AMBER Archive (2004)

Subject: Re: AMBER: Amber 7 on SGI: Sander MPI problem

From: Rohn Wood (llystrata_at_mac.com)
Date: Wed Apr 14 2004 - 18:48:58 CDT

I changed the modification below to

subroutie amflsh(lun) from subroutine amflsh(lun, istat)

and it appears things are now working. I still have failures depending
on the number of processors (test.sander will not complete successfully
if np > 8), but I can work with this.

Thanks...

Rohn

On Apr 14, 2004, at 11:28 AM, Rohn Wood wrote:

> Howdy Dave,
> Thanks for your time on this. I am not a fortran guy, so I may
> have botched this (I assumed it would puke during compile if I had):
>
>>
>> 1. post the exact change you made to
>> $AMBERHOME/src/Machines/standard/sys.f
>>
>
> c----------------------------------------------------------------------
> -
> subroutine amflsh(lun,istat)
> c wrapper for i/o buffer flushing routine
> c Author: George Seibel
> c
> c INPUT:
> c
> integer lun
> c ... logical unit number to flush
> c
> c --- most Unix (BSD, Convex, Sun, Stellar, SGI Iris...) ---
> c
> call flush(lun,istat)
> return
> end
>
>
>> 2. try commenting out the "call flush(lun)" statement in amflsh; that
>> is,
>> just have the amflsh routine return without doing anything.
>>
>
> I will try this as well.
>
> Thanks....
>
> Rohn
>
>
>>>
>>> MPI: --------stack traceback-------
>>> PC: 0x5ddb100 MPI_SGI_stacktraceback in /usr/lib32/libmpi.so
>>> PC: 0x5ddb544 first_arriver_handler in /usr/lib32/libmpi.so
>>> PC: 0x5ddb7d8 slave_sig_handler in /usr/lib32/libmpi.so
>>> PC: 0xfaee79c _sigtramp in /usr/lib32/libc.so.1
>>> PC: 0xa6ca7c0 flush_ in /usr/lib32/libfortran.so
>>> PC: 0x10164d6c amflsh in ../../exe/sander
>>> PC: 0x1000c150 sander in ../../exe/sander
>>> PC: 0xace9d74 main in /usr/lib32/libftn.so
>>
>> If you prevent amflsh above from calling "flush", then at least you
>> will
>> get different error :-) :-(
>>
>> ...hope this helps....dac
>>
>> --
>>
>> ==================================================================
>> David A. Case | e-mail: case_at_scripps.edu
>> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>> The Scripps Research Institute | phone: +1-858-784-9768
>> 10550 N. Torrey Pines Rd. | home page:
>> La Jolla CA 92037 USA | http://www.scripps.edu/case
>> ==================================================================
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