Matt/Barry My intention was to make sure that the code is bug free and since PETSc was pre-installed on the cluster with various compilers it was easier to test quickly rather than build all combinations myself. Performance is of absolutely no concern. Things were working fine with 3.1 but recently the OS (Cray Linux Env) was upgraded and so was PETSc (to 3.2). Matt I am attaching entire output. Tabrez --- stali@krakenpf2:~/meshes> which xterm /usr/bin/xterm stali@krakenpf2:~/meshes> aprun -n 1 ./defmod -f 2d_point_load_dyn_abc.inp -on_error_attach_debugger Reading input ... Reading mesh data ... Forming [K] ... Forming [M] & [M]^-1 ... Applying constraints ... Forming RHS ... Setting up solver ... Solving ... Time Step 0 [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/petsc-as/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: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [0]PETSC ERROR: PETSC: Attaching gdb to ./defmod of pid 26164 on display :0.0 on machine nid03538 Unable to start debugger in xterm: No such file or directory aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 _pmii_daemon(SIGCHLD): [NID 03538] [c12-3c2s4n2] [Mon Apr 2 22:50:09 2012] PE 0 exit signal Aborted Application 134950 exit codes: 134 Application 134950 resources: utime ~1s, stime ~0s On 04/02/2012 09:04 PM, Matthew Knepley wrote:
On Mon, Apr 2, 2012 at 8:57 PM, Barry Smith <[email protected] <mailto:[email protected]>> wrote:
On Apr 2, 2012, at 8:10 PM, Tabrez Ali wrote:
> Hello > > I am trying to debug a program using the switch '-on_error_attach_debugger' but the vendor/sysadmin built PETSc 3.2.00 is unable to start the debugger in xterm (see text below). But xterm is installed. What am I doing wrong? > > Btw the segfault happens during a call to MatMult but only with vendor/sysadmin supplied PETSc 3.2 with PGI and Intel compilers only and _not_ with CRAY or GNU compilers.
My advice, blow off "the vendor/sysadmin supplied PETSc 3.2" and just built it yourself so you can get real work done instead of trying to debug their mess. I promise the vendor one is not like a billion times faster or anything.
If you want to justify this to anyone (like a funder), just run both on ex5 for a large size and look at the flops on MatMult. That is probably your dominant cost (or your PC).
Matt
Barry
> > I also dont get the segfault if I build PETSc 3.2-p7 myself with PGI/Intel compilers. > > Any ideas on how to diagnose the problem? Unfortunately I cannot seem to run valgrind on this particular machine. > > Thanks in advance. > > Tabrez > > --- > > stali@krakenpf1:~/meshes> which xterm > /usr/bin/xterm > stali@krakenpf1:~/meshes> aprun -n 1 ./defmod -f 2d_point_load_dyn_abc.inp -on_error_attach_debugger > ... > ... > ... > [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/petsc-as/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: configure using --with-debugging=yes, recompile, link, and run > [0]PETSC ERROR: to get more information on the crash. > [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file > [0]PETSC ERROR: PETSC: Attaching gdb to ./defmod of pid 32384 on display localhost:20.0 on machine nid10649 > Unable to start debugger in xterm: No such file or directory > aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 > _pmii_daemon(SIGCHLD): [NID 10649] [c23-3c0s6n1] [Mon Apr 2 13:06:48 2012] PE 0 exit signal Aborted > Application 133198 exit codes: 134 > Application 133198 resources: utime ~1s, stime ~0s
-- 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