On Sun, Feb 22, 2015 at 1:03 PM, Barry Smith <bsm...@mcs.anl.gov> wrote:
> > Mark, > > I think it is ignoring the openmp pragmas I added. Can you please > configure with the additional argument --with-openmp > That works. Thanks, Mark > > Barry > > > On Feb 22, 2015, at 11:21 AM, Mark Adams <mfad...@lbl.gov> wrote: > > > > Barry, I get three errors with -ksp_converged_reason using your branch. > > > > Thanks, > > Mark > > > > Linear col_f_ solve converged due to CONVERGED_RTOL iterations 1 > > [1;31m[82]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > [0;39m [0;49m[82]PETSC ERROR: Argument out of range > > [82]PETSC ERROR: Too many pushes > > [82]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > > [82]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2014-g463f016 > GIT Date: 2015-02-21 11:26:56 -0600 > > [82]PETSC ERROR: ../../epsi/XGCa/xgca on a arch-xc30-optts-intel named > nid03897 by madams Sun Feb 22 09:12:35 2015 > > [82]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" > --download-parmetis --download-metis --with-ssl=0 --with-threadsafety > --with-log=0 --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn > --with-fortranlib-autodetect=0 > --with-hdf5-dir=/opt/cray/hdf5-parallel/1.8.13/intel/140/ > --with-shared-libraries=0 --with-x=0 --with-mpiexec=aprun LIBS=-lstdc++ > PETSC_ARCH=arch-xc30-optts-intel > PETSC_DIR=/global/homes/m/madams/petsc-barry > > [82]PETSC ERROR: #1 PetscViewerPushFormat() line 144 in > /global/u2/m/madams/petsc-barry/src/sys/classes/viewer/interface/viewa.c > > [82]PETSC ERROR: #2 KSPReasonViewFromOptionsUnsafe() line 424 in > /global/u2/m/madams/petsc-barry/src/ksp/ksp/interface/itfunc.c > > [82]PETSC ERROR: #3 KSPSolve() line 592 in > /global/u2/m/madams/petsc-barry/src/ksp/ksp/interface/itfunc.c > > Linear col_f_ solve converged due to CONVERGED_RTOL iterations 1 > > > > [snip] > > > > [13]PETSC ERROR: > ------------------------------------------------------------------------ > > [13]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [13]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > [13]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > > [13]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac > OS X to find memory corruption errors > > [13]PETSC ERROR: configure using --with-debugging=yes, recompile, link, > and run > > [13]PETSC ERROR: to get more information on the crash. > > Linear col_f_ solve converged due to CONVERGED_RTOL iterations 1 > > Linear col_f_ solve converged due to CONVERGED_RTOL iterations 1 > > [1;31m[13]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > [0;39m [0;49m[13]PETSC ERROR: Signal received > > [13]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > > [13]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2014-g463f016 > GIT Date: 2015-02-21 11:26:56 -0600 > > [13]PETSC ERROR: ../../epsi/XGCa/xgca on a arch-xc30-optts-intel named > nid00713 by madams Sun Feb 22 09:12:35 2015 > > [13]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" > --CXXOPTFLAGS="-fast -no-ipo" --FOPTFLAGS="-fast -no-ipo" > --download-parmetis --download-metis --with-ssl=0 --with-threadsafety > --with-log=0 --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC > --with-cxxlib-autodetect=0 --with-debugging=0 --with-fc=ftn > --with-fortranlib-autodetect=0 > --with-hdf5-dir=/opt/cray/hdf5-parallel/1.8.13/intel/140/ > --with-shared-libraries=0 --with-x=0 --with-mpiexec=aprun LIBS=-lstdc++ > PETSC_ARCH=arch-xc30-optts-intel > PETSC_DIR=/global/homes/m/madams/petsc-barry > > [13]PETSC ERROR: #1 User provided function() line 0 in unknown file > > Rank 13 [Sun Feb 22 09:13:04 2015] [c3-0c2s2n1] application called > MPI_Abort(MPI_COMM_WORLD, 59) - process 13 > > > > [snip] > > > > Linear col_f_ solve converged due to CONVERGED_RTOL iterations 1 > > forrtl: error (76): Abort trap signal > > Image PC Routine Line > Source > > xgca 0000000002E10A41 Unknown Unknown > Unknown > > xgca 0000000002E0F197 Unknown Unknown > Unknown > > xgca 0000000002DC5B24 Unknown Unknown > Unknown > > xgca 0000000002DC5936 Unknown Unknown > Unknown > > xgca 0000000002D59C64 Unknown Unknown > Unknown > > xgca 0000000002D60BE1 Unknown Unknown > Unknown > > xgca 00000000015217D0 Unknown Unknown > Unknown > > xgca 000000000152178B Unknown Unknown > Unknown > > xgca 0000000002E32271 Unknown Unknown > Unknown > > xgca 0000000002BDCE52 Unknown Unknown > Unknown > > xgca 0000000002BACDE3 Unknown Unknown > Unknown > > xgca 0000000000A6DAB9 Unknown Unknown > Unknown > > xgca 0000000000A6D394 Unknown Unknown > Unknown > > xgca 00000000015217D0 Unknown Unknown > Unknown > > xgca 00000000008BEE48 Unknown Unknown > Unknown > > xgca 00000000008BE456 Unknown Unknown > Unknown > > xgca 0000000000F0E10F Unknown Unknown > Unknown > > xgca 0000000000F0A1F2 Unknown Unknown > Unknown > > xgca 0000000000A373F2 Unknown Unknown > Unknown > > xgca 0000000000581957 petsc_lu_solver_ 973 > collisionf2.F90 > > xgca 000000000057EB05 col_f_picard_step 372 > collisionf2.F90 > > xgca 0000000000564D6A col_f_core_s_ 945 > collisionf.F90 > > xgca 000000000056325F f_collision_singl 254 > collisionf.F90 > > xgca 0000000000560409 f_collision_singl 350 > collisionf.F90 > > xgca 0000000002B1EF43 Unknown UnLinear > col_f_ solve converged due to CONVERGED_RTOL iterations 1 > > Linear col_f_ solve converged due to CONVERGED_RTOL iterations 1 > > Linear col_f_ solve converged due to CONVERGED_RTOL iterations 1 > > known Unknown > > > > > > On Sat, Feb 21, 2015 at 12:30 PM, Barry Smith <bsm...@mcs.anl.gov> > wrote: > > > > barry/threadsafety-kspconvergedreason-kspmonitor > > > > Note that as always the monitoring and converged reasons for the various > threads will be printed jumbled up > > > > In your own code make sure that any routines that use the default > viewers (like stdout) are in a omp critical section > > > > Barry > > > > > On Feb 20, 2015, at 8:22 PM, Mark Adams <mfad...@lbl.gov> wrote: > > > > > > OK, I have a code setup to test it so feel free to make branch and I > can test it. > > > Mark > > > > > > On Fri, Feb 20, 2015 at 7:13 PM, Barry Smith <bsm...@mcs.anl.gov> > wrote: > > > > > > Mark, > > > > > > Yes, after looking at the code it does make sense. The reason is > that Matt made me "improve" the -xxx_converged_reason to use viewers; but > in your case there will be multiple threads (each associated with different > KSP objects) each monkeying with the same (default) viewer thus possibly > corrupting it. > > > > > > I'll have to think a little bit about the best way to keep the > functionality but be thread safe. > > > > > > Barry > > > > > > > On Feb 20, 2015, at 5:57 PM, Mark Adams <mfad...@lbl.gov> wrote: > > > > > > > > Barry, > > > > > > > > We had a problem with the thread safe version and found, by pure > luck, that apparently if we use -ksp_converged_reason we get segv type > failure. Does this sound sensible? > > > > > > > > I can give you an executable and environment the run this on Edison > if that is useful. > > > > > > > > Thanks, > > > > Mark > > > > > > > > > > > > On Tue, Feb 17, 2015 at 9:27 PM, Barry Smith <bsm...@mcs.anl.gov> > wrote: > > > > > > > > You need to configure with --with-threadsafety and --with-log=0 > and --with-debugging=0 > > > > > > > > Eventually we'll support at least the debugging with thread safety. > > > > > > > > Barry > > > > > > > > Not sure about that strange message from the cray system. > > > > > > > > > > > > > On Feb 17, 2015, at 8:14 PM, Mark Adams <mfad...@lbl.gov> wrote: > > > > > > > > > > We have been testing master with a code that calls PETSc serial LU > solvers from threads. I have seen system messages with OMP (see way below) > and Robert (cc'ed) reported this useful stack trace. > > > > > > > > > > I have not modified my (non-thread) build. Perhaps I need to or > are there PETSc runtime options? > > > > > > > > > > This is a Cray XC30 with Intel. > > > > > > > > > > Thanks, > > > > > Mark > > > > > > > > > > SC[0;39mESC[0;49m[116]PETSC ERROR: Object is in wrong state > > > > > [116]PETSC ERROR: Logging event had unbalanced begin/end pairs > > > > > [116]PETSC ERROR: See > http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > > > > > [116]PETSC ERROR: Petsc Development GIT revision: > v3.5.3-1570-gcaf1481 GIT Date: 2015-02-07 17:34:17 -0600 > > > > > [116]PETSC ERROR: ./xgca_petsc36_col on a arch-xc30-opt64-intel > named nid05975 by rhager Tue Feb 17 10:46:32 2015 > > > > > [116]PETSC ERROR: Configure options --COPTFLAGS="-fast -no-ipo" > --CXXOPTFLAGS="-fast -no-ipoi" --FOPTFLAGS="-fast -no-ipo" --download-hypre > --download-superlu_dist -- > > > > > download-parmetis --download-metis --with-ssl=0 --with-cc=cc > --with-clib-autodetect=0 --with-cxx=CC --with-cxxlib-autodetect=0 > --with-debugging=0 --with-fc=ftn --with > > > > > -fortranlib-autodetect=0 > --with-hdf5-dir=/opt/cray/hdf5-parallel/1.8.13/intel/140/ > --with-shared-libraries=0 --with-x=0 --with-mpiexec=aprun LIBS=-lstdc++ > --with-64-b > > > > > it-indices PETSC_ARCH=arch-xc30-opt64-intel > PETSC_DIR=/global/u2/m/madams/petsc_master > > > > > [116]PETSC ERROR: #1 PetscLogEventEndDefault() line 694 in > /global/u2/m/madams/petsc_master/src/sys/logging/utils/eventlog.c > > > > > [116]PETSC ERROR: #2 MatLUFactorSymbolic() line 2894 in > /global/u2/m/madams/petsc_master/src/mat/interface/matrix.c > > > > > [116]PETSC ERROR: #3 PCSetUp_LU() line 127 in > /global/u2/m/madams/petsc_master/src/ksp/pc/impls/factor/lu/lu.c > > > > > [116]PETSC ERROR: #4 PCSetUp() line 918 in > /global/u2/m/madams/petsc_master/src/ksp/pc/interface/precon.c > > > > > [116]PETSC ERROR: #5 KSPSetUp() line 306 in > /global/u2/m/madams/petsc_master/src/ksp/ksp/interface/itfunc.c > > > > > [116]PETSC ERROR: #6 KSPSolve() line 503 in > /global/u2/m/madams/petsc_master/src/ksp/ksp/interface/itfunc.c > > > > > > > > > > > > > > > Other error message: > > > > > > > > > > > > > > > OMP: Error #13: Assertion failure at kmp_runtime.c(1588). > > > > > OMP: Hint: Please submit a bug report with this message, compile > and run commands used, and machine configuration info including native > compiler and operating system versions. Faster response will be obtained by > including all program sources. For information on submitting this issue, > please see http://www.intel.com/software/products/support/. > > > > > _pmiu_daemon(SIGCHLD): [NID 05979] [c7-3c0s6n3] [Tue Feb 17 > 15:14:43 2015] PE RANK 23 exit signal Killed > > > > > _pmiu_daemon(SIGCHLD): [NID 05976] [c7-3c0s6n0] [Tue Feb 17 > 15:14:43 2015] PE RANK 10 exit signal Killed > > > > > [NID 05979] 2015-02-17 15:14:43 Apid 10147992: initiated > application termination > > > > > [NID 05979] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 239]. Please contact admin for details. Killing > pid 18637(xgca) > > > > > [NID 05976] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 73]. Please contact admin for details. Killing > pid 15380(xgca) > > > > > [NID 05984] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 34636(xgca) > > > > > [NID 05988] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 59]. Please contact admin for details. Killing > pid 38496(xgca) > > > > > [NID 06019] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 11132(xgca) > > > > > [NID 05980] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 8320(xgca) > > > > > [NID 05993] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 46182(xgca) > > > > > [NID 06020] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 249]. Please contact admin for details. Killing > pid 23753(xgca) > > > > > [NID 05987] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 87]. Please contact admin for details. Killing > pid 11254(xgca) > > > > > [NID 05986] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 41]. Please contact admin for details. Killing > pid 6630(xgca) > > > > > [NID 05981] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 31]. Please contact admin for details. Killing > pid 10520(xgca) > > > > > [NID 05999] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 7]. Please contact admin for details. Killing > pid 1843(xgca) > > > > > [NID 05985] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 26498(xgca) > > > > > [NID 05998] 2015-02-17 15:14:43 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 209]. Please contact admin for details. Killing > pid 20387(xgca) > > > > > [NID 05994] 2015-02-17 15:14:53 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 39462(xgca) > > > > > [NID 05983] 2015-02-17 15:14:53 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 18598(xgca) > > > > > [NID 05995] 2015-02-17 15:14:54 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 42322(xgca) > > > > > [NID 05996] 2015-02-17 15:14:54 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 34248(xgca) > > > > > [NID 05978] 2015-02-17 15:14:55 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 9483(xgca) > > > > > [NID 05975] 2015-02-17 15:14:56 Apid 10147992: Cray HSN detected > critical error 0x4416[ptag 0]. Please contact admin for details. Killing > pid 11470(xgca) > > > > > Application 10147992 exit codes: 137 > > > > > Application 10147992 exit signals: Killed > > > > > Application 10147992 resources: utime ~2194s, stime ~199s, Rss > ~488560, inblocks ~908164, outblocks ~2571652 > > > > > > > > > > > > > > > > > > > > > > > > >
