From: philipp.coloc_at_gmx.de
Date: Wed Feb 10 2010 - 04:59:30 CST
Hi,
when trying to compile the new version of NAMD, I have problems like
Fatal Error by charmc in directory /usr/local/NAMD_2.7b2_Source/charm-6.1.3/mpi-linux-x86_64/tmp
Command mpicc -m64 -fPIC -I../bin/../include -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -I. -DCMK_MEMORY_BUILD_CHARMDEBUG -O -I/usr/mpi/gcc/openmpi-1.3.2/include -c memory.c -o ../lib/libmemory-charmdebug.o returned error code 1
charmc exiting...
when compiling charm.
Nonetheless, the compilation runs through and the pgm megatest gives no errors.
Then, I compile namd2 and when I run it, it crashes:
Signal: Segmentation fault (11)
Signal code: Invalid permissions (2)
Failing at address: 0x2b3a6505c000
[ 0] /lib64/libpthread.so.0 [0x306f00e4c0]
[ 1] /lib64/libc.so.6(memcpy+0x15b) [0x306e47b59b]
[ 2] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(_ZN8MOStream3PutEPcm+0x69) [0x7be529]
[ 3] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(_ZN10Parameters15send_ParametersEP8MOStream+0x1030) [0x7f4320]
[ 4] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(_ZN4Node11namdOneSendEv+0x92) [0x7e45f2]
[ 5] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(_ZN4Node7startupEv+0x845) [0x7e8185]
[ 6] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(CkDeliverMessageFree+0x38) [0x8b81c8]
[ 7] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(_Z15_processHandlerPvP11CkCoreState+0xc18) [0x8bdf26]
[ 8] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(CmiHandleMessage+0x27) [0x917828]
[ 9] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(CsdScheduleForever+0x64) [0x919328]
[10] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(CsdScheduler+0xd) [0x9193ab]
[11] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(_ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x28) [0x82dfd8]
[12] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(TclInvokeStringCommand+0x91) [0x939c78]
[13] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2 [0x96fac8]
[14] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(Tcl_EvalEx+0x176) [0x97010b]
[15] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(Tcl_EvalFile+0x134) [0x967b14]
[16] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(_ZN9ScriptTcl3runEPc+0x14) [0x82e204]
[17] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(_Z18after_backend_initiPPc+0x223) [0x4daf53]
[18] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(main+0x24) [0x4db034]
[19] /lib64/libc.so.6(__libc_start_main+0xf4) [0x306e41d974]
[20] /usr/local/NAMD_2.7b2_Source/Linux-x86_64-g++/namd2(_ZNSt19basic_ostringstreamIcSt11char_traitsIcESaIcEED1Ev+0x91) [0x4d78d9]
*** End of error message ***
I compiled NAMD_2.7b1 with exactly the same procedure and with the same mpi-installation and it runs without crashing.
Can you help me to figure this out?
Best,
Philipp
-- NEU: Mit GMX DSL über 1000,- ¿ sparen! http://portal.gmx.net/de/go/dsl02
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