[petsc-users] KSP_Solve crashes in debug mode
Sajid Ali Syed
sasyed at fnal.gov
Wed Feb 22 18:46:37 CST 2023
Via a checkpoint in `PetscOptionsCheckInitial_Private`, I can confirm that `checkstack` is set to `PETSC_TRUE` and this leads to no (additional) information about erroneous stack handling.
Thank You,
Sajid Ali (he/him) | Research Associate
Data Science, Simulation, and Learning Division
Fermi National Accelerator Laboratory
s-sajid-ali.github.io<http://s-sajid-ali.github.io>
________________________________
From: Sajid Ali Syed <sasyed at fnal.gov>
Sent: Wednesday, February 22, 2023 6:34 PM
To: Matthew Knepley <knepley at gmail.com>
Cc: Barry Smith <bsmith at petsc.dev>; petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] KSP_Solve crashes in debug mode
Hi Matt,
This is a trace from the same crash, but with `-checkstack` included in .petscrc : https://gist.github.com/s-sajid-ali/455b3982d47a31bff9e7ee211dd43991
I don't see any additional information regarding the possible cause.
Thank You,
Sajid Ali (he/him) | Research Associate
Data Science, Simulation, and Learning Division
Fermi National Accelerator Laboratory
s-sajid-ali.github.io<http://s-sajid-ali.github.io>
________________________________
From: Matthew Knepley <knepley at gmail.com>
Sent: Wednesday, February 22, 2023 6:28 PM
To: Sajid Ali Syed <sasyed at fnal.gov>
Cc: Barry Smith <bsmith at petsc.dev>; petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] KSP_Solve crashes in debug mode
On Wed, Feb 22, 2023 at 6:32 PM Sajid Ali Syed <sasyed at fnal.gov<mailto:sasyed at fnal.gov>> wrote:
Hi Matt,
Adding `-checkstack` does not prevent the crash, both on my laptop and on the cluster.
It will not prevent a crash. The output is intended to show us where the stack problem originates. Can you send the output?
Thanks,
Matt
What does prevent the crash (on my laptop at least) is changing `PETSCSTACKSIZE` from 64 to 256 here : https://github.com/petsc/petsc/blob/main/include/petscerror.h#L1153<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_petsc_petsc_blob_main_include_petscerror.h-23L1153&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=w-DPglgoOUOz8eiEyHKz0g&m=4O4e5ZFa8DyEfzEsYIIKt360UctxCt5KFvZxW811iBIqyNqK5hsslNaRmF9EKE7s&s=MnNgqJmNQ3g1IfdK3RejS4PSU0SSoTij4l0SxKbRCKM&e=>
Thank You,
Sajid Ali (he/him) | Research Associate
Data Science, Simulation, and Learning Division
Fermi National Accelerator Laboratory
s-sajid-ali.github.io<https://urldefense.proofpoint.com/v2/url?u=http-3A__s-2Dsajid-2Dali.github.io&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=w-DPglgoOUOz8eiEyHKz0g&m=4O4e5ZFa8DyEfzEsYIIKt360UctxCt5KFvZxW811iBIqyNqK5hsslNaRmF9EKE7s&s=8q2mKS3nKLeZnpV5HG37TS3K7ZYQ3hglpSFoDJHXJ3g&e=>
________________________________
From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Sent: Wednesday, February 22, 2023 5:23 PM
To: Sajid Ali Syed <sasyed at fnal.gov<mailto:sasyed at fnal.gov>>
Cc: Barry Smith <bsmith at petsc.dev<mailto:bsmith at petsc.dev>>; petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] KSP_Solve crashes in debug mode
On Wed, Feb 22, 2023 at 6:18 PM Sajid Ali Syed via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
One thing to note in relation to the trace attached in the previous email is that there are no warnings until the 36th call to KSP_Solve. The first error (as indicated by ASAN) occurs somewhere before the 40th call to KSP_Solve (part of what the application marks as turn 10 of the propagator). The crash finally occurs on the 43rd call to KSP_solve.
Looking at the trace, it appears that stack handling is messed up and eventually it causes the crash. This can happen when
PetscFunctionBegin is not matched up with PetscFunctionReturn. Can you try running this with
-checkstack
Thanks,
Matt
Thank You,
Sajid Ali (he/him) | Research Associate
Data Science, Simulation, and Learning Division
Fermi National Accelerator Laboratory
s-sajid-ali.github.io<https://urldefense.proofpoint.com/v2/url?u=http-3A__s-2Dsajid-2Dali.github.io&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=w-DPglgoOUOz8eiEyHKz0g&m=q5fD8r624Cr0Ow4AKTmgeLtq_M--q_KdGYMkBNiKOMDa8o82C8P97vdCRcxrqTCF&s=oNWxB3zDYTHODeZK9VCibIVqSo7DnwsJjSr6IgIPs2M&e=>
________________________________
From: Sajid Ali Syed <sasyed at fnal.gov<mailto:sasyed at fnal.gov>>
Sent: Wednesday, February 22, 2023 5:11 PM
To: Barry Smith <bsmith at petsc.dev<mailto:bsmith at petsc.dev>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] KSP_Solve crashes in debug mode
Hi Barry,
Thanks a lot for fixing this issue. I ran the same problem on a linux machine and have the following trace for the same crash (with ASAN turned on for both PETSc (on the latest commit of the branch) and the application) : https://gist.github.com/s-sajid-ali/85bdf689eb8452ef8702c214c4df6940<https://urldefense.proofpoint.com/v2/url?u=https-3A__gist.github.com_s-2Dsajid-2Dali_85bdf689eb8452ef8702c214c4df6940&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=w-DPglgoOUOz8eiEyHKz0g&m=q5fD8r624Cr0Ow4AKTmgeLtq_M--q_KdGYMkBNiKOMDa8o82C8P97vdCRcxrqTCF&s=Z8JyNKYXjUZE4DXYKvjxTOG4HZUA95U6z750WC6gUCo&e=>
The trace seems to indicate a couple of buffer overflows, one of which causes the crash. I'm not sure as to what causes them.
Thank You,
Sajid Ali (he/him) | Research Associate
Data Science, Simulation, and Learning Division
Fermi National Accelerator Laboratory
s-sajid-ali.github.io<https://urldefense.proofpoint.com/v2/url?u=http-3A__s-2Dsajid-2Dali.github.io&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=w-DPglgoOUOz8eiEyHKz0g&m=q5fD8r624Cr0Ow4AKTmgeLtq_M--q_KdGYMkBNiKOMDa8o82C8P97vdCRcxrqTCF&s=oNWxB3zDYTHODeZK9VCibIVqSo7DnwsJjSr6IgIPs2M&e=>
________________________________
From: Barry Smith <bsmith at petsc.dev<mailto:bsmith at petsc.dev>>
Sent: Wednesday, February 15, 2023 2:01 PM
To: Sajid Ali Syed <sasyed at fnal.gov<mailto:sasyed at fnal.gov>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] KSP_Solve crashes in debug mode
https://gitlab.com/petsc/petsc/-/merge_requests/6075<https://urldefense.proofpoint.com/v2/url?u=https-3A__gitlab.com_petsc_petsc_-2D_merge-5Frequests_6075&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=w-DPglgoOUOz8eiEyHKz0g&m=P7R0CW9R-fGNfm2q3yTL-ehqhM5N9-r8hHBLNgDetm9-7jxVqNsujIZ2hdnhVrVX&s=QwRI_DzGnCHagpaQSC4MPPEUnC4aAkbMwdG1eg_QUII&e=> should fix the possible recursive error condition Matt pointed out
On Feb 9, 2023, at 6:24 PM, Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:
On Thu, Feb 9, 2023 at 6:05 PM Sajid Ali Syed via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
I added “-malloc_debug” in a .petscrc file and ran it again. The backtrace from lldb is in the attached file. The crash now seems to be at:
Process 32660 stopped* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=2, address=0x16f603fb8)
frame #0: 0x0000000112ecc8f8 libpetsc.3.018.dylib`PetscFPrintf(comm=0, fd=0x0000000000000000, format=0x0000000000000000) at mprint.c:601
598 `PetscViewerASCIISynchronizedPrintf()`, `PetscSynchronizedFlush()`
599 @*/
600 PetscErrorCode PetscFPrintf(MPI_Comm comm, FILE *fd, const char format[], ...)
-> 601 {
602 PetscMPIInt rank;
603
604 PetscFunctionBegin;
(lldb) frame info
frame #0: 0x0000000112ecc8f8 libpetsc.3.018.dylib`PetscFPrintf(comm=0, fd=0x0000000000000000, format=0x0000000000000000) at mprint.c:601
(lldb)
The trace seems to indicate some sort of infinite loop causing an overflow.
Yes, I have also seen this. What happens is that we have a memory error. The error is reported inside PetscMallocValidate()
using PetscErrorPrintf, which eventually calls PetscCallMPI, which calls PetscMallocValidate again, which fails. We need to
remove all error checking from the prints inside Validate.
Thanks,
Matt
PS: I'm using a arm64 mac, so I don't have access to valgrind.
Thank You,
Sajid Ali (he/him) | Research Associate
Scientific Computing Division
Fermi National Accelerator Laboratory
s-sajid-ali.github.io<https://urldefense.proofpoint.com/v2/url?u=http-3A__s-2Dsajid-2Dali.github.io_&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=w-DPglgoOUOz8eiEyHKz0g&m=P7R0CW9R-fGNfm2q3yTL-ehqhM5N9-r8hHBLNgDetm9-7jxVqNsujIZ2hdnhVrVX&s=JA1u9AHcO8HqY5oCgbEy-ghtKRjURlRDwdmxP-9YJac&e=>
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--
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
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--
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/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cse.buffalo.edu_-7Eknepley_&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=w-DPglgoOUOz8eiEyHKz0g&m=4O4e5ZFa8DyEfzEsYIIKt360UctxCt5KFvZxW811iBIqyNqK5hsslNaRmF9EKE7s&s=LCxKjzvq3YbIyUcLuj1eoSiLF3MIZir2HjV9jHw4o0M&e=>
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