Re: [petsc-users] segfault after recent scientific linux upgrade

[Klaij, Christiaan]

Almost valgrind clean. We use intelmpi so we need a handfull of suppressions.

Chris


dr. ir. Christiaan Klaij  | Senior Researcher | Research & Development
MARIN | T +31 317 49 33 44 | mailto:c.kl...@marin.nl | http://www.marin.nl

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From: Satish Balay 
Sent: Thursday, December 07, 2017 6:07 PM
To: Klaij, Christiaan
Cc: petsc-users
Subject: Re: [petsc-users] segfault after recent scientific linux upgrade

Could you check if your code is valgrind clean?

Satish

On Thu, 7 Dec 2017, Klaij, Christiaan wrote:

> Satish,
>
> As a first try, I've kept petsc-3.7.5 and only replaced superlu
> by the new xsdk-0.2.0-rc1 version. Unfortunately, this doesn't
> fix the problem, see the backtrace below.
>
> Fande,
>
> Perhaps the problem is related to petsc, not superlu?
>
> What really puzzles me is that everything was working fine with
> petsc-3.7.5 and superlu_dist_5.3.1, it only broke after we
> updated Scientific Linux 7. So this bug (in petsc or in superlu)
> was already there but somehow not triggered before the SL7
> update?
>
> Chris
>
> (gdb) bt
> #0  0x2b38995fa30c in mc64wd_dist (n=0x3da6230, ne=0x2, ip=0x1,
> irn=0x3d424e0, a=0x3d82220, iperm=0x1000, num=0x7ffc505dd294,
> jperm=0x3d7a220, out=0x3d7e220, pr=0x3d82220, q=0x3d86220, l=0x3d8a220,
> u=0x3d8e230, d__=0x3d96230)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/mc64ad_dist.c:2322
> #1  0x2b38995f5f7b in mc64ad_dist (job=0x3da6230, n=0x2, ne=0x1,
> ip=0x3d424e0, irn=0x3d82220, a=0x1000, num=0x7ffc505dd2b0,
> cperm=0x3d8e230, liw=0x3d1acd0, iw=0x3d560f0, ldw=0x3d424e0, dw=0x3d0e530,
> icntl=0x3d7a220, info=0x2b3899615546 )
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/mc64ad_dist.c:596
> #2  0x2b3899615546 in dldperm_dist (job=0, n=0, nnz=0, colptr=0x3d424e0,
> adjncy=0x3d82220, nzval=0x1000, perm=0x4f00, u=0x1000, v=0x3d0e001)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/dldperm_dist.c:141
> #3  0x2b389960d286 in pdgssvx_ABglobal (options=0x3da6230, A=0x2,
> ScalePermstruct=0x1, B=0x3d424e0, ldb=64496160, nrhs=4096, grid=0x3d009f0,
> LUstruct=0x3d0df00, berr=0x1000,
> stat=0x2b389851da7d , 
> info=0x3d0df18)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/pdgssvx_ABglobal.c:716
> #4  0x2b389851da7d in MatLUFactorNumeric_SuperLU_DIST (F=0x3da6230, A=0x2,
> ---Type  to continue, or q  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  0x2b389852ca1a in MatLUFactorNumeric (fact=0x3da6230, mat=0x2,
> info=0x1)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/mat/interface/matrix.c:2996
> #6  0x2b38988856c7 in PCSetUp_LU (pc=0x3da6230)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/impls/factor/lu/lu.c:172
> #7  0x2b38987d4084 in PCSetUp (pc=0x3da6230)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/interface/precon.c:968
> #8  0x2b389891068d in KSPSetUp (ksp=0x3da6230)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/itfunc.c:390
> #9  0x2b389890c7be in KSPSolve (ksp=0x3da6230, b=0x2, x=0x2d18d90)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/itfunc.c:599
> #10 0x2b3898925142 in kspsolve_ (ksp=0x3da6230, b=0x2, x=0x1,
> __ierr=0x3d424e0)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/ftn-auto/itfuncf.c:261
> ---Type  to continue, or q  to quit---
> #11 0x00bccf71 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 0x00c2c9c5 in mass_momentum::mass_momentum_pressureprediction ()
> at mass_momentum.F90:989
> #13 0x00c0ffc1 in mass_momentum::mass_momentum_core ()
> at mass_momentum.F90:626
> #14 0x00c26a2c in mass_momentum::mass_momentum_systempcapply (
> aa_system=54952496, xx_system=47570896, rr_system=47572416, ierr=0)
> at mass_momentum.F90:919
> #15 0x2b3898891763 in ourshellapply (pc=0x3468230, x=0x2d5dfd0,
> y=0x2d5e5c0)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/impls/shell/ftn-custom/zshellpcf.c:41
> #16 0x2b389888e9be in PCApply_Shell (pc=0x3da6230, x=0x2, y=0x1)
> at 
> 

Re: [petsc-users] segfault after recent scientific linux upgrade

[Satish Balay]

Could you check if your code is valgrind clean?

Satish

On Thu, 7 Dec 2017, Klaij, Christiaan wrote:

> Satish,
> 
> As a first try, I've kept petsc-3.7.5 and only replaced superlu
> by the new xsdk-0.2.0-rc1 version. Unfortunately, this doesn't
> fix the problem, see the backtrace below.
> 
> Fande,
> 
> Perhaps the problem is related to petsc, not superlu?
> 
> What really puzzles me is that everything was working fine with
> petsc-3.7.5 and superlu_dist_5.3.1, it only broke after we
> updated Scientific Linux 7. So this bug (in petsc or in superlu)
> was already there but somehow not triggered before the SL7
> update?
> 
> Chris
> 
> (gdb) bt
> #0  0x2b38995fa30c in mc64wd_dist (n=0x3da6230, ne=0x2, ip=0x1,
> irn=0x3d424e0, a=0x3d82220, iperm=0x1000, num=0x7ffc505dd294,
> jperm=0x3d7a220, out=0x3d7e220, pr=0x3d82220, q=0x3d86220, l=0x3d8a220,
> u=0x3d8e230, d__=0x3d96230)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/mc64ad_dist.c:2322
> #1  0x2b38995f5f7b in mc64ad_dist (job=0x3da6230, n=0x2, ne=0x1,
> ip=0x3d424e0, irn=0x3d82220, a=0x1000, num=0x7ffc505dd2b0,
> cperm=0x3d8e230, liw=0x3d1acd0, iw=0x3d560f0, ldw=0x3d424e0, dw=0x3d0e530,
> icntl=0x3d7a220, info=0x2b3899615546 )
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/mc64ad_dist.c:596
> #2  0x2b3899615546 in dldperm_dist (job=0, n=0, nnz=0, colptr=0x3d424e0,
> adjncy=0x3d82220, nzval=0x1000, perm=0x4f00, u=0x1000, v=0x3d0e001)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/dldperm_dist.c:141
> #3  0x2b389960d286 in pdgssvx_ABglobal (options=0x3da6230, A=0x2,
> ScalePermstruct=0x1, B=0x3d424e0, ldb=64496160, nrhs=4096, grid=0x3d009f0,
> LUstruct=0x3d0df00, berr=0x1000,
> stat=0x2b389851da7d , 
> info=0x3d0df18)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/pdgssvx_ABglobal.c:716
> #4  0x2b389851da7d in MatLUFactorNumeric_SuperLU_DIST (F=0x3da6230, A=0x2,
> ---Type  to continue, or q  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  0x2b389852ca1a in MatLUFactorNumeric (fact=0x3da6230, mat=0x2,
> info=0x1)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/mat/interface/matrix.c:2996
> #6  0x2b38988856c7 in PCSetUp_LU (pc=0x3da6230)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/impls/factor/lu/lu.c:172
> #7  0x2b38987d4084 in PCSetUp (pc=0x3da6230)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/interface/precon.c:968
> #8  0x2b389891068d in KSPSetUp (ksp=0x3da6230)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/itfunc.c:390
> #9  0x2b389890c7be in KSPSolve (ksp=0x3da6230, b=0x2, x=0x2d18d90)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/itfunc.c:599
> #10 0x2b3898925142 in kspsolve_ (ksp=0x3da6230, b=0x2, x=0x1,
> __ierr=0x3d424e0)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/ftn-auto/itfuncf.c:261
> ---Type  to continue, or q  to quit---
> #11 0x00bccf71 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 0x00c2c9c5 in mass_momentum::mass_momentum_pressureprediction ()
> at mass_momentum.F90:989
> #13 0x00c0ffc1 in mass_momentum::mass_momentum_core ()
> at mass_momentum.F90:626
> #14 0x00c26a2c in mass_momentum::mass_momentum_systempcapply (
> aa_system=54952496, xx_system=47570896, rr_system=47572416, ierr=0)
> at mass_momentum.F90:919
> #15 0x2b3898891763 in ourshellapply (pc=0x3468230, x=0x2d5dfd0,
> y=0x2d5e5c0)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/impls/shell/ftn-custom/zshellpcf.c:41
> #16 0x2b389888e9be in PCApply_Shell (pc=0x3da6230, 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 0x2b38987d8800 in PCApply (pc=0x3da6230, x=0x2, y=0x1)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/interface/precon.c:482
> #18 0x2b389890c92a in KSPSolve (ksp=0x3da6230, b=0x2, x=0x2d5e5c0)
> at 
> /home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interf---Type
>   to continue, or q  to quit---
> ace/itfunc.c:631
> #19 0x2b3898925142 in kspsolve_ (ksp=0x3da6230, b=0x2, x=0x1,
> __ierr=0x3d424e0)
> at 
> 

Re: [petsc-users] segfault after recent scientific linux upgrade

[Klaij, Christiaan]

Fande,


That's what I did, I started the whole petsc config and build from scratch. The 
backtrace now says:


/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/mc64ad_dist.c:2322


instead of the old:


/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/SuperLU_DIST_5.1.3/SRC/mc64ad_dist.c:2322


which doesn't exist anymore. The entire install directory is new:


$ ls -lh /home/cklaij/ReFRESCO/Dev/trunk/Libs/install
drwxr-xr-x. 5 cklaij domain users   85 Dec  7 14:31 Linux-x86_64-Intel
drwxr-xr-x. 6 cklaij domain users   75 Dec  7 14:33 petsc-3.7.5


$ ls -lh /home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel
total 12K
drwxr-xr-x.  7 cklaij domain users 4.0K Dec  7 14:30 metis-5.1.0-p3
drwxrwxr-x.  7 cklaij domain users 4.0K Dec  7 14:30 parmetis-4.0.3-p3
drwxrwxr-x. 11 cklaij domain users 4.0K Dec  7 14:31 superlu_dist-xsdk-0.2.0-rc1

Chris


dr. ir. Christiaan Klaij | Senior Researcher | Research & Development
MARIN | T +31 317 49 33 44 | c.kl...@marin.nl | 
www.marin.nl

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  [Twitter] 
  [Facebook] 

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5-8


From: Kong, Fande 
Sent: Thursday, December 07, 2017 4:26 PM
To: Klaij, Christiaan
Cc: petsc-users
Subject: Re: [petsc-users] segfault after recent scientific linux upgrade



On Thu, Dec 7, 2017 at 8:15 AM, Klaij, Christiaan 
> wrote:
Satish,



As a first try, I've kept petsc-3.7.5 and only replaced superlu

by the new xsdk-0.2.0-rc1 version. Unfortunately, this doesn't

fix the problem, see the backtrace below.



Fande,



Perhaps the problem is related to petsc, not superlu?



What really puzzles me is that everything was working fine with

petsc-3.7.5 and superlu_dist_5.3.1, it only broke after we

updated Scientific Linux 7. So this bug (in petsc or in superlu)

was already there but somehow not triggered before the SL7

update?



Chris




I do not know how you installed PETSc. It looks like you are keeping using the 
old superlu_dist.  You have to delete the old package, and start from the 
scratch. PETSc does not automatically clean the old one. For me, I just simply 
"rm -rf $PETSC_ARCH" every time before I reinstall a new PETSc.


Fande,

Re: [petsc-users] segfault after recent scientific linux upgrade

[Kong, Fande]

On Thu, Dec 7, 2017 at 8:15 AM, Klaij, Christiaan  wrote:

> Satish,
>
>
>
> As a first try, I've kept petsc-3.7.5 and only replaced superlu
>
> by the new xsdk-0.2.0-rc1 version. Unfortunately, this doesn't
>
> fix the problem, see the backtrace below.
>
>
>
> Fande,
>
>
>
> Perhaps the problem is related to petsc, not superlu?
>
>
>
> What really puzzles me is that everything was working fine with
>
> petsc-3.7.5 and superlu_dist_5.3.1, it only broke after we
>
> updated Scientific Linux 7. So this bug (in petsc or in superlu)
>
> was already there but somehow not triggered before the SL7
>
> update?
>
>
>
> Chris
>
>
>
>
I do not know how you installed PETSc. It looks like you are keeping using
the old superlu_dist.  You have to delete the old package, and start from
the scratch. PETSc does not automatically clean the old one. For me, I just
simply "rm -rf $PETSC_ARCH" every time before I reinstall a new PETSc.


Fande,

Re: [petsc-users] segfault after recent scientific linux upgrade

[Klaij, Christiaan]

Satish,

As a first try, I've kept petsc-3.7.5 and only replaced superlu
by the new xsdk-0.2.0-rc1 version. Unfortunately, this doesn't
fix the problem, see the backtrace below.

Fande,

Perhaps the problem is related to petsc, not superlu?

What really puzzles me is that everything was working fine with
petsc-3.7.5 and superlu_dist_5.3.1, it only broke after we
updated Scientific Linux 7. So this bug (in petsc or in superlu)
was already there but somehow not triggered before the SL7
update?

Chris

(gdb) bt
#0  0x2b38995fa30c in mc64wd_dist (n=0x3da6230, ne=0x2, ip=0x1,
irn=0x3d424e0, a=0x3d82220, iperm=0x1000, num=0x7ffc505dd294,
jperm=0x3d7a220, out=0x3d7e220, pr=0x3d82220, q=0x3d86220, l=0x3d8a220,
u=0x3d8e230, d__=0x3d96230)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/mc64ad_dist.c:2322
#1  0x2b38995f5f7b in mc64ad_dist (job=0x3da6230, n=0x2, ne=0x1,
ip=0x3d424e0, irn=0x3d82220, a=0x1000, num=0x7ffc505dd2b0,
cperm=0x3d8e230, liw=0x3d1acd0, iw=0x3d560f0, ldw=0x3d424e0, dw=0x3d0e530,
icntl=0x3d7a220, info=0x2b3899615546 )
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/mc64ad_dist.c:596
#2  0x2b3899615546 in dldperm_dist (job=0, n=0, nnz=0, colptr=0x3d424e0,
adjncy=0x3d82220, nzval=0x1000, perm=0x4f00, u=0x1000, v=0x3d0e001)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/dldperm_dist.c:141
#3  0x2b389960d286 in pdgssvx_ABglobal (options=0x3da6230, A=0x2,
ScalePermstruct=0x1, B=0x3d424e0, ldb=64496160, nrhs=4096, grid=0x3d009f0,
LUstruct=0x3d0df00, berr=0x1000,
stat=0x2b389851da7d , info=0x3d0df18)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/Linux-x86_64-Intel/superlu_dist-xsdk-0.2.0-rc1/SRC/pdgssvx_ABglobal.c:716
#4  0x2b389851da7d in MatLUFactorNumeric_SuperLU_DIST (F=0x3da6230, A=0x2,
---Type  to continue, or q  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  0x2b389852ca1a in MatLUFactorNumeric (fact=0x3da6230, mat=0x2,
info=0x1)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/mat/interface/matrix.c:2996
#6  0x2b38988856c7 in PCSetUp_LU (pc=0x3da6230)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/impls/factor/lu/lu.c:172
#7  0x2b38987d4084 in PCSetUp (pc=0x3da6230)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/interface/precon.c:968
#8  0x2b389891068d in KSPSetUp (ksp=0x3da6230)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/itfunc.c:390
#9  0x2b389890c7be in KSPSolve (ksp=0x3da6230, b=0x2, x=0x2d18d90)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/itfunc.c:599
#10 0x2b3898925142 in kspsolve_ (ksp=0x3da6230, b=0x2, x=0x1,
__ierr=0x3d424e0)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/ftn-auto/itfuncf.c:261
---Type  to continue, or q  to quit---
#11 0x00bccf71 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 0x00c2c9c5 in mass_momentum::mass_momentum_pressureprediction ()
at mass_momentum.F90:989
#13 0x00c0ffc1 in mass_momentum::mass_momentum_core ()
at mass_momentum.F90:626
#14 0x00c26a2c in mass_momentum::mass_momentum_systempcapply (
aa_system=54952496, xx_system=47570896, rr_system=47572416, ierr=0)
at mass_momentum.F90:919
#15 0x2b3898891763 in ourshellapply (pc=0x3468230, x=0x2d5dfd0,
y=0x2d5e5c0)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/impls/shell/ftn-custom/zshellpcf.c:41
#16 0x2b389888e9be in PCApply_Shell (pc=0x3da6230, 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 0x2b38987d8800 in PCApply (pc=0x3da6230, x=0x2, y=0x1)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/pc/interface/precon.c:482
#18 0x2b389890c92a in KSPSolve (ksp=0x3da6230, b=0x2, x=0x2d5e5c0)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interf---Type
  to continue, or q  to quit---
ace/itfunc.c:631
#19 0x2b3898925142 in kspsolve_ (ksp=0x3da6230, b=0x2, x=0x1,
__ierr=0x3d424e0)
at 
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.5/src/ksp/ksp/interface/ftn-auto/itfuncf.c:261
#20 0x00c1b0ea in mass_momentum::mass_momentum_krylov ()
at mass_momentum.F90:777
#21 0x00c0d242 in mass_momentum::mass_momentum_simple ()
at mass_momentum.F90:548
#22 0x00c0841f in 

Re: [petsc-users] Boundary condition IS

[Matthew Knepley]

On Thu, Dec 7, 2017 at 2:23 AM, Mohammad Hassan Baghaei <
mhbagh...@mail.sjtu.edu.cn> wrote:

> Hello
>
> I am using DMPlex to construct a fully circular 2D domain for my PDEs. As
> I am discretizing the PDEs using finite difference method,
>

How do you do FD on an unstructured mesh?


> I need to know , to define the layout of PetscSection, how I can find the
> boundary condition IS. I know the location of the boundaries in Sieve
> chart. However, I noticed that I need to know the Index Set of that
> location. Can I use the Sieve point number for Index Set. It seems I think
> I am not familiar with IS. Can you help me? Thank for your help.
>

I like Yann's response. You can simplify the processing somewhat:

  1) You can use DMPlexLabelComplete() to add in edges and vertices on the
boundary

  2) You can use DMPlexComputeCellGeometryFVM to compute the centroid

  Thanks,

Matt


> Amir
>



-- 
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/ 

Re: [petsc-users] segfault after recent scientific linux upgrade

[Klaij, Christiaan]

Thanks Satish, I will give it shot and let you know.

Chris


dr. ir. Christiaan Klaij  | Senior Researcher | Research & Development
MARIN | T +31 317 49 33 44 | mailto:c.kl...@marin.nl | http://www.marin.nl

MARIN news: 
http://www.marin.nl/web/News/News-items/MARIN-at-Marintec-China-Shanghai-December-58-1.htm


From: Satish Balay 
Sent: Wednesday, December 06, 2017 6:05 PM
To: Klaij, Christiaan
Cc: Fande Kong; petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] segfault after recent scientific linux upgrade

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 | 
> www.marin.nl
>
> [LinkedIn] [YouTube] 
>   [Twitter] 
>   [Facebook] 
> 
> MARIN news: Seminar ‘Blauwe toekomst: versnellen van innovaties door 
> samenwerken
>
> 
> From: Fande Kong 
> 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 
> > 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 
> 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:
> ...
> 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  0x2ba501c132bc 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
> 2322if (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