output error)
>>>>> Abort(805946511) on node 31 (rank 31 in comm 256): Fatal error in
>>>>> PMPI_Probe: Other MPI error, error stack:
>>>>> PMPI_Probe(118)...............: MPI_Probe(src=MPI_ANY_SOURCE, tag=7,
>>>>> comm=0xc4000015, status=0x7fff9538b7a0) failed
>>>>> MPID_Probe(159)...............:
>>>>> progress_test(100)............:
>>>>> MPIDI_OFI_handle_cq_error(949): OFI poll failed
>>>>> (ofi_events.c:951:MPIDI_OFI_handle_cq_error:Input/output error)
>>>>> Abort(1179791) on node 73 (rank 73 in comm 0): Fatal error in
>>>>> PMPI_Test: Other MPI error, error stack:
>>>>> PMPI_Test(188)................: MPI_Test(request=0x5b638d4,
>>>>> flag=0x7ffd755119cc, status=0x7ffd755121b0) failed
>>>>> MPIR_Test(73).................:
>>>>> MPIR_Test_state(33)...........:
>>>>> progress_test(100)............:
>>>>> MPIDI_OFI_handle_cq_error(949): OFI poll failed
>>>>> (ofi_events.c:951:MPIDI_OFI_handle_cq_error:Input/output error)
>>>>> ```
>>>>>
>>>>> Thank you very much for your time and consideration.
>>>>>
>>>>> Best wishes,
>>>>> Zongze
>>>>>
>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their
>>>> experiments is infinitely more interesting than any results to which their
>>>> experiments lead.
>>>> -- Norbert Wiener
>>>>
>>>> https://www.cse.buffalo.edu/~knepley/
>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>
>>> --
>>> Best wishes,
>>> Zongze
>>>
>>
>>
>> --
>> Stefano
>>
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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