AMBER Archive (2002)

Subject: Re: MPI_BCAST error

From: Nathan A. Baker (baker_at_cholla.wustl.edu)
Date: Wed Dec 18 2002 - 19:31:47 CST

Dear Scott --

Thank you for your help. We will try varying the compiler options to
see if we can track down the problem, but per others' advice, we'll
likely just switch to sander in the future.

Thanks again,

Nathan

Scott Brozell <sbrozell_at_scripps.edu> (12-18-2002 13:24:55-0800):
>Hello,
>
>I have not encountered that message.
>It generally indicates that a receive buffer is too small.
>Since mpi_bcast produces the error and since the problem is
>sporadic, the cause is probably a dangling pointer, which in Fortran
>means an out of bounds array index or some other type of corrupted memory.
>
>One approach to finding the problem is to build gibbs with the
>compiler's automatic array bounds checking, stack checking,
>etc. turned on.
>
>Scott Brozell, Ph.D. | e-mail: sbrozell_at_scripps.edu
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-8754
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA | http://www.scripps.edu/~sbrozell
>
>On Wed, 18 Dec 2002, Nathan A. Baker wrote:
>
>> Hi All --
>>
>> Has anyone encountered the message:
>>
>> -----------------------------------------------------
>> 1 - MPI_BCAST : Message truncated
>> [1] Aborting program !
>> [1] Aborting program!
>> Child process exited unexpectedly 0
>>
>>
>> ** Signal 134519144 **
>>
>>
>> End of diagnostics
>> -----------------------------------------------------
>>
>> when running Gibbs using shared memory MPI (MPICH with device
>> ch_shmem)?
>>
>> We've ran into this a few times (very randomly, some runs work & some
>> runs die in the middle with this error) on our Linux cluster and are
>> tyring to find the problem.
>>
>> Thanks for your help!
>>
>> -- Nathan Baker
>>
>>
>> --
>> Nathan A. Baker, Assistant Professor
>> Washington University in St. Louis School of Medicine
>> Dept. of Biochemistry and Molecular Biophysics
>> Center for Computational Biology
>> 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
>> Phone: (314) 362-2040, Fax: (314) 362-0234
>> URL: http://www.biochem.wustl.edu/~baker
>>
>
End of message from Scott Brozell. 

-- 
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone:  (314) 362-2040, Fax:  (314) 362-0234
URL:  http://www.biochem.wustl.edu/~baker