On 18/6/2012 10:58 PM, Barry Smith wrote: > On Jun 18, 2012, at 9:54 PM, TAY wee-beng wrote: > >> 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. > Then likely it is an Intel compiler bug. Does this happen with the gnu > gfortran compiler combined with gcc as the c compiler? > > Barry I have not tested. I'm also using intel fortran with VS2008 in windows 7 64bit. Do I have to re-build PETSc to test with gcc and gfortran?
Thanks. >>> 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
