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<p>Dear all,</p>
<p>I have emailed the K computer helpdesk and they have given their
reply:</p>
<p><i><b>This is HPCI helpdesk.
</b></i><i><b><br>
</b></i>
<i><b><br>
</b></i><i><b>Sorry for making you wait.
</b></i><i><b><br>
</b></i><i><b>We have received the investigation results from
Operation Division.
</b></i><i><b><br>
</b></i>
<i><b><br>
</b></i><i><b>The cause of SIGSEGV by the Fujitsu compiler is
that the implementation of
</b></i><i><b><br>
</b></i><i><b>the Fortran pointer is different from the
Intel/GNU compiler.
</b></i><i><b><br>
</b></i>
<i><b><br>
</b></i><i><b>In the Fujitsu compiler, interoperability of the
Fortran pointer and C language
</b></i><i><b><br>
</b></i><i><b>is implemented by the Fortran pointer interface of
Fujitsu.
</b></i><i><b><br>
</b></i><i><b>* The implementation of the Fortran pointer is
processor-dependent.*
</b></i><i><b><br>
</b></i>
<i><b><br>
</b></i><i><b>On the other hand, PETSc is implemented assuming
of the Fortran pointer interface of
</b></i><i><b><br>
</b></i><i><b>the Intel/GNU compiler.
</b></i><i><b><br>
</b></i>
<i><b><br>
</b></i><i><b>The PETSc routine cannot correctly interpret the
Fortran pointer of Fujitsu
</b></i><i><b><br>
</b></i><i><b>because the implementation of the Fortran pointer
of the Fujitsu compiler
</b></i><i><b><br>
</b></i><i><b>and the Intel/GNU compiler is different, and it
terminates abnormally at execution.
</b></i><i><b><br>
</b></i>
<i><b><br>
</b></i><i><b>Please avoid the use of the Fortran pointer as a
workaround.
</b></i><i><b><br>
</b></i>
<i><b><br>
</b></i><i><b>The sample program of PETSc which does not use the
Fotran pointer (ex4f etc.)
</b></i><i><b><br>
</b></i><i><b>runs normaly without getting SIGSEGV.
</b></i></p>
<p>Hence, they advice avoiding the use of pointers. I made use of
VecGetArrayF90 but I believe I can also use VecGetArray.</p>
<p>But what about DMDAVecGetArrayF90 and DMDAVecRestoreArrayF90? Can
I use DMDAVecGetArray and DMDAVecRestoreArray instead in Fortran,
thus avoiding using pointers? I remember my segmentation fault
always happens when calling DMDAVecGetArrayF90 and
DMDAVecRestoreArrayF90.</p>
<p>In other words, can I use DMDA in Fortran w/o using any pointer?<br>
</p>
<p><br>
</p>
<pre class="moz-signature" cols="72">Thank you
Yours sincerely,
TAY wee-beng</pre>
<div class="moz-cite-prefix">On 10/6/2016 11:00 AM, Barry Smith
wrote:<br>
</div>
<blockquote
cite="mid:6E84C554-39F0-4BB6-92D0-D2443BA79989@mcs.anl.gov"
type="cite">
<pre wrap="">
Without knowing the specifics of how this machine's Fortran compiler passes Fortran pointers to subroutines we cannot resolve this problem. This information can only be obtained from the experts on the this machine.
Barry
</pre>
<blockquote type="cite">
<pre wrap="">On Jun 9, 2016, at 9:28 PM, TAY wee-beng <a class="moz-txt-link-rfc2396E" href="mailto:zonexo@gmail.com"><zonexo@gmail.com></a> wrote:
Hi,
The current solution cannot work. May I know if there's any other solution to try. Meanwhile, I've also email the K computer helpdesk for help.
Thank you
Yours sincerely,
TAY wee-beng
On 3/6/2016 10:33 PM, Satish Balay wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Sorry - I'm not sure whats hapenning with this compiler.
[for a build without the patch I sent ] - can you edit
PETSC_ARCH/include/petscconf.h and remove the lines
#ifndef PETSC_HAVE_F90_2PTR_ARG
#define PETSC_HAVE_F90_2PTR_ARG 1
#endif
And then build the libraries [do not run configure again].
Does this make a difference for this example?
Satish
On Fri, 3 Jun 2016, TAY wee-beng wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
Is there any update to the issue below?
No hurry, just to make sure that the email is sent successfully.
Thanks
-------- Forwarded Message --------
Subject: Re: [petsc-users] Error with PETSc on K computer
Date: Thu, 2 Jun 2016 10:25:22 +0800
From: TAY wee-beng <a class="moz-txt-link-rfc2396E" href="mailto:zonexo@gmail.com"><zonexo@gmail.com></a>
To: petsc-users <a class="moz-txt-link-rfc2396E" href="mailto:petsc-users@mcs.anl.gov"><petsc-users@mcs.anl.gov></a>
Hi Satish,
The X9 option is :
Provides a different interpretation under Fortran 95 specifications
for any parts not conforming to the language specifications of this
compiler
I just patched and re-compiled but it still can't work. I've attached the
configure.log for both builds.
FYI, some parts of the PETSc 3.6.3 code were initially patch to make it work
with the K computer system:
$ diff -u petsc-3.6.3/config/BuildSystem/config/package.py.org
petsc-3.6.3/config/BuildSystem/config/package.py
--- petsc-3.6.3/config/BuildSystem/config/package.py.org 2015-12-04
14:06:42.000000000 +0900
+++ petsc-3.6.3/config/BuildSystem/config/package.py 2016-01-22
11:09:37.000000000 +0900
@@ -174,7 +174,7 @@
return ''
def getSharedFlag(self,cflags):
- for flag in ['-PIC', '-fPIC', '-KPIC', '-qpic']:
+ for flag in ['-KPIC', '-fPIC', '-PIC', '-qpic']:
if cflags.find(flag) >=0: return flag
return ''
$ diff -u petsc-3.6.3/config/BuildSystem/config/setCompilers.py.org
petsc-3.6.3/config/BuildSystem/config/setCompilers.py
--- petsc-3.6.3/config/BuildSystem/config/setCompilers.py.org 2015-07-23
00:22:46.000000000 +0900
+++ petsc-3.6.3/config/BuildSystem/config/setCompilers.py 2016-01-22
11:10:05.000000000 +0900
@@ -1017,7 +1017,7 @@
self.pushLanguage(language)
#different compilers are sensitive to the order of testing these
flags. So separete out GCC test.
if config.setCompilers.Configure.isGNU(self.getCompiler()): testFlags =
['-fPIC']
- else: testFlags = ['-PIC', '-fPIC', '-KPIC','-qpic']
+ else: testFlags = ['-KPIC', '-fPIC', '-PIC','-qpic']
for testFlag in testFlags:
try:
self.logPrint('Trying '+language+' compiler flag '+testFlag)
$ diff -u petsc-3.6.3/config/BuildSystem/config/packages/openmp.py.org
petsc-3.6.3/config/BuildSystem/config/packages/openmp.py
--- petsc-3.6.3/config/BuildSystem/config/packages/openmp.py.org 2016-01-25
15:42:23.000000000+0900
+++ petsc-3.6.3/config/BuildSystem/config/packages/openmp.py 2016-01-22
17:13:52.000000000 +0900
@@ -19,7 +19,8 @@
self.found = 0
self.setCompilers.pushLanguage('C')
#
- for flag in ["-fopenmp", # Gnu
+ for flag in ["-Kopenmp", # Fujitsu
+ "-fopenmp", # Gnu
"-qsmp=omp",# IBM XL C/C++
"-h omp", # Cray. Must come after XL because XL
interprets this option as meaning"-soname omp"
"-mp", # Portland Group
$ diff -u ./petsc-3.6.3/config/BuildSystem/config/compilers.py.org
./petsc-3.6.3/config/BuildSystem/config/compilers.py
--- ./petsc-3.6.3/config/BuildSystem/config/compilers.py.org 2015-06-10
06:24:49.000000000 +0900
+++ ./petsc-3.6.3/config/BuildSystem/config/compilers.py 2016-02-19
11:56:12.000000000 +0900
@@ -164,7 +164,7 @@
def checkCLibraries(self):
'''Determines the libraries needed to link with C'''
oldFlags = self.setCompilers.LDFLAGS
- self.setCompilers.LDFLAGS += ' -v'
+ self.setCompilers.LDFLAGS += ' -###'
self.pushLanguage('C')
(output, returnCode) = self.outputLink('', '')
self.setCompilers.LDFLAGS = oldFlags
@@ -413,7 +413,7 @@
def checkCxxLibraries(self):
'''Determines the libraries needed to link with C++'''
oldFlags = self.setCompilers.LDFLAGS
- self.setCompilers.LDFLAGS += ' -v'
+ self.setCompilers.LDFLAGS += ' -###'
self.pushLanguage('Cxx')
(output, returnCode) = self.outputLink('', '')
self.setCompilers.LDFLAGS = oldFlags
Thank you
Yours sincerely,
TAY wee-beng
On 2/6/2016 3:18 AM, Satish Balay wrote:
</pre>
<blockquote type="cite">
<pre wrap="">What does -X9 in --FFLAGS="-X9 -O0" do?
can you send configure.log for this build?
And does the attached patch make a difference with this example?
[suggest doing a separate temporary build of PETSc - in a different source
location - to check this.]
Satish
On Wed, 1 Jun 2016, TAY wee-beng wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Satish,
Only partially working:
[t00196@b04-036 tutorials]$ mpiexec -n 2 ./ex4f90
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.
Vec Object:Vec Object:initial vector:initial vector: 1 MPI processes
type: seq
10
20
30
40
50
60
1 MPI processes
type: seq
10
20
30
40
50
60
[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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>
[1]PETSC ERROR: or tryhttp://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] F90Array1dCreate line 50
/.global/volume2/home/hp150306/t00196/source/petsc-3.6.3/src/sys/f90-src/f90_cwrap.c
[1]PETSC ERROR: --------------------- Error Message
------------------------------------------[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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>
[0]PETSC ERROR: or tryhttp://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] F90Array1dCreate line 50
/.global/volume2/home/hp150306/t00196/source/petsc-3.6.3/src/sys/f90-src/f90_cwrap.c
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: Signal received
[1]PETSC ERROR: Seehttp://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: ./ex4f90 on a petsc-3.6.3_debug named b04-036 by Unknown
Wed
Jun 1 13:23:41 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 in unknown file
--------------------------------------------------------------------------
[mpi::mpi-api::mpi-abort]
MPI_ABORT was invoked on rank 1 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.
--------------------------------------------------------------------------
[b04-036:28998]
/opt/FJSVtclang/GM-1.2.0-20/lib64/libmpi.so.0(orte_errmgr_base_error_abort+0x84)
[0xffffffff11360404]
[b04-036:28998]
/opt/FJSVtclang/GM-1.2.0-20/lib64/libmpi.so.0(ompi_mpi_abort+0x51c)
[0xffffffff1110391c]
[b04-036:28998]
/opt/FJSVtclang/GM-1.2.0-20/lib64/libmpi.so.0(MPI_Abort+0x6c)
[0xffffffff1111b5ec]
[b04-036:28998]
/opt/FJSVtclang/GM-1.2.0-20/lib64/libtrtmet_c.so.1(MPI_Abort+0x2c)
[0xffffffff00281bf0]
[b04-036:28998] ./ex4f90 [0x292548]
[b04-036:28998] ./ex4f90 [0x29165c]
[b04-036:28998]
/opt/FJSVxosmmm/lib64/libmpgpthread.so.1(_IO_funlockfile+0x5c)
[0xffffffff121e1974]
[b04-036:28998] ./ex4f90 [0x9f6748]
[b04-036:28998] ./ex4f90 [0x9f0ea4]
[b04-036:28998] ./ex4f90 [0x2c76a0]
[b04-036:28998] ./ex4f90(MAIN__+0x38c) [0x10688c]
[b04-036:28998] ./ex4f90(main+0xec) [0x268e91c]
[b04-036:28998] /lib64/libc.so.6(__libc_start_main+0x194)
[0xffffffff138cb81c]
[b04-036:28998] ./ex4f90 [0x1063ac]
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch
system) has told this process to end
[1]PETSC ERROR: Tr--------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: Seehttp://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: ./ex4f90 on a petsc-3.6.3_debug named b04-036 by Unknown
Wed
Jun 1 13:23:41 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
--------------------------------------------------------------------------
[mpi::mpi-api::mpi-abort]
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.
--------------------------------------------------------------------------
[b04-036:28997]
/opt/FJSVtclang/GM-1.2.0-20/lib64/libmpi.so.0(orte_errmgr_base_error_abort+0x84)
[0xffffffff11360404]
[b04-036:28997]
/opt/FJSVtclang/GM-1.2.0-20/lib64/libmpi.so.0(ompi_mpi_abort+0x51c)
[0xffffffff1110391c]
[b04-036:28997]
/opt/FJSVtclang/GM-1.2.0-20/lib64/libmpi.so.0(MPI_Abort+0x6c)
[0xffffffff1111b5ec]
[b04-036:28997]
/opt/FJSVtclang/GM-1.2.0-20/lib64/libtrtmet_c.so.1(MPI_Abort+0x2c)
[0xffffffff00281bf0]
[b04-036:28997] ./ex4f90 [0x292548]
[b04-036:28997] ./ex4f90 [0x29165c]
[b04-036:28997]
/opt/FJSVxosmmm/lib64/libmpgpthread.so.1(_IO_funlockfile+0x5c)
[0xffffffff121e1974]
[b04-036:28997] ./ex4f90 [0x9f6748]
[b04-036:28997] ./ex4f90 [0x9f0ea4]
[b04-036:28997] ./ex4f90 [0x2c76a0]
[b04-036:28997] ./ex4f90(MAIN__+0x38c) [0x10688c]
[b04-036:28997] ./ex4f90(main+0xec) [0x268e91c]
[b04-036:28997] /lib64/libc.so.6(__libc_start_main+0x194)
[0xffffffff138cb81c]
[b04-036:28997] ./ex4f90 [0x1063ac]
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch
system) has told this process to end
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>
[0]PETSC ERROR: or tryhttp://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] F90Array1dCreate line 50
/.global/volume2/home/hp150306/t00196/source/petsc-3.6.3/src/sys/f90-src/f90_cwrap.c
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: Seehttp://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: ./ex4f90 on a petsc-3.6.3_debug named b04-036 by Unknown
Wed
Jun 1 13:23:41 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-debuy option -start_in_debugger or
-on_error_attach_debugger
[1]PETSC ERROR: or see
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>
[1]PETSC ERROR: or tryhttp://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] F90Array1dCreate line 50
/.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: Seehttp://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: ./ex4f90 on a petsc-3.6.3_debug named b04-036 by Unknown
Wed
Jun 1 13:23:41 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: #2 User provided function() line 0 in unknown file
gging=1 --useThreads=0 --with-hypre=1
--with-hypre-dir=/home/hp150306/t00196/lib/hypre-2.10.0b-p4
[0]PETSC ERROR: #2 User provided function() line 0 in unknown file
[ERR.] PLE 0019 plexec One of MPI processes was
aborted.(rank=0)(nid=0x04180034)(CODE=1938,793745140674134016,15104)
[t00196@b04-036 tutorials]$
[ERR.] PLE 0021 plexec The interactive job has aborted with the
signal.(sig=24)
[INFO] PJM 0083 pjsub Interactive job 5211401 completed.
Thank you
Yours sincerely,
TAY wee-beng
On 1/6/2016 12:21 PM, Satish Balay wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Do PETSc examples using VecGetArrayF90() work?
say src/vec/vec/examples/tutorials/ex4f90.F
Satish
On Tue, 31 May 2016, TAY wee-beng wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*</a>
*//*[1]PETSC ERROR: or tryhttp://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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*</a>
*//*[3]PETSC ERROR: or tryhttp://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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*</a>
*//*[0]PETSC ERROR: or tryhttp://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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*</a>
*//*[2]PETSC ERROR: or tryhttp://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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*</a>
*//*[0]PETSC ERROR: or tryhttp://valgrind.org on GNU/linux and Apple
Mac
OS X
to find memory corruption errors*//*
*//*[1]PETSC ERROR: or see
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind*//*</a>
*//*[1]PETSC ERROR: or tryhttp://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
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
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*//*
*/
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