search

CISM / cism-documentation

Source code for documentation for CISM. The acual documentation can be found at https://cism.github.io/data/cism_documentation_v2_1.pdf
0 stars 1 forks source link

uofcalgary-CISM #3

Open uofcalgary opened 8 years ago

uofcalgary commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

@uofcalgary , can you list the following:

uofcalgary commented 8 years ago

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 commented 8 years ago

@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 commented 8 years ago

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 commented 8 years ago

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.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/CISM/cism-documentation/issues/3#issuecomment-243867622, or mute the thread https://github.com/notifications/unsubscribe-auth/AD_QEn7PUeHcNXd5-HN-R50hrZhYinKbks5qldCNgaJpZM4Jv-kd .