[petsc-users] superlu_dist segfault
Stefano Zampini
stefano.zampini at gmail.com
Sun Nov 1 04:09:42 CST 2020
More importantly,
==43569== Conditional jump or move depends on uninitialised value(s)
==43569== at 0x1473C515: pzgstrs (pzgstrs.c:1074)
==43569== by 0x146F5E72: pzgssvx (pzgssvx.c:1422)
==43569== by 0x58C3FE5: MatMatSolve_SuperLU_DIST (superlu_dist.c:242)
==43569== by 0x55FB716: MatMatSolve (matrix.c:3485)
==43569== by 0x40465D: main (superlu_test.c:59)
You should run using valgrind's option --track-origins=yes to
understand the reason for this.
Il giorno dom 1 nov 2020 alle ore 11:53 Barry Smith <bsmith at petsc.dev> ha
scritto:
>
>
> You can sometimes use -on_error_attach_debugger noxterm and it will try
> to attach just in the console you started the job. If you are lucky this
> works and you use bt and see the stack and look at variables. But if
> multiple ranks crash the debugger will get confused and even if only one
> crashes if it is not rank zero the stty can get messed up so you cannot
> type to control the debugger.
>
> The valgrind information is very valuable, likely Sherry can look at
> those lines and have a really good idea what the problem is, for example,
>
> Address 0x266e5ac0 is 0 bytes after a block of size 35,520 alloc'd
>
>
> means that for some reason the code is writing past the end of an
> allocated array, either because the array allocated was not long enough or
> the code has some issue where it wants to write further than it should.
> This kind of thing is very common and usually easy to debug by someone who
> knows the code once they know exactly what line of code is problematic.
> Since it shows exactly where the memory was allocated and exactly where it
> went out of bounds.
>
> Barry
>
>
> On Nov 1, 2020, at 1:21 AM, Marius Buerkle <mbuerkle at web.de> wrote:
>
> Hi,
>
> I cannot use on_error_attach_debugger as X forwarding does not work on the
> system. Is it possible to dump the gdb output to file instead?
>
> I run it through valgrind. It seems there is some problem during calls in
> superlu_dist but I don't know if this eventually causes the seg fault. I
> think this is the relevant output:
>
> ==43569== Conditional jump or move depends on uninitialised value(s)
> ==43569== at 0x1473C515: pzgstrs (pzgstrs.c:1074)
> ==43569== by 0x146F5E72: pzgssvx (pzgssvx.c:1422)
> ==43569== by 0x58C3FE5: MatMatSolve_SuperLU_DIST (superlu_dist.c:242)
> ==43569== by 0x55FB716: MatMatSolve (matrix.c:3485)
> ==43569== by 0x40465D: main (superlu_test.c:59)
> ==43569==
> ==43569== Use of uninitialised value of size 8
> ==43569== at 0x1473C554: pzgstrs (pzgstrs.c:1077)
> ==43569== by 0x146F5E72: pzgssvx (pzgssvx.c:1422)
> ==43569== by 0x58C3FE5: MatMatSolve_SuperLU_DIST (superlu_dist.c:242)
> ==43569== by 0x55FB716: MatMatSolve (matrix.c:3485)
> ==43569== by 0x40465D: main (superlu_test.c:59)
> ==43569==
> ==43569== Use of uninitialised value of size 8
> ==43569== at 0x1473C55A: pzgstrs (pzgstrs.c:1077)
> ==43569== by 0x146F5E72: pzgssvx (pzgssvx.c:1422)
> ==43569== by 0x58C3FE5: MatMatSolve_SuperLU_DIST (superlu_dist.c:242)
> ==43569== by 0x55FB716: MatMatSolve (matrix.c:3485)
> ==43569== by 0x40465D: main (superlu_test.c:59)
> ==43569==
> ==43569== Invalid write of size 8
> ==43569== at 0x1473C554: pzgstrs (pzgstrs.c:1077)
> ==43569== by 0x146F5E72: pzgssvx (pzgssvx.c:1422)
> ==43569== by 0x58C3FE5: MatMatSolve_SuperLU_DIST (superlu_dist.c:242)
> ==43569== by 0x55FB716: MatMatSolve (matrix.c:3485)
> ==43569== by 0x40465D: main (superlu_test.c:59)
> ==43569== Address 0x266e5ac0 is 0 bytes after a block of size 35,520
> alloc'd
> ==43569== at 0x4C2D814: memalign (vg_replace_malloc.c:906)
> ==43569== by 0x4C2D97B: posix_memalign (vg_replace_malloc.c:1070)
> ==43569== by 0x1464D488: superlu_malloc_dist (memory.c:127)
> ==43569== by 0x1473C451: pzgstrs (pzgstrs.c:1044)
> ==43569== by 0x146F5E72: pzgssvx (pzgssvx.c:1422)
> ==43569== by 0x58C3FE5: MatMatSolve_SuperLU_DIST (superlu_dist.c:242)
> ==43569== by 0x55FB716: MatMatSolve (matrix.c:3485)
> ==43569== by 0x40465D: main (superlu_test.c:59)
> ==43569==
> ==43569== Invalid write of size 8
> ==43569== at 0x1473C55A: pzgstrs (pzgstrs.c:1077)
> ==43569== by 0x146F5E72: pzgssvx (pzgssvx.c:1422)
> ==43569== by 0x58C3FE5: MatMatSolve_SuperLU_DIST (superlu_dist.c:242)
> ==43569== by 0x55FB716: MatMatSolve (matrix.c:3485)
> ==43569== by 0x40465D: main (superlu_test.c:59)
> ==43569== Address 0x266e5ad0 is 16 bytes after a block of size 35,520
> alloc'd
> ==43569== at 0x4C2D814: memalign (vg_replace_malloc.c:906)
> ==43569== by 0x4C2D97B: posix_memalign (vg_replace_malloc.c:1070)
> ==43569== by 0x1464D488: superlu_malloc_dist (memory.c:127)
> ==43569== by 0x1473C451: pzgstrs (pzgstrs.c:1044)
> ==43569== by 0x146F5E72: pzgssvx (pzgssvx.c:1422)
> ==43569== by 0x58C3FE5: MatMatSolve_SuperLU_DIST (superlu_dist.c:242)
> ==43569== by 0x55FB716: MatMatSolve (matrix.c:3485)
> ==43569== by 0x40465D: main (superlu_test.c:59)
> ==43569==
>
> I also attached the whole log. Does this make any sense? The problem seems
> to be around where I get the original segfault.
>
> best,
> marius
>
>
> *Gesendet:* Samstag, 31. Oktober 2020 um 04:07 Uhr
> *Von:* "Barry Smith" <bsmith at petsc.dev>
> *An:* "Marius Buerkle" <mbuerkle at web.de>
> *Cc:* "Xiaoye S. Li" <xsli at lbl.gov>, "petsc-users at mcs.anl.gov" <
> petsc-users at mcs.anl.gov>, "Sherry Li" <xiaoye at nersc.gov>
> *Betreff:* Re: [petsc-users] superlu_dist segfault
>
> Have you run it yet with valgrind, good be memory corruption earlier that
> causes a later crash, crashes that occur at different places for the same
> run are almost always due to memory corruption.
>
> If valgrind is clean you can run with -on_error_attach_debugger and if
> the X forwarding is set up it will open a debugger on the crashing process
> and you can type bt to see exactly where it is crashing, at what line
> number and code line.
>
> Barry
>
>
>
> On Oct 29, 2020, at 1:04 AM, Marius Buerkle <mbuerkle at web.de> wrote:
>
> Hi Sherry,
>
> I used only 1 OpenMP thread and I also recompiled PETSC in debug mode with
> OpenMP turned off. But did not help.
>
> Here is the output I can get from SuperLu during the PETSC run
> Nonzeros in L 29519630
> Nonzeros in U 29519630
> nonzeros in L+U 58996711
> nonzeros in LSUB 4509612
> ** Memory Usage **********************************
> ** NUMfact space (MB): (sum-of-all-processes)
> L\U : 952.18 | Total : 1980.60
> ** Total highmark (MB):
> Sum-of-all : 12401.85 | Avg : 387.56 | Max : 387.56
> **************************************************
> **************************************************
> **** Time (seconds) ****
> EQUIL time 0.06
> ROWPERM time 1.03
> COLPERM time 1.01
> SYMBFACT time 0.45
> DISTRIBUTE time 0.33
> FACTOR time 0.90
> Factor flops 2.225916e+11 Mflops 247438.62
> SOLVE time 0.000
> **************************************************
>
> I tried all available ordering options for Colperm
> (NATURAL,MMD_AT_PLUS_A,MMD_ATA,METIS_AT_PLUS_A), save for parmetis which
> always crashes. For Rowperm I used NOROWPERM, LargeDiag_MC64. All gives the
> same seg. fault.
>
>
> *Gesendet:* Donnerstag, 29. Oktober 2020 um 14:14 Uhr
> *Von:* "Xiaoye S. Li" <xsli at lbl.gov>
> *An:* "Marius Buerkle" <mbuerkle at web.de>
> *Cc:* "Zhang, Hong" <hzhang at mcs.anl.gov>, "petsc-users at mcs.anl.gov" <
> petsc-users at mcs.anl.gov>, "Sherry Li" <xiaoye at nersc.gov>
> *Betreff:* Re: Re: Re: [petsc-users] superlu_dist segfault
> Hong: thanks for the diagnosis!
>
> Marius: how many OpenMP threads are you using per MPI task?
> In an earlier email, you mentioned the allocation failure at the following
> line:
> if ( !(lsum = (doublecomplex*) SUPERLU_MALLOC(sizelsum*num_thread *
> sizeof(doublecomplex)))) ABORT("Malloc fails for lsum[].");
>
> this is in the solve phase. I think when we do some OpenMP optimization,
> we allowed several data structures to grow with OpenMP threads. You can
> try to use 1 thread.
>
> The RHS and X memories are easy to compute. However, in order to gauge
> how much memory is used in the factorization, can you print out the number
> of nonzeros in the L and U factors? What ordering option are you using?
> The sparse matrix A looks pretty small.
>
> The code can also print out the working storage used during
> factorization. I am not sure how this printing can be turned on through
> PETSc.
>
> Sherry
>
> On Wed, Oct 28, 2020 at 9:43 PM Marius Buerkle <mbuerkle at web.de> wrote:
>
>> Thanks for the swift reply.
>>
>> I also realized if I reduce the number of RHS then it works. But I am
>> running the code on a cluster with 256GB ram / node. One dense matrix
>> would be around ~30 Gb so 60 Gb, which is large but does exceed the
>> memory of even one node and I also get the seg fault if I run it on several
>> nodes. Moreover, it works well with MUMPS and MKL_CPARDISO solver. The
>> maxium memory used when using MUMPS is around 150 Gb during the solver
>> phase but for SuperLU_dist it crashed even before reaching the solver
>> phase. Could there be such a large difference in memory usage between
>> SuperLu_dist and MUMPS ?
>>
>>
>> best,
>>
>> marius
>>
>> *Gesendet:* Donnerstag, 29. Oktober 2020 um 10:10 Uhr
>> *Von:* "Zhang, Hong" <hzhang at mcs.anl.gov>
>> *An:* "Marius Buerkle" <mbuerkle at web.de>
>> *Cc:* "petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>, "Sherry Li" <
>> xiaoye at nersc.gov>
>> *Betreff:* Re: Re: [petsc-users] superlu_dist segfault
>> Marius,
>> I tested your code with petsc-release on my mac laptop using np=2 cores.
>> I first tested a small matrix data file successfully. Then I switch to your
>> data file and run out of memory, likely due to the dense matrices B and X.
>> I got an error "Your system has run out of application memory" from my
>> laptop.
>>
>> The sparse matrix A has size 42549 by 42549. Your code creates dense
>> matrices B and X with the same size -- a huge memory requirement!
>> By replacing B and X with size 42549 by nrhs (nrhs =< 4000), I had the
>> code run well with np=2. Note the error message you got
>> [23]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>>
>> The modified code I used is attached.
>> Hong
>>
>> ------------------------------
>> *From:* Marius Buerkle <mbuerkle at web.de>
>> *Sent:* Tuesday, October 27, 2020 10:01 PM
>> *To:* Zhang, Hong <hzhang at mcs.anl.gov>
>> *Cc:* petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>; Sherry Li <
>> xiaoye at nersc.gov>
>> *Subject:* Aw: Re: [petsc-users] superlu_dist segfault
>>
>> Hi,
>>
>> I recompiled PETSC with debug option, now I get a seg fault at a
>> different position
>>
>> [23]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [23]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [23]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [23]PETSC ERROR: or see
>> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> [23]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>> OS X to find memory corruption errors
>> [23]PETSC ERROR: likely location of problem given in stack below
>> [23]PETSC ERROR: --------------------- Stack Frames
>> ------------------------------------
>> [23]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>> available,
>> [23]PETSC ERROR: INSTEAD the line number of the start of the
>> function
>> [23]PETSC ERROR: is given.
>> [23]PETSC ERROR: [23] SuperLU_DIST:pzgssvx line 242
>> /home/cdfmat_marius/prog/petsc/git/release/petsc/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
>> [23]PETSC ERROR: [23] MatMatSolve_SuperLU_DIST line 211
>> /home/cdfmat_marius/prog/petsc/git/release/petsc/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
>> [23]PETSC ERROR: [23] MatMatSolve line 3466
>> /home/cdfmat_marius/prog/petsc/git/release/petsc/src/mat/interface/matrix.c
>> [23]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [23]PETSC ERROR: Signal received
>>
>> I made a small reproducer. The matrix is a bit too big so I cannot
>> attach it directly to the email, but I put it in the cloud
>> https://1drv.ms/u/s!AqZsng1oUcKzjYxGMGHojLRG09Sf1A?e=7uHnmw
>>
>> Best,
>> Marius
>>
>>
>> *Gesendet:* Dienstag, 27. Oktober 2020 um 23:11 Uhr
>> *Von:* "Zhang, Hong" <hzhang at mcs.anl.gov>
>> *An:* "Marius Buerkle" <mbuerkle at web.de>, "petsc-users at mcs.anl.gov" <
>> petsc-users at mcs.anl.gov>, "Sherry Li" <xiaoye at nersc.gov>
>> *Betreff:* Re: [petsc-users] superlu_dist segfault
>> Marius,
>> It fails at the line 1075 in file
>> /home/petsc3.14.release/arch-linux-c-debug/externalpackages/git.superlu_dist/SRC/pzgstrs.c
>> if ( !(lsum = (doublecomplex*)SUPERLU_MALLOC(sizelsum*num_thread *
>> sizeof(doublecomplex)))) ABORT("Malloc fails for lsum[].");
>>
>> We do not know what it means. You may use a debugger to check the values
>> of the variables involved.
>> I'm cc'ing Sherry (superlu_dist developer), or you may send us a
>> stand-alone short code that reproduce the error. We can help on its
>> investigation.
>> Hong
>>
>>
>> ------------------------------
>> *From:* petsc-users <petsc-users-bounces at mcs.anl.gov> on behalf of
>> Marius Buerkle <mbuerkle at web.de>
>> *Sent:* Tuesday, October 27, 2020 8:46 AM
>> *To:* petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
>> *Subject:* [petsc-users] superlu_dist segfault
>>
>> Hi,
>>
>> When using MatMatSolve with superlu_dist I get a segmentation fault:
>>
>> Malloc fails for lsum[]. at line 1075 in file
>> /home/petsc3.14.release/arch-linux-c-debug/externalpackages/git.superlu_dist/SRC/pzgstrs.c
>>
>> The matrix size is not particular big and I am using the petsc release
>> branch and superlu_dist is v6.3.0 I think.
>>
>> Best,
>> Marius
>>
> <valgrind.tar.gz>
>
>
>
--
Stefano
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