May 2009 - petsc-users - mailman3.cels.anl.gov

memory check: error message from valgrind
by (Rebecca) Xuefei YUAN 06 May '09

06 May '09

Hi, I am using valgrind to check the memory leaking and it turned out that I got 3 errors and they were happening at the the PetscInitialize(), and DACreate2d() line 79: PetscInitialize(&argc, &argv, (char*)0, help); line 84: ierr = DACreate2d(comm,DA_XPERIODIC,DA_STENCIL_BOX, -5, -5, PETSC_DECIDE, PETSC_DECIDE, 4, 2, 0, 0, &da);CHKERRQ(ierr); What could be wrong here? Thanks! The following is the message from valgrind ----------------------------------------------------------------- valgrind --leak-check=full --show-reachable=yes --tool=memcheck ./vdthpffxmhd -options_file option_ffxmhd>output ==26665== Memcheck, a memory error detector. ==26665== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al. ==26665== Using LibVEX rev 1804, a library for dynamic binary translation. ==26665== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP. ==26665== Using valgrind-3.3.0-Debian, a dynamic binary instrumentation framework. ==26665== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al. ==26665== For more details, rerun with: -v ==26665== ==26665== Invalid read of size 4 ==26665== at 0x40151F9: (within /lib/ld-2.7.so) ==26665== by 0x4005C59: (within /lib/ld-2.7.so) ==26665== by 0x4007A87: (within /lib/ld-2.7.so) ==26665== by 0x4011533: (within /lib/ld-2.7.so) ==26665== by 0x400D5C5: (within /lib/ld-2.7.so) ==26665== by 0x4010F4D: (within /lib/ld-2.7.so) ==26665== by 0x42C0291: (within /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x400D5C5: (within /lib/ld-2.7.so) ==26665== by 0x42C0454: __libc_dlopen_mode (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x429A186: __nss_lookup_function (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x429A29F: (within /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x429BEC5: __nss_hosts_lookup (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== Address 0x432af8c is 36 bytes inside a block of size 37 alloc'd ==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207) ==26665== by 0x4008021: (within /lib/ld-2.7.so) ==26665== by 0x4011533: (within /lib/ld-2.7.so) ==26665== by 0x400D5C5: (within /lib/ld-2.7.so) ==26665== by 0x4010F4D: (within /lib/ld-2.7.so) ==26665== by 0x42C0291: (within /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x400D5C5: (within /lib/ld-2.7.so) ==26665== by 0x42C0454: __libc_dlopen_mode (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x429A186: __nss_lookup_function (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x429A29F: (within /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x429BEC5: __nss_hosts_lookup (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x42A0782: gethostbyname_r (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== ==26665== Invalid read of size 4 ==26665== at 0x40151E3: (within /lib/ld-2.7.so) ==26665== by 0x4005C59: (within /lib/ld-2.7.so) ==26665== by 0x4007A87: (within /lib/ld-2.7.so) ==26665== by 0x4011533: (within /lib/ld-2.7.so) ==26665== by 0x400D5C5: (within /lib/ld-2.7.so) ==26665== by 0x4010F4D: (within /lib/ld-2.7.so) ==26665== by 0x42C0291: (within /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x400D5C5: (within /lib/ld-2.7.so) ==26665== by 0x42C0454: __libc_dlopen_mode (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x429A186: __nss_lookup_function (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x4731FFB: (within /lib/tls/i686/cmov/libnss_compat-2.7.so) ==26665== by 0x473313C: _nss_compat_getpwuid_r (in /lib/tls/i686/cmov/libnss_compat-2.7.so) ==26665== Address 0x432c1f8 is 32 bytes inside a block of size 35 alloc'd ==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207) ==26665== by 0x4008021: (within /lib/ld-2.7.so) ==26665== by 0x4011533: (within /lib/ld-2.7.so) ==26665== by 0x400D5C5: (within /lib/ld-2.7.so) ==26665== by 0x4010F4D: (within /lib/ld-2.7.so) ==26665== by 0x42C0291: (within /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x400D5C5: (within /lib/ld-2.7.so) ==26665== by 0x42C0454: __libc_dlopen_mode (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x429A186: __nss_lookup_function (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x4731FFB: (within /lib/tls/i686/cmov/libnss_compat-2.7.so) ==26665== by 0x473313C: _nss_compat_getpwuid_r (in /lib/tls/i686/cmov/libnss_compat-2.7.so) ==26665== by 0x4246D15: getpwuid_r (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== ==26665== ERROR SUMMARY: 3 errors from 2 contexts (suppressed: 41 from 1) ==26665== malloc/free: in use at exit: 64,352 bytes in 87 blocks. ==26665== malloc/free: 2,472 allocs, 2,385 frees, 3,015,115 bytes allocated. ==26665== For counts of detected errors, rerun with: -v ==26665== searching for pointers to 87 not-freed blocks. ==26665== checked 1,120,136 bytes. ==26665== ==26665== ==26665== 32 bytes in 2 blocks are still reachable in loss record 1 of 5 ==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207) ==26665== by 0x871B2A8: MPID_VCRT_Create (mpid_vc.c:62) ==26665== by 0x8718C6A: MPID_Init (mpid_init.c:116) ==26665== by 0x86F1C3B: MPIR_Init_thread (initthread.c:288) ==26665== by 0x86F175D: PMPI_Init (init.c:106) ==26665== by 0x86355A1: PetscInitialize (pinit.c:503) ==26665== by 0x804B627: main (vdthpffxmhd.c:79) ==26665== ==26665== ==26665== 156 (36 direct, 120 indirect) bytes in 1 blocks are definitely lost in loss record 2 of 5 ==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207) ==26665== by 0x429A3E2: (within /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x429AC2D: __nss_database_lookup (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x4731FDB: ??? ==26665== by 0x473313C: ??? ==26665== by 0x4246D15: getpwuid_r (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x424665D: getpwuid (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x8644D41: PetscGetUserName (fuser.c:68) ==26665== by 0x8602528: PetscErrorPrintfInitialize (errtrace.c:68) ==26665== by 0x863565B: PetscInitialize (pinit.c:518) ==26665== by 0x804B627: main (vdthpffxmhd.c:79) ==26665== ==26665== ==26665== 40 bytes in 5 blocks are indirectly lost in loss record 3 of 5 ==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207) ==26665== by 0x4299FBB: __nss_lookup_function (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x4731FFB: ??? ==26665== by 0x473313C: ??? ==26665== by 0x4246D15: getpwuid_r (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x424665D: getpwuid (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x8644D41: PetscGetUserName (fuser.c:68) ==26665== by 0x8602528: PetscErrorPrintfInitialize (errtrace.c:68) ==26665== by 0x863565B: PetscInitialize (pinit.c:518) ==26665== by 0x804B627: main (vdthpffxmhd.c:79) ==26665== ==26665== ==26665== 80 bytes in 5 blocks are indirectly lost in loss record 4 of 5 ==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207) ==26665== by 0x428739B: tsearch (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x4299F7D: __nss_lookup_function (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x4731FFB: ??? ==26665== by 0x473313C: ??? ==26665== by 0x4246D15: getpwuid_r (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x424665D: getpwuid (in /lib/tls/i686/cmov/libc-2.7.so) ==26665== by 0x8644D41: PetscGetUserName (fuser.c:68) ==26665== by 0x8602528: PetscErrorPrintfInitialize (errtrace.c:68) ==26665== by 0x863565B: PetscInitialize (pinit.c:518) ==26665== by 0x804B627: main (vdthpffxmhd.c:79) ==26665== ==26665== ==26665== 64,164 bytes in 74 blocks are still reachable in loss record 5 of 5 ==26665== at 0x4022AB8: malloc (vg_replace_malloc.c:207) ==26665== by 0x8610BE4: PetscMallocAlign (mal.c:40) ==26665== by 0x8611CD3: PetscTrMallocDefault (mtr.c:194) ==26665== by 0x81DE577: DACreate2d (da2.c:364) ==26665== by 0x804B701: main (vdthpffxmhd.c:84) ==26665== ==26665== LEAK SUMMARY: ==26665== definitely lost: 36 bytes in 1 blocks. ==26665== indirectly lost: 120 bytes in 10 blocks. ==26665== possibly lost: 0 bytes in 0 blocks. ==26665== still reachable: 64,196 bytes in 76 blocks. ==26665== suppressed: 0 bytes in 0 blocks. ------------------------------------------------------------------ -- (Rebecca) Xuefei YUAN Department of Applied Physics and Applied Mathematics Columbia University Tel:917-399-8032 www.columbia.edu/~xy2102

3 3

implementing my own mat vec multiplayer
by Damian Kaleta 05 May '09

05 May '09

Hi, I was wondering if PETSc will allow me to implement my own matrix- vector multiplayer when I use Linear solvers (KSP). If it is possible, how can I achieve that? Thank you, Damian Kaleta

2 1

Some strange results running in PETSc.
by (Rebecca) Xuefei YUAN 05 May '09

05 May '09

Hi, I am running some codes and stores the solution in the text file. However, I found that some results are wired in the sense that some processors are "eating" my (i,j) index and the corresponding solution. For example, the solution at time step =235 on processor 6 is right, but at time step = 236 on processor 6, one grid solution is missing and thus the order of the index is wrong. In the attached two files: hp.solution.dt0.16700.n90.t235.p6 (right one) hp.solution.dt0.16700.n90.t236.p6 (wrong one) for example, in hp.solution.dt0.16700.n90.t235.p6 (right one) i j --------------------------------------------------------------------------------------------------------------------------------------------------------------------- 50 14 3.3212491928636803e-02 7.2992225179014901e-03 2.9841295384404947e+00 2.2004855368148415e-02 51 14 4.0287965701667774e-02 2.5401878231124070e-03 2.9201873761746322e+00 2.6251864239477816e-02 52 14 4.7084950235070790e-02 -1.5367647745423544e-03 2.8460826176461214e+00 3.1550405800570377e-02 53 14 5.3394938807608198e-02 -3.8189091837479271e-03 2.7618414550374171e+00 3.4078755072804334e-02 -------------------------------------------------------------------------------------------------------------------------------------------------------------------- however, in hp.solution.dt0.16700.n90.t236.p6 (wrong one) i j --------------------------------------------------------------------------------------------------------------------------------------------------------------------- 50 14 3.1239406700376452e-02 8.5179559039992043e-03 2.9840003096148520e+00 2.1760859158622522e-02 51 14 3.8032143218986063e-02 3.6341965920997721e-03 2.9198035731818854e+00 2.6200771510346648e-02 53 14 5.0661309132451274e-02 -2.9274557377189617e-03 2.7606822480069755e+00 3.4021016413777964e-02 54 14 5.6049570141121191e-02 -2.8111244430837979e-03 2.6669503598276267e+00 3.8855104759650566e-02 -------------------------------------------------------------------------------------------------------------------------------------------------------------------- the (i,j) = (52,14) is missing and as a result, one grid point solution is missing. I did not understand how this happens and why this happens? Any ideas? Thanks very much! Cheers, Rebecca -- (Rebecca) Xuefei YUAN Department of Applied Physics and Applied Mathematics Columbia University Tel:917-399-8032 www.columbia.edu/~xy2102

3 3

Additive multilevel Schwarz preconditioner
by Nguyen, Hung V ERDC-ITL-MS 05 May '09

05 May '09

Hello, Does PETSc supports additive multilevel Schwarz preconditioner? If yes, how to set/run it? Thanks, -hung

2 2

Duplicating MATSeqAIJ matrix to other PEs
by Keita Teranishi 05 May '09

05 May '09

Hi, I have been trying to copy a MatSeqAIJ matrix on PE0 to the rest of the PEs so that every PE has the exactly the same matrix. What is the best way to do that? Thanks in advance, ================================ Keita Teranishi Scientific Library Group Cray, Inc. keita(a)cray.com ================================

2 1

installation Petsc 3.0.0 and parmetis
by Fredrik Bengzon 05 May '09

05 May '09

Hi Petsc team I've installed petsc 3.0.0 with parmetis for use with superlu_dist. Everything compiles well, but when I link with my application code I get undefined reference to METIS_mCPartGraphRecursive2. Do I need to set any LD paths or something pointing to the 'externalpackages' directory or should this be taken care of by Petsc? Regards, Fredrik Bengzon

2 1

MPIAIJ and MatSetValuesBlocked
by Ryan Yan 05 May '09

05 May '09

Hi, all, I am using MPIAIJ for my matrix A, but when I call the function MatSetValuesBlocked, I got the error: PetscPrintf(PETSC_COMM_WORLD, "breakpoint 1\n"); ierr = MatSetValuesBlocked(A,1,&irow,1,(col_ind+icol),temp_vector,INSERT_VALUES); PetscPrintf(PETSC_COMM_WORLD, "breakpoint 2\n"); breakpoint 1 [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: No support for this operation for this object type! [0]PETSC ERROR: Mat type mpiaij! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 15, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: /home/vyan2000/local/PPETSc/petsc-2.3.3-p15/src/ksp/ksp/examples/tutorials/ttt2/kspex1reader_binmpiaij on a linux-gnu named vyan2000-linux by vyan2000 Fri May 1 17:58:48 2009 [0]PETSC ERROR: Libraries linked from /home/vyan2000/local/PPETSc/petsc-2.3.3-p15/lib/linux-gnu-c-debug [0]PETSC ERROR: Configure run at Thu Feb 5 21:10:10 2009 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/lib/ --with-debugger=gdb --with-shared=0 --download-hypre=1 --download-parmetis=1 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: MatSetValuesBlocked() line 1289 in src/mat/interface/matrix.c breakpoint 2 Is it the reason that MatSetValuesBlocked only works for MPIBAIJ or SeqBAIJ? Thanks, Yan

8 15

Cast matrix as a vector?
by liu chang 03 May '09

03 May '09

I'm using TAO's LMVM method for optimize a dense matrix, but TAO expects its input as a Vec. Do I have to copy the content back and forth between a Mat and a Vec? Can I somehow cast the Mat into a Vec? Both the Mat and the Vec are distributed evenly across the processes so ideally there doesn't need to be any copying at all. Thanks, Liu Chang

2 3

Convex optimization with linear constraint?
by liu chang 03 May '09

03 May '09

I'm using PETSc + TAO's LMVM method for a convex optimization problem. As the project progresses, it's clear that some linear constraints are also needed, the problem now looks like: minimize f(vec_x) (f is neither linear or quadratic, but is convex) subject to A * vec_x = vec_b As LMVM does not support linear constraints, I'm looking for another solver. TAO lists several functions dealing with constraints, but they're all in the developer section, and in the samples linked from the manual I haven't found one that's linearly constrained. Is there a suitable one in TAO? Liu Chang

2 2