AMBER Archive (2009)

Subject: Re: [AMBER] pmemd failure

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Nov 08 2009 - 13:08:53 CST


On Sun, Nov 8, 2009 at 6:00 PM, Robert Duke <rduke_at_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_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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