July 2008 - petsc-dev - mailman3.cels.anl.gov

Re: problem with PetscSynchronizedFPrintf (fwd)
by Barry Smith 21 Jul '08

21 Jul '08

Matt, You have to be careful here. You use PetscMalloc() here, are you positive this routine will never be called BEFORE PetscMalloc() is setup for (sometime in PetscInitialize), or after PetscMalloc() is taken down (somewhere in PetscFinalize())? Is there someway you can make sure that it is safe? In a few places on setup I have to use a raw malloc instead of PetscMalloc(), I don't want you to have to do that here. I'm not saying to change back the code, just to be careful and check it. Barry On Jul 21, 2008, at 2:47 PM, Matthew Knepley wrote: > I made this change because synchronized printing was cutting off my > stuff. Now the queue is dynamically allocated so it can accomodate > any size string. > > I tried ex7 and it runs fine for me, even under valgrind. > > Shi, can you reproduce this with a Sieve example? > > Matt > > On Mon, Jul 21, 2008 at 2:37 PM, Satish Balay <balay(a)mcs.anl.gov> > wrote: >> Looks like this could be related to changeset 9e3fbe04a926 >> >> --> mprint.h <-- >> >> - char string[QUEUESTRINGSIZE]; >> + char *string; >> >> So now strings needs to use malloc()/free()? >> >> Matt - you can reproduce this issue with dm/ao/examples/tests/ex7.c >> >> Satish >> >> On Mon, 21 Jul 2008, Satish Balay wrote: >> >>> >>> ---------- Forwarded message ---------- >>> Date: Sun, 20 Jul 2008 22:39:13 -0700 (PDT) >>> From: Shi Jin <jinzishuai(a)yahoo.com> >>> Subject: problem with PetscSynchronizedFPrintf >>> To: petsc-dev(a)mcs.anl.gov >>> >>> Hi, >>> >>> I recently updated my petsc-dev and found my previously working >>> code is having trouble running in parallel. I've narrowed it down >>> to the calls to PetscSynchronizedFPrintf. Even if I don't have >>> those, I will have errors at the end of my MPI runs like: >>> [1]PETSC ERROR: PetscMemzero() line 189 in src/sys/utils/memc.c >>> [1]PETSC ERROR: PetscViewerASCIISynchronizedPrintf() line 859 in >>> src/sys/viewer/impls/ascii/filev.c >>> [1]PETSC ERROR: PetscMemoryShowUsage() line 367 in src/sys/memory/ >>> mtr.c >>> [1]PETSC ERROR: PetscFinalize() line 675 in src/sys/objects/pinit.c >>> [1]PETSC ERROR: completeSection() line 163 in main.cxx >>> [0]0:Return code = 0, signaled with Interrupt >>> [0]1:Return code = 85 >>> >>> Since the same code was running fine before the update. I am >>> wondering if it is something recently introduced. >>> Thanks a lot. >>> >>> -- >>> Shi Jin, PhD >>> >>> >>> >>> >>> >>> >> >> > > > > -- > 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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Re: problem with PetscSynchronizedFPrintf (fwd)
by Satish Balay 21 Jul '08

21 Jul '08

Matt - Perhaps ex7 is a different Problem. But it does crash for me. And I noticed the following code: >>>>>>>>>>> ierr = PetscNew(struct _PrintfQueue,&next);CHKERRQ(ierr); if (queue) {queue->next = next; queue = next;} else {queuebase = queue = next;} queuelength++; string = next->string; ierr = PetscMemzero(string,QUEUESTRINGSIZE);CHKERRQ(ierr); <<<<<<<<< i.e 'next' is allocated - here is no malloc for 'next->string'. But its being zeroed in PetscMemzero() - hence the crash with ex7 for me. Satish --------------------------------------------- asterix:/home/balay/spetsc/src/dm/ao/examples/tests>mpiexec -n 2 ./ex7 Number of elements in ordering 10 PETSc->App App->PETSc 0 0 0 0 1 5 1 2 2 1 2 4 3 6 3 6 4 2 4 8 5 7 5 1 6 3 6 3 7 8 7 5 8 4 8 7 9 9 9 9 [1]PETSC ERROR: --------------------- Error Message ------------------------------------ [1]PETSC ERROR: Null argument, when expecting valid pointer! [1]PETSC ERROR: Trying to zero at a null pointer! [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: Petsc Development Version 2.3.3, Patch 13, unknown HG revision: unknown [1]PETSC ERROR: See docs/changes/index.html for recent updates. [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [1]PETSC ERROR: See docs/index.html for manual pages. [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: ./ex7 on a asterix64 named asterix by balay Mon Jul 21 14:51:02 2008 [1]PETSC ERROR: Libraries linked from /home/balay/spetsc/lib [1]PETSC ERROR: Configure run at Mon Jul 21 10:38:52 2008 [1]PETSC ERROR: Configure options --with-mpi-dir=/home/balay/soft/linux64/mpich2-1.0.7 --with-shared=1 PETSC_ARCH=asterix64 [1]PETSC ERROR: ----------------------------[0] Number of indices in (stride) set 5 [0] 0 0 [0] 1 2 [0] 2 4 [0] 3 6 [0] 4 8 -------------------------------------------- [1]PETSC ERROR: PetscMemzero() line 189 in src/sys/utils/memc.c [1]PETSC ERROR: PetscViewerASCIISynchronizedPrintf() line 859 in src/sys/viewer/impls/ascii/filev.c [1]PETSC ERROR: ISView_Stride() line 231 in src/vec/is/impls/stride/stride.c [1]PETSC ERROR: ISView() line 398 in src/vec/is/interface/index.c [1]PETSC ERROR: main() line 31 in src/dm/ao/examples/tests/ex7.c application called MPI_Abort(MPI_COMM_WORLD, 85) - process 1[cli_1]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 85) - process 1 [0]0:Return code = 0, signaled with Interrupt [0]1:Return code = 85 asterix:/home/balay/spetsc/src/dm/ao/examples/tests> On Mon, 21 Jul 2008, Matthew Knepley wrote: > I made this change because synchronized printing was cutting off my > stuff. Now the queue is dynamically allocated so it can accomodate > any size string. > > I tried ex7 and it runs fine for me, even under valgrind. > > Shi, can you reproduce this with a Sieve example? > > Matt > > On Mon, Jul 21, 2008 at 2:37 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > Looks like this could be related to changeset 9e3fbe04a926 > > > > --> mprint.h <-- > > > > - char string[QUEUESTRINGSIZE]; > > + char *string; > > > > So now strings needs to use malloc()/free()? > > > > Matt - you can reproduce this issue with dm/ao/examples/tests/ex7.c > > > > Satish

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Re: problem with PetscSynchronizedFPrintf (fwd)
by Matthew Knepley 21 Jul '08

21 Jul '08

I made this change because synchronized printing was cutting off my stuff. Now the queue is dynamically allocated so it can accomodate any size string. I tried ex7 and it runs fine for me, even under valgrind. Shi, can you reproduce this with a Sieve example? Matt On Mon, Jul 21, 2008 at 2:37 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > Looks like this could be related to changeset 9e3fbe04a926 > > --> mprint.h <-- > > - char string[QUEUESTRINGSIZE]; > + char *string; > > So now strings needs to use malloc()/free()? > > Matt - you can reproduce this issue with dm/ao/examples/tests/ex7.c > > Satish > > On Mon, 21 Jul 2008, Satish Balay wrote: > >> >> ---------- Forwarded message ---------- >> Date: Sun, 20 Jul 2008 22:39:13 -0700 (PDT) >> From: Shi Jin <jinzishuai(a)yahoo.com> >> Subject: problem with PetscSynchronizedFPrintf >> To: petsc-dev(a)mcs.anl.gov >> >> Hi, >> >> I recently updated my petsc-dev and found my previously working code is having trouble running in parallel. I've narrowed it down to the calls to PetscSynchronizedFPrintf. Even if I don't have those, I will have errors at the end of my MPI runs like: >> [1]PETSC ERROR: PetscMemzero() line 189 in src/sys/utils/memc.c >> [1]PETSC ERROR: PetscViewerASCIISynchronizedPrintf() line 859 in src/sys/viewer/impls/ascii/filev.c >> [1]PETSC ERROR: PetscMemoryShowUsage() line 367 in src/sys/memory/mtr.c >> [1]PETSC ERROR: PetscFinalize() line 675 in src/sys/objects/pinit.c >> [1]PETSC ERROR: completeSection() line 163 in main.cxx >> [0]0:Return code = 0, signaled with Interrupt >> [0]1:Return code = 85 >> >> Since the same code was running fine before the update. I am wondering if it is something recently introduced. >> Thanks a lot. >> >> -- >> Shi Jin, PhD >> >> >> >> >> >> > > -- 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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Re: problem with PetscSynchronizedFPrintf (fwd)
by Satish Balay 21 Jul '08

21 Jul '08

Looks like this could be related to changeset 9e3fbe04a926 --> mprint.h <-- - char string[QUEUESTRINGSIZE]; + char *string; So now strings needs to use malloc()/free()? Matt - you can reproduce this issue with dm/ao/examples/tests/ex7.c Satish On Mon, 21 Jul 2008, Satish Balay wrote: > > ---------- Forwarded message ---------- > Date: Sun, 20 Jul 2008 22:39:13 -0700 (PDT) > From: Shi Jin <jinzishuai(a)yahoo.com> > Subject: problem with PetscSynchronizedFPrintf > To: petsc-dev(a)mcs.anl.gov > > Hi, > > I recently updated my petsc-dev and found my previously working code is having trouble running in parallel. I've narrowed it down to the calls to PetscSynchronizedFPrintf. Even if I don't have those, I will have errors at the end of my MPI runs like: > [1]PETSC ERROR: PetscMemzero() line 189 in src/sys/utils/memc.c > [1]PETSC ERROR: PetscViewerASCIISynchronizedPrintf() line 859 in src/sys/viewer/impls/ascii/filev.c > [1]PETSC ERROR: PetscMemoryShowUsage() line 367 in src/sys/memory/mtr.c > [1]PETSC ERROR: PetscFinalize() line 675 in src/sys/objects/pinit.c > [1]PETSC ERROR: completeSection() line 163 in main.cxx > [0]0:Return code = 0, signaled with Interrupt > [0]1:Return code = 85 > > Since the same code was running fine before the update. I am wondering if it is something recently introduced. > Thanks a lot. > > -- > Shi Jin, PhD > > > > > >

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problem with PetscSynchronizedFPrintf (fwd)
by Satish Balay 21 Jul '08

21 Jul '08

---------- Forwarded message ---------- Date: Sun, 20 Jul 2008 22:39:13 -0700 (PDT) From: Shi Jin <jinzishuai(a)yahoo.com> Subject: problem with PetscSynchronizedFPrintf To: petsc-dev(a)mcs.anl.gov Hi, I recently updated my petsc-dev and found my previously working code is having trouble running in parallel. I've narrowed it down to the calls to PetscSynchronizedFPrintf. Even if I don't have those, I will have errors at the end of my MPI runs like: [1]PETSC ERROR: PetscMemzero() line 189 in src/sys/utils/memc.c [1]PETSC ERROR: PetscViewerASCIISynchronizedPrintf() line 859 in src/sys/viewer/impls/ascii/filev.c [1]PETSC ERROR: PetscMemoryShowUsage() line 367 in src/sys/memory/mtr.c [1]PETSC ERROR: PetscFinalize() line 675 in src/sys/objects/pinit.c [1]PETSC ERROR: completeSection() line 163 in main.cxx [0]0:Return code = 0, signaled with Interrupt [0]1:Return code = 85 Since the same code was running fine before the update. I am wondering if it is something recently introduced. Thanks a lot. -- Shi Jin, PhD

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Re: Petsc Repository
by Hong Zhang 18 Jul '08

18 Jul '08

Yong, petsc.cs.iit.edu is back now. Thanks, Hong On Fri, 18 Jul 2008, Hong Zhang wrote: > > Yong, > > Please check if the petsc machine is running? > Thanks, > > Hong > > On Fri, 18 Jul 2008, Satish Balay wrote: > >> Matt, >> >> Looks like the machine is down. >> >> Perhaps everyone can just grab the nightly traball for now.. >> ftp://info.mcs.anl.gov/pub/petsc/petsc-dev.tar.gz >> >> Satish >> >> On Fri, 18 Jul 2008, Matthew Knepley wrote: >> >>> I cannot ping petsc.cs.iit.edu. I have a tutorial scheduled for 8:30am and >>> was planning for everyone to pull and build. >>> >>> Matt >>> >>> >> >> > >

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vacation next Mon and Tue
by Hong Zhang 18 Jul '08

18 Jul '08

I'll take vacation next Mon and Tue (July 21-22). Hong

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Petsc Repository
by Hong Zhang 18 Jul '08

18 Jul '08

Yong, Please check if the petsc machine is running? Thanks, Hong On Fri, 18 Jul 2008, Satish Balay wrote: > Matt, > > Looks like the machine is down. > > Perhaps everyone can just grab the nightly traball for now.. > ftp://info.mcs.anl.gov/pub/petsc/petsc-dev.tar.gz > > Satish > > On Fri, 18 Jul 2008, Matthew Knepley wrote: > >> I cannot ping petsc.cs.iit.edu. I have a tutorial scheduled for 8:30am and >> was planning for everyone to pull and build. >> >> Matt >> >> > >

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Re: Repository
by Satish Balay 18 Jul '08

18 Jul '08

Matt, Looks like the machine is down. Perhaps everyone can just grab the nightly traball for now.. ftp://info.mcs.anl.gov/pub/petsc/petsc-dev.tar.gz Satish On Fri, 18 Jul 2008, Matthew Knepley wrote: > I cannot ping petsc.cs.iit.edu. I have a tutorial scheduled for 8:30am and > was planning for everyone to pull and build. > > Matt > >

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Repository
by Matthew Knepley 18 Jul '08

18 Jul '08

I cannot ping petsc.cs.iit.edu. I have a tutorial scheduled for 8:30am and was planning for everyone to pull and build. Matt -- 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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