On 18/6/2012 10:36 PM, Barry Smith wrote: > Do PETSc examples run on this system. cd src/snes/examples/tutorials; make > ex19 ; then run ex19 on a bunch of nodes of the cluster, does it run > correctly? Repeat with ex5f > > Barry ex19 and ex5f both run w/o problem.
[wtay at hpc12:tutorials]$ mpiexec -np 2 ./ex19 lid velocity = 0.0625, prandtl # = 1, grashof # = 1 Number of SNES iterations = 2 [wtay at hpc12:tutorials]$ mpiexec -np 4 ./ex19 lid velocity = 0.0625, prandtl # = 1, grashof # = 1 Number of SNES iterations = 2 [wtay at hpc12:tutorials]$ ./ex5f Number of SNES iterations = 4 [wtay at hpc12:tutorials]$ mpiexec -np 2 ./ex5f Number of SNES iterations = 4 [wtay at hpc12:tutorials]$ mpiexec -np 4 ./ex5f Number of SNES iterations = 4 [wtay at hpc12:tutorials]$ The problem seems to lie in DMDAVecGetArrayF90 and DMDAVecRestoreArrayF90. I have reported this problem before when I convert ex29 from C to Fortran. It works in Vs2008 windows but not in linux. I wonder if it has some bugs or compatibility problem. > > On Jun 18, 2012, at 9:21 PM, TAY wee-beng wrote: > >> On 18/6/2012 9:52 PM, Matthew Knepley wrote: >>> On Mon, Jun 18, 2012 at 7:30 PM, TAY wee-beng<zonexo at gmail.com> wrote: >>> >>> On 17/6/2012 2:33 PM, Jed Brown wrote: >>>> On Sun, Jun 17, 2012 at 7:26 AM, TAY wee-beng<zonexo at gmail.com> wrote: >>>> >>>> On 16/6/2012 9:24 AM, Jed Brown wrote: >>>>> It depends how you want to solve the problem. I usually group all dofs >>>>> together. There is a 2D Stokes+Thermodynamics example in SNES ex30 (or >>>>> 31?). >>>>> >>>> I tried to understand ex30. I have some questions since it's in C and I'm >>>> using to Fortran programming. >>>> >>>> This looks about right, see src/dm/examples/tutorials/ex11f90.F. >>> I tried to build and run ex11f90 in linux. However, it's not working: >>> >>> I have attached the run and valgrind output: >>> >>> It appears to be a problem with your MPI. >>> >>> Matt >> Is there anyway to solve this problem? I'm running on a cluster using >> openmpi 1.5.3 and I've no admin rights. >>> >>> run output: >>> >>> [wtay at hpc12:tutorials]$ ./ex11f90 >>> [0]PETSC ERROR: >>> ------------------------------------------------------------------------ >>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>> probably memory access out of range >>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >>> [0]PETSC ERROR: or see >>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR: >>> or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory >>> corruption errors >>> [0]PETSC ERROR: likely location of problem given in stack below >>> [0]PETSC ERROR: --------------------- Stack Frames >>> ------------------------------------ >>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, >>> [0]PETSC ERROR: INSTEAD the line number of the start of the function >>> [0]PETSC ERROR: is given. >>> [0]PETSC ERROR: --------------------- Error Message >>> ------------------------------------ >>> [0]PETSC ERROR: Signal received! >>> [0]PETSC ERROR: >>> ------------------------------------------------------------------------ >>> [0]PETSC ERROR: Petsc Development HG revision: >>> f3b998b41b349e16d47fe42b0e223d3462737e05 HG Date: Fri Jun 15 17:50:32 2012 >>> -0500 >>> [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: ./ex11f90 on a petsc-3.3 named hpc12 by wtay Tue Jun 19 >>> 03:22:52 2012 >>> [0]PETSC ERROR: Libraries linked from >>> /home/wtay/Lib/petsc-3.3-dev_shared_debug/lib >>> [0]PETSC ERROR: Configure run at Sun Jun 17 16:51:29 2012 >>> [0]PETSC ERROR: Configure options --with-mpi-dir=/opt/openmpi-1.5.3/ >>> --with-blas-lapack-dir=/opt/intelcpro-11.1.059/mkl/lib/em64t/ >>> --with-debugging=1 --download-hypre=1 >>> --prefix=/home/wtay/Lib/petsc-3.3-dev_shared_debug --known-mpi-shared=1 >>> --with-shared-libraries >>> [0]PETSC ERROR: >>> ------------------------------------------------------------------------ >>> [0]PETSC ERROR: User provided function() line 0 in unknown directory >>> unknown file >>> -------------------------------------------------------------------------- >>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>> with errorcode 59. >>> >>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> You may or may not see output from other processes, depending on >>> exactly when Open MPI kills them. >>> -------------------------------------------------------------------------- >>> >>> valgrind output: >>> >>> ==6027== Memcheck, a memory error detector >>> ==6027== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al. >>> ==6027== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info >>> ==6027== Command: ex11f90 >>> ==6027== >>> ==6027== Invalid read of size 8 >>> ==6027== at 0xA60148D: _wordcopy_fwd_dest_aligned (in >>> /lib64/libc-2.12.so) >>> ==6027== by 0xA5FB11D: __GI_memmove (in /lib64/libc-2.12.so) >>> ==6027== by 0xA6027DB: argz_insert (in /lib64/libc-2.12.so) >>> ==6027== by 0x95CAF25: lt_argz_insert (ltdl.c:1679) >>> ==6027== by 0x95CB7D0: foreachfile_callback (ltdl.c:1718) >>> ==6027== by 0x95CB4F1: foreach_dirinpath (ltdl.c:710) >>> ==6027== by 0x95CB580: lt_dlforeachfile (ltdl.c:1865) >>> ==6027== by 0x95DB999: mca_base_component_find >>> (mca_base_component_find.c:301) >>> ==6027== by 0x95DC4B0: mca_base_components_open >>> (mca_base_components_open.c:128) >>> ==6027== by 0x95F7CE7: opal_paffinity_base_open >>> (paffinity_base_open.c:112) >>> ==6027== by 0x95C39FE: opal_init (opal_init.c:307) >>> ==6027== by 0x95815A4: orte_init (orte_init.c:78) >>> ==6027== Address 0xb39d9a8 is 40 bytes inside a block of size 43 alloc'd >>> ==6027== at 0x4C267BA: malloc (vg_replace_malloc.c:263) >>> ==6027== by 0x95CA358: lt__malloc (lt__alloc.c:54) >>> ==6027== by 0x95CB751: foreachfile_callback (ltdl.c:1764) >>> ==6027== by 0x95CB4F1: foreach_dirinpath (ltdl.c:710) >>> ==6027== by 0x95CB580: lt_dlforeachfile (ltdl.c:1865) >>> ==6027== by 0x95DB999: mca_base_component_find >>> (mca_base_component_find.c:301) >>> ==6027== by 0x95DC4B0: mca_base_components_open >>> (mca_base_components_open.c:128) >>> ==6027== by 0x95F7CE7: opal_paffinity_base_open >>> (paffinity_base_open.c:112) >>> ==6027== by 0x95C39FE: opal_init (opal_init.c:307) >>> ==6027== by 0x95815A4: orte_init (orte_init.c:78) >>> ==6027== by 0x95432AE: ompi_mpi_init (ompi_mpi_init.c:350) >>> ==6027== by 0x955938F: PMPI_Init (pinit.c:84) >>> ==6027== >>> ==6027== Syscall param writev(vector[...]) points to uninitialised byte(s) >>> ==6027== at 0xA65692B: writev (in /lib64/libc-2.12.so) >>> ==6027== by 0xC9A2C56: mca_oob_tcp_msg_send_handler (oob_tcp_msg.c:249) >>> ==6027== by 0xC9A417C: mca_oob_tcp_peer_send (oob_tcp_peer.c:204) >>> ==6027== by 0xC9A67FC: mca_oob_tcp_send_nb (oob_tcp_send.c:167) >>> ==6027== by 0xC3953B5: orte_rml_oob_send (rml_oob_send.c:136) >>> ==6027== by 0xC3955FF: orte_rml_oob_send_buffer (rml_oob_send.c:270) >>> ==6027== by 0xCDB1E87: modex (grpcomm_bad_module.c:573) >>> ==6027== by 0x95436F1: ompi_mpi_init (ompi_mpi_init.c:682) >>> ==6027== by 0x955938F: PMPI_Init (pinit.c:84) >>> ==6027== by 0x8AB4FF4: MPI_INIT (pinit_f.c:75) >>> ==6027== by 0x50ED97E: petscinitialize_ (zstart.c:299) >>> ==6027== by 0x40881C: MAIN__ (ex11f90.F:43) >>> ==6027== Address 0xed30cd1 is 161 bytes inside a block of size 256 alloc'd >>> ==6027== at 0x4C268B2: realloc (vg_replace_malloc.c:632) >>> ==6027== by 0x95C4F22: opal_dss_buffer_extend >>> (dss_internal_functions.c:63) >>> ==6027== by 0x95C5A64: opal_dss_copy_payload (dss_load_unload.c:164) >>> ==6027== by 0x95A1246: orte_grpcomm_base_pack_modex_entries >>> (grpcomm_base_modex.c:861) >>> ==6027== by 0xCDB1E3C: modex (grpcomm_bad_module.c:563) >>> ==6027== by 0x95436F1: ompi_mpi_init (ompi_mpi_init.c:682) >>> ==6027== by 0x955938F: PMPI_Init (pinit.c:84) >>> ==6027== by 0x8AB4FF4: MPI_INIT (pinit_f.c:75) >>> ==6027== by 0x50ED97E: petscinitialize_ (zstart.c:299) >>> ==6027== by 0x40881C: MAIN__ (ex11f90.F:43) >>> ==6027== by 0x4087AB: main (in >>> /home/wtay/Codes/petsc-dev/src/dm/examples/tutorials/ex11f90) >>> ==6027== >>> ==6027== Invalid read of size 8 >>> ==6027== at 0x50FC6D8: vecview_ (zvectorf.c:56) >>> ==6027== by 0x408A05: MAIN__ (ex11f90.F:56) >>> ==6027== by 0xEE1CC2F: ??? >>> ==6027== by 0xEE5A0AF: ??? >>> ==6027== by 0x6F5C9F: ??? (in >>> /home/wtay/Codes/petsc-dev/src/dm/examples/tutorials/ex11f90) >>> ==6027== by 0x4962FF: ??? (in >>> /home/wtay/Codes/petsc-dev/src/dm/examples/tutorials/ex11f90) >>> ==6027== by 0x6F5C9F: ??? (in >>> /home/wtay/Codes/petsc-dev/src/dm/examples/tutorials/ex11f90) >>> ==6027== by 0x7FEFFFC13: ??? >>> ==6027== Address 0xfffffffffffffeb8 is not stack'd, malloc'd or (recently) >>> free'd >>> ==6027== >>> >>> >>> >>>> >>>> >>>> Supposed I have a field - u,v,w,p, so in order to use them, I do the >>>> following: >>>> >>>> type field >>>> >>>> real u,v,w,p >>>> >>>> end type field >>>> >>>> type(field), pointer :: field1(:,:,:) -> make a derived variable >>>> >>>> Also: >>>> >>>> Vec field_local,field_global >>>> >>>> call DMDACreate3d with dof = 4 >>>> >>>> call DMCreateGlobalVector(da, field_local,ierr) >>>> >>>> call DMCreateLocalVector(da,field_global,ierr) >>>> >>>> call DMGetLocalVector(da, field_local,ierr) -> To insert values >>>> >>>> call DMDAVecGetArrayF90(da, field_local,field1,ierr) >>>> >>>> do k = zs, zs + zm - 1 >>>> >>>> do j = ys, ys + ym -1 >>>> >>>> do i = xs, xs + xm - 1 >>>> >>>> field1(i,j,k)%u = ... -> evaluate u,v,w,p etc >>>> >>>> end do >>>> >>>> end do >>>> >>>> call DMDAVecRestoreArrayF90(da,field_local,field1,ierr) >>>> >>>> call DMLocalToGlobalBegin(da,field_local,INSERT_VALUES,field_global,ierr) >>>> >>>> call DMLocalToGlobalEnd(da,field_local,INSERT_VALUES,field_global,ierr) >>>> >>>> call DMRestoreLocalVector(da,field_local,ierr) >>>> >>>> Is this the correct way? >>>> >>>> Also, supposed I now want to solve my u,v,w momentum eqns. Although >>>> they're not coupled together, I believe it's faster if I assemble them >>>> into 1 big matrix. >>>> >>>> So for Ax = b, x = >>>> (field(1,1,1)%u,field(1,1,1)%v,field(1,1,1)%w,field(2,1,1)%u.... ) >>>> >>>> For b, do I duplicate a Vec similar to field_local? >>>> >>>> What about matrix A? Do I use the MatSetValuesStencil? >>>> >>>> Yes >>>> >>>> >>>> Lastly, the type field contains u,v,w and p. However, I'm only solving >>>> u,v,w. Do I have to skip some values or use identity matrix to solve it? >>>> >>>> Why not make a field that contains only u,v,w. I don't see what you're >>>> trying to do. >>> >>> >>> -- >>> 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
