On Sun, Nov 8, 2009 at 6:00 PM, Robert Duke <rduke.email.unc.edu> wrote:
> PMEMD does not do vacuum simulations. I am assuming that there was a proper
> error msg from the master,
I could not see anything more than I have posted, also because of
mistakenly ntpr=0.
Sorry for the misuse of pmemd.
Thanks
francesco
> 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.gmail.com>
> To: "Amber" <amber.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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Sun Nov 08 2009 - 11:30:02 PST
