[petsc-users] segfault after recent scientific linux upgrade

Tue Dec 5 09:30:56 CST 2017

I would like to suggest you to use PETSc-3.8.x. Then the bug should go
away. It is a known bug related to the reuse of the factorization pattern.

Fande,

On Tue, Dec 5, 2017 at 8:07 AM, Klaij, Christiaan <C.Klaij at marin.nl> wrote:

> I'm running production software with petsc-3.7.5 and, among
> others, superlu_dist 5.1.3 on scientific linux 7.4.
>
> After a recent update of SL7.4, notably of the kernel and glibc,
> we found that superlu is somehow broken. Below's a backtrace of a
> serial example. Is this a known issue? Could you please advice on
> how to proceed (preferably while keeping 3.7.5 for now).
>
> Thanks,
> Chris
>
> $ gdb ./refresco ./core.9810
> GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-100.el7
> Copyright (C) 2013 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.
> html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>...
> Reading symbols from /home/cklaij/ReFRESCO/Dev/trunk/Suites/testSuite/
> FlatPlate_laminar/calcs/Grid64x64/refresco...done.
> [New LWP 9810]
> Missing separate debuginfo for /home/cklaij/ReFRESCO/Dev/
> trunk/Libs/install/licensing-1.55.0/sll/lib64/libssl.so.10
> Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/68/
> 6a25d0a83d002183c835fa5694a8110c78d3bc.debug
> Missing separate debuginfo for /home/cklaij/ReFRESCO/Dev/
> trunk/Libs/install/licensing-1.55.0/sll/lib64/libcrypto.so.10
> Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/68/
> d2958189303f421b1082abc33fd87338826c65.debug
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib64/libthread_db.so.1".
> Core was generated by `./refresco'.
> Program terminated with signal 11, Segmentation fault.
> #0  0x00002ba501c132bc in mc64wd_dist (n=0x5213270, ne=0x2, ip=0x1,
>     irn=0x51af520, a=0x51ef260, iperm=0x1000, num=0x7ffc545b2d94,
>     jperm=0x51e7260, out=0x51eb260, pr=0x51ef260, q=0x51f3260, l=0x51f7260,
>     u=0x51fb270, d__=0x5203270)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_
> 64-Intel/SuperLU_DIST_5.1.3/SRC/mc64ad_dist.c:2322
> 2322    if (iperm[i__] != 0 || iperm[i0] == 0) {
> Missing separate debuginfos, use: debuginfo-install
> bzip2-libs-1.0.6-13.el7.x86_64 glibc-2.17-196.el7.x86_64
> keyutils-libs-1.5.8-3.el7.x86_64 krb5-libs-1.15.1-8.el7.x86_64
> libcom_err-1.42.9-10.el7.x86_64 libgcc-4.8.5-16.el7.x86_64
> libselinux-2.5-11.el7.x86_64 libstdc++-4.8.5-16.el7.x86_64
> libxml2-2.9.1-6.el7_2.3.x86_64 numactl-libs-2.0.9-6.el7_2.x86_64
> pcre-8.32-17.el7.x86_64 xz-libs-5.2.2-1.el7.x86_64 zlib-1.2.7-17.el7.x86_64
> (gdb) bt
> #0  0x00002ba501c132bc in mc64wd_dist (n=0x5213270, ne=0x2, ip=0x1,
>     irn=0x51af520, a=0x51ef260, iperm=0x1000, num=0x7ffc545b2d94,
>     jperm=0x51e7260, out=0x51eb260, pr=0x51ef260, q=0x51f3260, l=0x51f7260,
>     u=0x51fb270, d__=0x5203270)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_
> 64-Intel/SuperLU_DIST_5.1.3/SRC/mc64ad_dist.c:2322
> #1  0x00002ba501c0ef2b in mc64ad_dist (job=0x5213270, n=0x2, ne=0x1,
>     ip=0x51af520, irn=0x51ef260, a=0x1000, num=0x7ffc545b2db0,
>     cperm=0x51fb270, liw=0x5187d10, iw=0x51c3130, ldw=0x51af520,
> dw=0x517b570,
>     icntl=0x51e7260, info=0x2ba501c2e556 <dldperm_dist+614>)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_
> 64-Intel/SuperLU_DIST_5.1.3/SRC/mc64ad_dist.c:596
> #2  0x00002ba501c2e556 in dldperm_dist (job=0, n=0, nnz=0,
> colptr=0x51af520,
>     adjncy=0x51ef260, nzval=0x1000, perm=0x4f00, u=0x1000, v=0x517b001)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_
> 64-Intel/SuperLU_DIST_5.1.3/SRC/dldperm_dist.c:141
> #3  0x00002ba501c26296 in pdgssvx_ABglobal (options=0x5213270, A=0x2,
>     ScalePermstruct=0x1, B=0x51af520, ldb=85914208, nrhs=4096,
> grid=0x516da30,
>     LUstruct=0x517af40, berr=0x1000,
>     stat=0x2ba500b36a7d <MatLUFactorNumeric_SuperLU_DIST+2349>,
> info=0x517af58)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_
> 64-Intel/SuperLU_DIST_5.1.3/SRC/pdgssvx_ABglobal.c:716
> #4  0x00002ba500b36a7d in MatLUFactorNumeric_SuperLU_DIST (F=0x5213270,
> A=0x2,
> ---Type <return> to continue, or q <return> to quit---
>     info=0x1)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c:419
> #5  0x00002ba500b45a1a in MatLUFactorNumeric (fact=0x5213270, mat=0x2,
>     info=0x1)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/mat/interface/matrix.c:2996
> #6  0x00002ba500e9e6c7 in PCSetUp_LU (pc=0x5213270)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/ksp/pc/impls/factor/lu/lu.c:172
> #7  0x00002ba500ded084 in PCSetUp (pc=0x5213270)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/ksp/pc/interface/precon.c:968
> #8  0x00002ba500f2968d in KSPSetUp (ksp=0x5213270)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/ksp/ksp/interface/itfunc.c:390
> #9  0x00002ba500f257be in KSPSolve (ksp=0x5213270, b=0x2, x=0x4193510)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/ksp/ksp/interface/itfunc.c:599
> #10 0x00002ba500f3e142 in kspsolve_ (ksp=0x5213270, b=0x2, x=0x1,
>     __ierr=0x51af520)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/ksp/ksp/interface/ftn-auto/itfuncf.c:261
> ---Type <return> to continue, or q <return> to quit---
> #11 0x0000000000bccf71 in petsc_solvers::petsc_solvers_solve (
>     regname='massTransport', rhs_c=..., phi_c=..., tol=0.01, maxiter=500,
>     res0=-9.2559631349317831e+61, usediter=0, .tmp.REGNAME.len_V$1790=13)
>     at petsc_solvers.F90:580
> #12 0x0000000000c2c9c5 in mass_momentum::mass_momentum_pressureprediction
> ()
>     at mass_momentum.F90:989
> #13 0x0000000000c0ffc1 in mass_momentum::mass_momentum_core ()
>     at mass_momentum.F90:626
> #14 0x0000000000c26a2c in mass_momentum::mass_momentum_systempcapply (
>     aa_system=76390912, xx_system=68983024, rr_system=68984544, ierr=0)
>     at mass_momentum.F90:919
> #15 0x00002ba500eaa763 in ourshellapply (pc=0x48da200, x=0x41c98f0,
>     y=0x41c9ee0)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/ksp/pc/impls/shell/ftn-custom/zshellpcf.c:41
> #16 0x00002ba500ea79be in PCApply_Shell (pc=0x5213270, x=0x2, y=0x1)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/ksp/pc/impls/shell/shellpc.c:124
> #17 0x00002ba500df1800 in PCApply (pc=0x5213270, x=0x2, y=0x1)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/ksp/pc/interface/precon.c:482
> #18 0x00002ba500f2592a in KSPSolve (ksp=0x5213270, b=0x2, x=0x41c9ee0)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interf---Type
> <return> to continue, or q <return> to quit---
> ace/itfunc.c:631
> #19 0x00002ba500f3e142 in kspsolve_ (ksp=0x5213270, b=0x2, x=0x1,
>     __ierr=0x51af520)
>     at /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/
> src/ksp/ksp/interface/ftn-auto/itfuncf.c:261
> #20 0x0000000000c1b0ea in mass_momentum::mass_momentum_krylov ()
>     at mass_momentum.F90:777
> #21 0x0000000000c0d242 in mass_momentum::mass_momentum_simple ()
>     at mass_momentum.F90:548
> #22 0x0000000000c0841f in mass_momentum::mass_momentum_solve ()
>     at mass_momentum.F90:465
> #23 0x000000000041b5ec in refresco () at refresco.F90:259
> #24 0x000000000041999e in main ()
> #25 0x00002ba508c98c05 in __libc_start_main () from /lib64/libc.so.6
> #26 0x00000000004198a3 in _start ()
> (gdb)
>
>
> dr. ir. Christiaan Klaij  | Senior Researcher | Research & Development
> MARIN | T +31 317 49 33 44 | mailto:C.Klaij at marin.nl | http://www.marin.nl
>
> MARIN news: http://www.marin.nl/web/News/News-items/Seminar-Blauwe-
> toekomst-versnellen-van-innovaties-door-samenwerken.htm
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20171205/56280bba/attachment.html>