[FLASH-USERS] Running Flash4 with OpenMPI+Intel
Asif ud-Doula
auu4 at psu.edu
Sun May 26 12:06:50 EDT 2013
Thanks Michael,
I now compiled Sedov with -auto -2d flag, and using gdg I was able to
track the error to:
Program received signal SIGSEGV, Segmentation fault.
0x00000000005df429 in amr_refine_derefine () at
mpi_amr_refine_derefine.F90:489
489 level_cell_sizes(1:ndim,i) = .5*level_cell_sizes(1:ndim,i-1)
Asif
On 5/24/13 10:16 PM, Michael Sabino wrote:
> It looks like pointer memory allocation is failing for OpenMPI. I would
> try a different version of OpenMPI.
> Can you tell me what instruction it is attempting to execute at
> opal_memory_ptmalloc2_int_malloc()+(~0x260-0x2aa) and
> opal_memory_ptmalloc2_malloc+(~0x10-0x59)?
> You can enter the offset in hte, or use gdb.
>
> Http://hte(dot)sourceforge(dot)net
>
> Thanks,
>
> Michael Sabino
>
> On Fri, May 24, 2013 at 11:05 AM, Asif ud-Doula <auu4 at psu.edu
> <mailto:auu4 at psu.edu>> wrote:
>
> Hi Everyone,
> I am having some trouble running the latest version of Flash on
> linux cluster with OpenMPI 1.6.1 version along with Intel
> (composer_xe_2011_sp1.8.27). There seems to be some memory
> allocation issues. Note that it compiles just fine.
>
>
> I have tried the standard ./setup Sedov -auto -2d and tried to run
> it with e.g. 4 processes with flash.par virtually unchanged. Here is
> the error I receive when I run it in an interactive mode:
>
> RuntimeParameters_read: ignoring unknown parameter "order"...
> RuntimeParameters_read: ignoring unknown parameter "slopeLimiter"...
> RuntimeParameters_read: ignoring unknown parameter
> "LimitedSlopeBeta"...
> RuntimeParameters_read: ignoring unknown parameter "use_avisc"...
> RuntimeParameters_read: ignoring unknown parameter
> "use_flattening"...
> RuntimeParameters_read: ignoring unknown parameter "use_upwindTVD"...
> RuntimeParameters_read: ignoring unknown parameter "RiemannSolver"...
> RuntimeParameters_read: ignoring unknown parameter "entropy"...
> RuntimeParameters_read: ignoring unknown parameter "shockDetect"...
>
> flash4:27361 terminated with signal 11 at PC=2b66b15f539a
> SP=7fff34566480. Backtrace:
>
> flash4:27362 terminated with signal 11 at PC=2b506c4cd39a
> SP=7fffd1113480. Backtrace:
>
> flash4:27363 terminated with signal 11 at PC=2b812071539a
> SP=7fffd2f31780. Backtrace:
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1(opal___memory_ptmalloc2_int_malloc+__0x2aa)[0x2b506c4cd39a]
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1(opal___memory_ptmalloc2_int_malloc+__0x2aa)[0x2b812071539a]
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1(opal___memory_ptmalloc2_malloc+0x59)[__0x2b506c4d0659]
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1(opal___memory_ptmalloc2_malloc+0x59)[__0x2b8120718659]
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1(+__0x110346)[0x2b8120718346]
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1(+__0x110346)[0x2b506c4d0346]
> /home/1232/FLASH4/object/__flash4(for_allocate+0x164)[__0x6a4544]
> /home/1232/FLASH4/object/__flash4(for_allocate+0x164)[__0x6a4544]
> /home/1232/FLASH4/object/__flash4(namevaluell_data_mp___namevaluell_addreal_+0x35c)[__0x632bbc]
> /home/1232/FLASH4/object/__flash4(namevaluell_data_mp___namevaluell_addreal_+0x35c)[__0x632bbc]
> /home/1232/FLASH4/object/__flash4(namevaluell_bcast_+__0x1e6f)[0x631f5f]
> /home/1232/FLASH4/object/__flash4(namevaluell_bcast_+__0x1e6f)[0x631f5f]
> /home/1232/FLASH4/object/__flash4(runtimeparameters___bcast_+0x12)[0x46edb2]
> /home/1232/FLASH4/object/__flash4(runtimeparameters___bcast_+0x12)[0x46edb2]
> /home/1232/FLASH4/object/__flash4(runtimeparameters_init___+0x265)[0x46f3c5]
> /home/1232/FLASH4/object/__flash4(runtimeparameters_init___+0x265)[0x46f3c5]
> /home/1232/FLASH4/object/__flash4(driver_initflash_+0x35)__[0x430245]
> /home/1232/FLASH4/object/__flash4(driver_initflash_+0x35)__[0x430245]
> /home/1232/FLASH4/object/__flash4(MAIN__+0x42)[0x435802]
> /home/1232/FLASH4/object/__flash4(MAIN__+0x42)[0x435802]
> /home/1232/FLASH4/object/__flash4(main+0x3c)[0x42b1dc]
> /home/1232/FLASH4/object/__flash4(main+0x3c)[0x42b1dc]
> /lib64/libc.so.6(__libc_start___main+0xfd)[0x2b506db26cdd]
> /lib64/libc.so.6(__libc_start___main+0xfd)[0x2b8121d6ecdd]
> /home/1232/FLASH4/object/__flash4[0x42b0d9]
> /home/1232/FLASH4/object/__flash4[0x42b0d9]
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1(opal___memory_ptmalloc2_int_malloc+__0x2aa)[0x2b66b15f539a]
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1(opal___memory_ptmalloc2_malloc+0x59)[__0x2b66b15f8659]
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1(+__0x110346)[0x2b66b15f8346]
> /home/1232/FLASH4/object/__flash4(for_allocate+0x164)[__0x6a4544]
> /home/1232/FLASH4/object/__flash4(namevaluell_data_mp___namevaluell_addreal_+0x35c)[__0x632bbc]
> /home/1232/FLASH4/object/__flash4(namevaluell_bcast_+__0x1e6f)[0x631f5f]
> /home/1232/FLASH4/object/__flash4(runtimeparameters___bcast_+0x12)[0x46edb2]
> /home/1232/FLASH4/object/__flash4(runtimeparameters_init___+0x265)[0x46f3c5]
> /home/1232/FLASH4/object/__flash4(driver_initflash_+0x35)__[0x430245]
> /home/1232/FLASH4/object/__flash4(MAIN__+0x42)[0x435802]
> /home/1232/FLASH4/object/__flash4(main+0x3c)[0x42b1dc]
> /lib64/libc.so.6(__libc_start___main+0xfd)[0x2b66b2c4ecdd]
> /home/1232/FLASH4/object/__flash4[0x42b0d9]
>
>
> Just to provide you with more information about the system:
> * uname -a
> Linux n106 2.6.32-279.19.1.el6.x86_64 #1 SMP Tue Dec 18 17:22:54 CST
> 2012 x86_64 x86_64 x86_64 GNU/Linux
>
> * ldd flash4
> linux-vdso.so.1 => (0x00007fff8d5d0000)
> libhdf5.so.7 =>
> /opt/shared/hdf5/1.8.8-__intel64/lib/libhdf5.so.7 (0x00002ab4a4f58000)
> libmpi.so.1 =>
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi.so.1 (0x00002ab4a54f8000)
> libm.so.6 => /lib64/libm.so.6 (0x00002ab4a5908000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00002ab4a5b90000)
> libz.so.1 => /lib64/libz.so.1 (0x00002ab4a5db0000)
> libmpi_f90.so.1 =>
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi_f90.so.1
> (0x00002ab4a5fc8000)
> libmpi_f77.so.1 =>
> /opt/shared/openmpi/1.6.1-__intel64/lib/libmpi_f77.so.1
> (0x00002ab4a61d0000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00002ab4a6408000)
> librt.so.1 => /lib64/librt.so.1 (0x00002ab4a6610000)
> libnsl.so.1 => /lib64/libnsl.so.1 (0x00002ab4a6818000)
> libutil.so.1 => /lib64/libutil.so.1 (0x00002ab4a6a38000)
> libc.so.6 => /lib64/libc.so.6 (0x00002ab4a6c40000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002ab4a6fd8000)
> libimf.so =>
> /home/software/intel/composer___xe_2011_sp1.8.273/compiler/__lib/intel64/libimf.so
> (0x00002ab4a71f0000)
> libsvml.so =>
> /home/software/intel/composer___xe_2011_sp1.8.273/compiler/__lib/intel64/libsvml.so
> (0x00002ab4a75c0000)
> libintlc.so.5 =>
> /home/software/intel/composer___xe_2011_sp1.8.273/compiler/__lib/intel64/libintlc.so.5
> (0x00002ab4a7d38000)
> /lib64/ld-linux-x86-64.so.2 (0x00002ab4a4d30000)
> libifport.so.5 =>
> /home/software/intel/composer___xe_2011_sp1.8.273/compiler/__lib/intel64/libifport.so.5
> (0x00002ab4a7e88000)
> libifcore.so.5 =>
> /home/software/intel/composer___xe_2011_sp1.8.273/compiler/__lib/intel64/libifcore.so.5
> (0x00002ab4a7fc0000)
> libifcoremt.so.5 =>
> /home/software/intel/composer___xe_2011_sp1.8.273/compiler/__lib/intel64/libifcoremt.so.5
> (0x00002ab4a8208000)
>
>
> I wonder if you have encountered a similar issue, or perhaps have a
> suggestion for me. Thank you in advance for your time and help,
>
> Asif
>
>
> --
> __________________________________
> Asif ud-Doula
> Assistant Professor of Physics
> Penn State Worthington Scranton
> 120 Ridge View Drive
> Dunmore, PA 18512
> USA
> tel. +1-570-963-2582 <tel:%2B1-570-963-2582>
> __________________________________
>
>
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