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 > <mailto: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: 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120618/47eef88b/attachment-0001.html>
