petsc 3.7 - and 3.8 both default to superlu_dist snapshot:
self.gitcommit = 'xsdk-0.2.0-rc1'
If using petsc-3.7 - you can use latest maint-3.7 [i.e 3.7.7+]
[3.7.7 is a latest bugfix update to 3.7 - so there should be no reason to stick
to 3.7.5]
But if you really want to stick to 3.7.5 you can use:
--download-superlu_dist=1 --download-superlu_dist-commit=xsdk-0.2.0-rc1
Satish
On Wed, 6 Dec 2017, Klaij, Christiaan wrote:
> Fande,
>
> Thanks, that's good to know. Upgrading to 3.8.x is definitely my
> long-term plan, but is there anything I can do short-term to fix
> the problem while keeping 3.7.5?
>
> Chris
>
> dr. ir. Christiaan Klaij | Senior Researcher | Research & Development
> MARIN | T +31 317 49 33 44 | c.kl...@marin.nl<mailto:c.kl...@marin.nl> |
> www.marin.nl<http://www.marin.nl>
>
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>
> ________________________________
> From: Fande Kong <fdkong...@gmail.com>
> Sent: Tuesday, December 05, 2017 4:30 PM
> To: Klaij, Christiaan
> Cc: petsc-users@mcs.anl.gov
> Subject: Re: [petsc-users] segfault after recent scientific linux upgrade
>
> 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.kl...@marin.nl<mailto:c.kl...@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.kl...@marin.nl<mailto:c.kl...@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
>
>
>
>
>
