uofcalgary-CISM

[uofcalgary]

Hi,
I'm working with remote computer (jasper-westgrid). when I run CISM, cism_driver ice_sheet.config, under a job script, I see an issue like this:

[kam1967@jasper jobs]$ cism_driver ice_sheet.config
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
cism_driver 000000000047FDAC Unknown Unknown Unknown
cism_driver 000000000048124F Unknown Unknown Unknown
cism_driver 000000000041E61A Unknown Unknown Unknown
cism_driver 000000000041DD95 Unknown Unknown Unknown
cism_driver 000000000041DBBC Unknown Unknown Unknown
libc.so.6 0000003BCEC1ED5D Unknown Unknown Unknown
cism_driver 000000000041DAB9 Unknown Unknown Unknown

what's the problem? can someone help me?

Thanks,
Kambiz

[stephenprice]

Can you please post your "ice_sheet.config.log" file? Also, it might be useful if you build and run in debug mode so that you have access to more useful debug output. It would also be helpful to have access to more information, like is this a parallel or serial build? What sort of platform and OS are you working on? What compilers / versions are you using?

[uofcalgary]

Hi Stephenprice,

The log file is a empty file (attached). this is a parallel build. I'm working on Linux and CISM 2.0.5.
how can I run in debug mode? let me know please.

Thanks, Kambiz

ice_sheet.config.log.txt

[stephenprice]

Are you building with an intel compiler? You might look at the first response at this link for a few compiler options that should give you more specific information as to where the error is occurring. Those compiler options would be included by editing the compile line in whatever build script you are currently using.

Also, you might try executing your run command on the command line first (vs. in a script) to see if it works, e.g.:

./cism_driver ./ice_sheet.config

... where you first make sure that "cism_driver" and "ice_sheet.config" are defined in the current directory you are trying to run from.

[matthewhoffman]

@uofcalgary , can you list the following:

• specific flavor of linux and version
• compiler and version
• netCDF library version
• attach a copy of the build script and/or build command you are using

[uofcalgary]

LSB Version :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description: CentOS release 6.6 (Final)
Release: 6.6
Codename: Final

Linux jasper.westgrid.ca 2.6.32-504.23.4.el6.x86_64 #1 SMP Tue Jun 9 20:57:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)

Linux version 2.6.32-504.23.4.el6.x86_64 (mockbuild@c6b9.bsys.dev.centos.org) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) ) #1 SMP Tue Jun 9 20:57:37 UTC 2015

netcdf library version 4.1.1 of Jan 30 2014 05:31:22 $

you can see the builds here:

cism-master.zip

[stephenprice]

@uofcalgary, it might be useful for us to see the other information that comes along with your build (presumably you are using some altered version of the "linux-gnu" build scripts?). Can you provide a link to the actual directory under the ./builds subdir, including all of the files that come along with the build process?

BTW, if you are using gcc, some additional debug options you might try including in your compilation line are listed here and here. You would add any of those options to this line of the build script (e.g., by altering line 52 of "linux-gnu-cmake":

-D CMAKE_Fortran_FLAGS="-g -O2 -ffree-line-length-none -fPIC -fno-range-check" \

One other thing to try right away would be to remove the '-O2' option and see if you see the same errors when building a non-optimized version of the code.

[uofcalgary]

Please take a look at the following on/off of some options:
CISM_BINARY_DIR:STATIC=/lustre/jasper/software-build6/cism/cism-2.0.5/builds/linux-gnu/build-parallel
CISM_BUILD_CISM_DRIVER:BOOL=ON
CISM_BUILD_EXTRA_EXECUTABLES:BOOL=OFF
CISM_BUILD_SIMPLE_GLIDE:BOOL=OFF
CISM_COUPLED:BOOL=OFF
CISM_ENABLE_BISICLES:BOOL=OFF
CISM_ENABLE_FELIX:UNINITIALIZED=OFF
CISM_EXTRA_LIBS:STRING=-mkl=sequential
CISM_FORCE_FORTRAN_LINKER:BOOL=OFF
CISM_GNU:BOOL=ON
CISM_INCLUDE_IMPLICIT_LINK_LIBRARIES:BOOL=ON
CISM_MPI_INC_DIR:UNINITIALIZED=/global/software/openmpi/openmpi-1.6.5-intel/include
CISM_MPI_LIB_DIR:UNINITIALIZED=/global/software/openmpi/openmpi-1.6.5-intel/lib
CISM_MPI_MODE:BOOL=ON
CISM_NETCDFF_FOUND:PATH=/global/software/netcdf/netcdf-4.1.3/lib
CISM_NETCDF_DIR:UNINITIALIZED=/global/software/netcdf/netcdf-4.1.3
CISM_NETCDF_LIBS:STRING=netcdff
CISM_NO_EXECUTABLE:BOOL=OFF
CISM_SERIAL_MODE:BOOL=OFF
CISM_SOURCEMOD_DIR:BOOL=OFF
CISM_SOURCE_DIR:STATIC=/lustre/jasper/software-build6/cism/cism-2.0.5
CISM_STATIC_LINKING:BOOL=OFF
CISM_TRILINOS_DIR:UNINITIALIZED=/global/software/trilinos/trilinos-12.6.3/
CISM_USE_DEFAULT_IO:BOOL=OFF
CISM_USE_GPTL_INSTRUMENTATION:BOOL=OFF
CISM_USE_MPI_WITH_SLAP:BOOL=OFF
CISM_USE_TRILINOS:BOOL=OFF
CMAKE_PROJECT_NAME:STATIC=CISM

what do you think? please let me know.

[matthewhoffman]

Another thing to try is doing a serial build and see if that fares any
better.

On Aug 31, 2016 1:05 PM, "uofcalgary" notifications@github.com wrote:

Please take a look at the following on/off of some options:
CISM_BINARY_DIR:STATIC=/lustre/jasper/software-build6/
cism/cism-2.0.5/builds/linux-gnu/build-parallel
CISM_BUILD_CISM_DRIVER:BOOL=ON
CISM_BUILD_EXTRA_EXECUTABLES:BOOL=OFF
CISM_BUILD_SIMPLE_GLIDE:BOOL=OFF
CISM_COUPLED:BOOL=OFF
CISM_ENABLE_BISICLES:BOOL=OFF
CISM_ENABLE_FELIX:UNINITIALIZED=OFF
CISM_EXTRA_LIBS:STRING=-mkl=sequential
CISM_FORCE_FORTRAN_LINKER:BOOL=OFF
CISM_GNU:BOOL=ON
CISM_INCLUDE_IMPLICIT_LINK_LIBRARIES:BOOL=ON
CISM_MPI_INC_DIR:UNINITIALIZED=/global/software/openmpi/openmpi-1.6.
5-intel/include
CISM_MPI_LIB_DIR:UNINITIALIZED=/global/software/openmpi/openmpi-1.6.
5-intel/lib
CISM_MPI_MODE:BOOL=ON
CISM_NETCDFF_FOUND:PATH=/global/software/netcdf/netcdf-4.1.3/lib
CISM_NETCDF_DIR:UNINITIALIZED=/global/software/netcdf/netcdf-4.1.3
CISM_NETCDF_LIBS:STRING=netcdff
CISM_NO_EXECUTABLE:BOOL=OFF
CISM_SERIAL_MODE:BOOL=OFF
CISM_SOURCEMOD_DIR:BOOL=OFF
CISM_SOURCE_DIR:STATIC=/lustre/jasper/software-build6/cism/cism-2.0.5
CISM_STATIC_LINKING:BOOL=OFF
CISM_TRILINOS_DIR:UNINITIALIZED=/global/software/trilinos/trilinos-12.6.3/
CISM_USE_DEFAULT_IO:BOOL=OFF
CISM_USE_GPTL_INSTRUMENTATION:BOOL=OFF
CISM_USE_MPI_WITH_SLAP:BOOL=OFF
CISM_USE_TRILINOS:BOOL=OFF
CMAKE_PROJECT_NAME:STATIC=CISM

what do you think? please let me know.

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