[FLASH-USERS] Running Flash4 with OpenMPI+Intel

Asif ud-Doula auu4 at psu.edu
Fri May 24 12:05:12 EDT 2013 

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
________________________________

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