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*//*
*/
--
Thank you
Yours sincerely,
TAY wee-beng
