AMBER Archive (2009)

Subject: Re: [AMBER] pmemd failure

From: Robert Duke (rduke_at_email.unc.edu)
Date: Sun Nov 08 2009 - 11:00:52 CST

PMEMD does not do vacuum simulations. I am assuming that there was a proper
error msg from the master, and the rest of this stuff below is from a messy
mpi "cleanup" of the other processors...
Regards - Bob Duke
----- Original Message -----
From: "Francesco Pietra" <chiendarret_at_gmail.com>
To: "Amber" <amber_at_ambermd.org>
Sent: Sunday, November 08, 2009 11:52 AM
Subject: [AMBER] pmemd failure

> 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
>
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>
>

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