Do PETSc examples using VecGetArrayF90() work? say src/vec/vec/examples/tutorials/ex4f90.F
Satish On Tue, 31 May 2016, TAY wee-beng wrote: > Hi, > > I'm trying to run my MPI CFD code on Japan's K computer. My code can run if I > didn't make use of the PETSc DMDAVecGetArrayF90 subroutine. If it's called > > call DMDAVecGetArrayF90(da_u,u_local,u_array,ierr) > > I get the error below. I have no problem with my code on other clusters using > the new Intel compilers. I used to have problems with DM when using the old > Intel compilers. Now on the K computer, I'm using Fujitsu's Fortran compiler. > How can I troubleshoot? > > Btw, I also tested on the ex13f90 example and it didn't work too. The error is > below. > > > My code error: > > /* size_x,size_y,size_z 76x130x136*//* > *//* total grid size = 1343680*//* > *//* recommended cores (50k / core) = 26.87360000000000*//* > *//* 0*//* > *//* 1*//* > *//* 1*//* > *//*[3]PETSC ERROR: [1]PETSC ERROR: > ------------------------------------------------------------------------*//* > *//*[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range*//* > *//*[1]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger*//* > *//*[1]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//* > *//*[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X > to find memory corruption errors*//* > *//*[1]PETSC ERROR: likely location of problem given in stack below*//* > *//*[1]PETSC ERROR: --------------------- Stack Frames > ------------------------------------*//* > *//*[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available,*//* > *//*[1]PETSC ERROR: INSTEAD the line number of the start of the > function*//* > *//*[1]PETSC ERROR: is given.*//* > *//*[1]PETSC ERROR: [1] F90Array3dCreate line 244 > /.global/volume2/home/hp150306/t00196/source/petsc-3.6.3/src/sys/f90-src/f90_cwrap.c*//* > *//* 1*//* > *//*------------------------------------------------------------------------*//* > *//*[3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range*//* > *//*[3]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger*//* > *//*[3]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//* > *//*[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X > to find memory corruption errors*//* > *//*[3]PETSC ERROR: likely location of problem given in stack below*//* > *//*[3]PETSC ERROR: --------------------- Stack Frames > ------------------------------------*//* > *//*[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: [0] F90Array3dCreate line 244 > /.global/volume2/home/hp150306/t00196/source/petsc-3.6.3/src/sys/f90-src/f90_cwrap.c*//* > *//*[0]PETSC ERROR: --------------------- Error Message > ----------------------------------------- 1*//* > *//*[2]PETSC ERROR: > ------------------------------------------------------------------------*//* > *//*[2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range*//* > *//*[2]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger*//* > *//*[2]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//* > *//*[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X > to find memory corruption errors*//* > *//*[2]PETSC ERROR: likely location of problem given in stack below*//* > *//*[2]PETSC ERROR: --------------------- Stack Frames > ------------------------------------*//* > *//*[2]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available,*//* > *//*[2]PETSC ERROR: INSTEAD the line number of the start of the > function*//* > *//*[2]PETSC ERROR: is given.*//* > *//*[2]PETSC ERROR: [2] F90Array3dCreate line 244 > /.global/volume2/home/hp150306/t00196/source/petsc-3.6.3/src/sys/f90-src/f90_cwrap.c*//* > *//*[2]PETSC ERROR: --------------------- Error Message > -----------------------------------------[3]PETSC ERROR: Note: The EXACT line > numbers in the stack are not available,*//* > *//*[3]PETSC ERROR: INSTEAD the line number of the start of the > function*//* > *//*[3]PETSC ERROR: is given.*//* > *//*[3]PETSC ERROR: [3] F90Array3dCreate line 244 > /.global/volume2/home/hp150306/t00196/source/petsc-3.6.3/src/sys/f90-src/f90_cwrap.c*//* > *//*[3]PETSC ERROR: --------------------- Error Message > --------------------------------------------------------------*//* > *//*[3]PETSC ERROR: Signal received*//* > *//*[3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting.*//* > *//*[3]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015*//* > *//*[3]PETSC ERROR: ./a-debug.out on a petsc-3.6.3_debug named b04-036 by > Unknown Wed Jun 1 12:54:34 2016*//* > *//*[3]PETSC ERROR: Configure options --with-cc=mpifcc --with-cxx=mpiFCC > --with-fc=mpifrt --with-64-bit-pointers=1 --CC=mpifcc --CFLAGS="-Xg -O0" > --CXX=mpiFCC --CXXFLAGS="-Xg -O0" --FC=mpifrt --FFLAGS="-X9 -O0" --LD_SHARED= > --LDDFLAGS= --with-openmp=1 --with-mpiexec=mpiexec --known-endian=big > --with-shared----------------------*//* > *//*[0]PETSC ERROR: Signal received*//* > *//*[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting.*//* > *//*[0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015*//* > *//*[0]PETSC ERROR: ./a-debug.out on a petsc-3.6.3_debug named b04-036 by > Unknown Wed Jun 1 12:54:34 2016*//* > *//*[0]PETSC ERROR: Configure options --with-cc=mpifcc --with-cxx=mpiFCC > --with-fc=mpifrt --with-64-bit-pointers=1 --CC=mpifcc --CFLAGS="-Xg -O0" > --CXX=mpiFCC --CXXFLAGS="-Xg -O0" --FC=mpifrt --FFLAGS="-X9 -O0" --LD_SHARED= > --LDDFLAGS= --with-openmp=1 --with-mpiexec=mpiexec --known-endian=big > --with-shared-libraries=0 --with-blas-lapack-lib=-SSL2 > --with-scalapack-lib=-SCALAPACK > --prefix=/home/hp150306/t00196/lib/petsc-3.6.3_debug > --with-fortran-interfaces=1 --with-debugging=1 --useThreads=0 --with-hypre=1 > --with-hypre-dir=/home/hp150306/t00196/lib/hypre-2.10.0b-p4*//* > *//*[0]PETSC ERROR: #1 User provided function() line 0 in unknown file*//* > *//*--------------------------------------------------------------------------*//* > *//*[m---------------------*//* > *//*[2]PETSC ERROR: Signal received*//* > *//*[2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting.*//* > *//*[2]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015*//* > *//*[2]PETSC ERROR: ./a-debug.out on a petsc-3.6.3_debug named b04-036 by > Unknown Wed Jun 1 12:54:34 2016*//* > *//*[2]PETSC ERROR: Configure options --with-cc=mpifcc --with-cxx=mpiFCC > --with-fc=mpifrt --with-64-bit-pointers=1 --CC=mpifcc --CFLAGS="-Xg -O0" > --CXX=mpiFCC --CXXFLAGS="-Xg -O0" --FC=mpifrt --FFLAGS="-X9 -O0" --LD_SHARED= > --LDDFLAGS= --with-openmp=1 --with-mpiexec=mpiexec --known-endian=big > --with-shared-libraries=0 --with-blas-lapack-lib=-SSL2 > --with-scalapack-lib=-SCALAPACK > --prefix=/home/hp150306/t00196/lib/petsc-3.6.3_debug > --with-fortran-interfaces=1 --with-debugging=1 --useThreads=0 --with-hypre=1 > --with-hypre-dir=/home/hp150306/t00196/lib/hypre-2.10.0b-p4*//* > *//*[2]PETSC ERROR: #1 User provided function() line 0 in unknown file*//* > *//*--------------------------------------------------------------------------*//* > *//*[m[1]PETSC ERROR: --------------------- Error Message > --------------------------------------------------------------*//* > *//*[1]PETSC ERROR: Signal received*//* > *//*[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting.*//* > *//*[1]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015*//* > *//*[1]PETSC ERROR: ./a-debug.out on a petsc-3.6.3_debug named b04-036 by > Unknown Wed Jun 1 12:54:34 2016*//* > *//*[1]PETSC ERROR: Configure options --with-cc=mpifcc --with-cxx=mpiFCC > --with-fc=mpifrt --with-64-bit-pointers=1 --CC=mpifcc --CFLAGS="-Xg -O0" > --CXX=mpiFCC --CXXFLAGS="-Xg -O0" --FC=mpifrt --FFLAGS="-X9 -O0" --LD_SHARED= > --LDDFLAGS= --with-openmp=1 --with-mpiexec=mpiexec --known-endian=big > --with-shared-libraries=0 --with-blas-lapack-lib=-SSL2 > --with-scalapack-lib=-SCALAPACK > --prefix=/home/hp150306/t00196/lib/petsc-3.6.3_debug > --with-fortran-interfaces=1 --with-debugging=1 --useThreads=0 --with-hypre=1 > --with-hypre-dir=/home/hp150306/t00196/lib/hypre-2.10.0b-p4*//* > *//*[1]PETSC ERROR: #1 User provided function() line 0 ilibraries=0 > --with-blas-lapack-lib=-SSL2 --with-scalapack-lib=-SCALAPACK > --prefix=/home/hp150306/t00196/lib/petsc-3.6.3_debug > --with-fortran-interfaces=1 --with-debugging=1 --useThreads=0 --with-hypre=1 > --with-hypre-dir=/home/hp150306/t00196/lib/hypre-2.10.0b-p4*//* > *//*[3]PETSC ERROR: #1 User provided function() line 0 in unknown file*//* > *//*--------------------------------------------------------------------------*//* > *//*[mpi::mpi-api::mpi-abort]*//* > *//*MPI_ABORT was invoked on rank 3 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.*//* > *//*--------------------------------------------------------------------------*//* > *//*[b04-036:28416] > /opt/FJSVtclang/GM-1.2.0-20/lib64/libmpi.so.0(orte_errmgr_base_error_abort+0x84) > [0xffffffff11360404]*//* > *//*[b04-036:28416] > /opt/FJSVtclang/GM-1.2.0-20/lib64/libmpi.so.0(ompi_mpi_abort+0x51c) > [0xffffffff1110391c]*//* > *//*[b04-036:28416] /opt/FJSVtclang/GM-1.2.0-2pi::mpi-api::mpi-abort]*//* > *//*MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD*//* > *//*with errorcode 59.*/ > > ex13f90 error: > > > /*[t00196@b04-036 tutorials]$ mpiexec -np 2 ./ex13f90*//* > *//*jwe1050i-w The hardware barrier couldn't be used and continues processing > using the software barrier.*//* > *//*taken to (standard) corrective action, execution continuing.*//* > *//*jwe1050i-w The hardware barrier couldn't be used and continues processing > using the software barrier.*//* > *//*taken to (standard) corrective action, execution continuing.*//* > *//* Hi! We're solving van der Pol using 2 processes.*//* > *//* > *//* t x1 x2*//* > *//*[1]PETSC ERROR: > ------------------------------------------------------------------------*//* > *//*[1]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal > memory access*//* > *//*[1]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger*//* > *//*[0]PETSC ERROR: > ------------------------------------------------------------------------*//* > *//*[0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal > memory access*//* > *//*[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*//* > *//*[1]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//* > *//*[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X > to find memory corruption errors*//* > *//*[1]PETSC ERROR: likely location of problem given in stack below*//* > *//*[1]PETSC ERROR: --------------------- Stack Frames > ------------------------------------*//* > *//*[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available,*//* > *//*[1]PETSC ERROR: INSTEAD the line number of the start of the > function*//* > *//*[1]PETSC ERROR: is given.*//* > *//*[1]PETSC ERROR: [1] F90Array4dCreate line 337 > /.global/volume2/home/hp150306/t00196/source/petsc-3.6.3/src/sys/f90-src/f90_cwrap.c*//* > *//*[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: [0] F90Array4dCreate line 337 > /.global/volume2/home/hp150306/t00196/source/petsc-3.6.3/src/sys/f90-src/f90_cwrap.c*//* > *//*[1]PETSC ERROR: --------------------- Error Message > --------------------------------------------------------------*//* > *//*[1]PETSC ERROR: Signal received*//* > *//*[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting.*//* > *//*[1]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015*//* > *//*[1]PETSC ERROR: ./ex13f90 on a petsc-3.6.3_debug named b04-036 by Unknown > Wed Jun 1 13:04:34 2016*//* > *//*[1]PETSC ERROR: Configure options --with-cc=mpifcc --with-cxx=mpiFCC > --with-fc=mpifrt --with-64-bit-pointers=1 --CC=mpifcc --CFLAGS="-Xg -O0" > --CXX=mpiFCC --CXXFLAGS="-Xg -O0" --FC=mpifrt --FFLAGS="-X9 -O0" --LD_SHARED= > --LDDFLAGS= --with-openmp=1 --with-mpiexec=mpiexec --known-endian=big > --with-shared-libraries=0 --with-blas-lapack-lib=-SSL2 > --with-scalapack-lib=-SCALAPACK > --prefix=/home/hp150306/t00196/lib/petsc-3.6.3_debug > --with-fortran-interfaces=1 --with-debugging=1 --useThreads=0 --with-hypre=1 > --with-hyp*//* > */ > > >
