Trying in vacuo relaxation with pmemd in AMBER10 (which software
unused for a few months), segmentation fault occurred, while
sander.MPI worked nicely with the same command below. The same problem
on two different machines with 4 or 8 logical amd opterons, shared
memory. pmemd worked nicely in the past and I did not touch AMBER10 in
the meantime. I wonder whether the following screen output suggests
how to restore pmemd.
Both pmemd and openmpi-1.2.6 compiled with Intel
Command:
mpirun -np 8 $AMBERHOME/exe/pmemd -O -i min1.in -o mod21_min1.out -c
mod21.inpcrd -p mod21.prmtop -r mod21_min1.rst 2>&1 | tee fileout
[deb64:03609] MPI_ABORT invoked on rank 0 in communicator
MPI_COMM_WORLD with errorcode 1
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
libc.so.6 00007F8241E26190 Unknown Unknown Unknown
libopen-pal.so.0 00007F8242A02725 Unknown Unknown Unknown
libopen-pal.so.0 00007F8242A034F7 Unknown Unknown Unknown
libopen-pal.so.0 00007F82429FF6D7 Unknown Unknown Unknown
libopen-pal.so.0 00007F8242A00390 Unknown Unknown Unknown
libopen-pal.so.0 00007F82429FA0CE Unknown Unknown Unknown
libmpi.so.0 00007F8242F10D70 Unknown Unknown Unknown
mca_coll_tuned.so 00007F823BA1F5A5 Unknown Unknown Unknown
mca_coll_tuned.so 00007F823BA2018B Unknown Unknown Unknown
mca_coll_tuned.so 00007F823BA19D9A Unknown Unknown Unknown
libmpi.so.0 00007F8242F25EBE Unknown Unknown Unknown
libmpi_f77.so.0 00007F82431B7A80 Unknown Unknown Unknown
pmemd 000000000041A068 Unknown Unknown Unknown
pmemd 00000000004E5768 Unknown Unknown Unknown
pmemd 000000000041A022 Unknown Unknown Unknown
libc.so.6 00007F8241E121A6 Unknown Unknown Unknown
pmemd 0000000000419F69 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
mca_btl_sm.so 00007FDA3BE42D54 Unknown Unknown Unknown
mca_bml_r2.so 00007FDA3C24F429 Unknown Unknown Unknown
libopen-pal.so.0 00007FDA423EE0F9 Unknown Unknown Unknown
libmpi.so.0 00007FDA42904D70 Unknown Unknown Unknown
mca_coll_tuned.so 00007FDA3B413362 Unknown Unknown Unknown
mca_coll_tuned.so 00007FDA3B41418B Unknown Unknown Unknown
mca_coll_tuned.so 00007FDA3B40DD9A Unknown Unknown Unknown
libmpi.so.0 00007FDA42919EBE Unknown Unknown Unknown
libmpi_f77.so.0 00007FDA42BABA80 Unknown Unknown Unknown
pmemd 000000000041A068 Unknown Unknown Unknown
pmemd 00000000004E5768 Unknown Unknown Unknown
pmemd 000000000041A022 Unknown Unknown Unknown
libc.so.6 00007FDA418061A6 Unknown Unknown Unknown
pmemd 0000000000419F69 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
mca_btl_sm.so 00007FEE2BEEDD4A Unknown Unknown Unknown
mca_bml_r2.so 00007FEE2C2FA429 Unknown Unknown Unknown
libopen-pal.so.0 00007FEE324990F9 Unknown Unknown Unknown
libmpi.so.0 00007FEE329AFD70 Unknown Unknown Unknown
mca_coll_tuned.so 00007FEE2B4BE362 Unknown Unknown Unknown
mca_coll_tuned.so 00007FEE2B4BF18B Unknown Unknown Unknown
mca_coll_tuned.so 00007FEE2B4B8D9A Unknown Unknown Unknown
libmpi.so.0 00007FEE329C4EBE Unknown Unknown Unknown
libmpi_f77.so.0 00007FEE32C56A80 Unknown Unknown Unknown
pmemd 000000000041A068 Unknown Unknown Unknown
pmemd 00000000004E5768 Unknown Unknown Unknown
pmemd 000000000041A022 Unknown Unknown Unknown
libc.so.6 00007FEE318B11A6 Unknown Unknown Unknown
pmemd 0000000000419F69 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
libmpi.so.0 00007FA54B99FD70 Unknown Unknown Unknown
mca_coll_tuned.so 00007FA5444AE362 Unknown Unknown Unknown
mca_coll_tuned.so 00007FA5444AF18B Unknown Unknown Unknown
mca_coll_tuned.so 00007FA5444A8D9A Unknown Unknown Unknown
libmpi.so.0 00007FA54B9B4EBE Unknown Unknown Unknown
libmpi_f77.so.0 00007FA54BC46A80 Unknown Unknown Unknown
pmemd 000000000041A068 Unknown Unknown Unknown
pmemd 00000000004E5768 Unknown Unknown Unknown
pmemd 000000000041A022 Unknown Unknown Unknown
libc.so.6 00007FA54A8A11A6 Unknown Unknown Unknown
pmemd 0000000000419F69 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
mca_btl_sm.so 00007FF8F50A9D73 Unknown Unknown Unknown
mca_bml_r2.so 00007FF8F54B6429 Unknown Unknown Unknown
libopen-pal.so.0 00007FF8FB6550F9 Unknown Unknown Unknown
libmpi.so.0 00007FF8FBB6BD70 Unknown Unknown Unknown
mca_coll_tuned.so 00007FF8F467A5A5 Unknown Unknown Unknown
mca_coll_tuned.so 00007FF8F467B18B Unknown Unknown Unknown
mca_coll_tuned.so 00007FF8F4674D9A Unknown Unknown Unknown
libmpi.so.0 00007FF8FBB80EBE Unknown Unknown Unknown
libmpi_f77.so.0 00007FF8FBE12A80 Unknown Unknown Unknown
pmemd 000000000041A068 Unknown Unknown Unknown
pmemd 00000000004E5768 Unknown Unknown Unknown
pmemd 000000000041A022 Unknown Unknown Unknown
libc.so.6 00007FF8FAA6D1A6 Unknown Unknown Unknown
pmemd 0000000000419F69 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
mca_btl_sm.so 00007F9C7EA43CE9 Unknown Unknown Unknown
mca_bml_r2.so 00007F9C7EE50429 Unknown Unknown Unknown
libopen-pal.so.0 00007F9C84FEF0F9 Unknown Unknown Unknown
libmpi.so.0 00007F9C85505D70 Unknown Unknown Unknown
mca_coll_tuned.so 00007F9C7E0145A5 Unknown Unknown Unknown
mca_coll_tuned.so 00007F9C7E01518B Unknown Unknown Unknown
mca_coll_tuned.so 00007F9C7E00ED9A Unknown Unknown Unknown
libmpi.so.0 00007F9C8551AEBE Unknown Unknown Unknown
libmpi_f77.so.0 00007F9C857ACA80 Unknown Unknown Unknown
pmemd 000000000041A068 Unknown Unknown Unknown
pmemd 00000000004E5768 Unknown Unknown Unknown
pmemd 000000000041A022 Unknown Unknown Unknown
libc.so.6 00007F9C844071A6 Unknown Unknown Unknown
pmemd 0000000000419F69 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
mca_btl_sm.so 00007FC2820231A1 Unknown Unknown Unknown
mca_bml_r2.so 00007FC28242F429 Unknown Unknown Unknown
libopen-pal.so.0 00007FC2885CE0F9 Unknown Unknown Unknown
libmpi.so.0 00007FC288AE4D70 Unknown Unknown Unknown
mca_coll_tuned.so 00007FC2815F35A5 Unknown Unknown Unknown
mca_coll_tuned.so 00007FC2815F418B Unknown Unknown Unknown
mca_coll_tuned.so 00007FC2815EDD9A Unknown Unknown Unknown
libmpi.so.0 00007FC288AF9EBE Unknown Unknown Unknown
libmpi_f77.so.0 00007FC288D8BA80 Unknown Unknown Unknown
pmemd 000000000041A068 Unknown Unknown Unknown
pmemd 00000000004E5768 Unknown Unknown Unknown
pmemd 000000000041A022 Unknown Unknown Unknown
libc.so.6 00007FC2879E61A6 Unknown Unknown Unknown
pmemd 0000000000419F69 Unknown Unknown Unknown
Thanks
francesco pietra
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Nov 08 2009 - 09:00:02 PST
