AMBER Archive (2004)

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

From: David A. Case (
Date: Tue Apr 13 2004 - 19:37:04 CDT

On Tue, Apr 13, 2004, Rohn Wood wrote:

> Compiling Amber with Machine.sgi_mpi results in a bad sander module
> (see errors below under PROBLEM). I have seen a few references to this
> problem on the list, but no clear resolution. The only solution that
> included a code modification was found at:
> However, this fix did not work for me.

This sure _looks_ like the flush problem listed above, since your programs
(see below) are failing exactly in flush. Can you do the following:

1. post the exact change you made to $AMBERHOME/src/Machines/standard/sys.f

2. try commenting out the "call flush(lun)" statement in amflsh; that is,
just have the amflsh routine return without doing anything.

> MPI: --------stack traceback-------
> PC: 0x5ddb100 MPI_SGI_stacktraceback in /usr/lib32/
> PC: 0x5ddb544 first_arriver_handler in /usr/lib32/
> PC: 0x5ddb7d8 slave_sig_handler in /usr/lib32/
> PC: 0xfaee79c _sigtramp in /usr/lib32/
> PC: 0xa6ca7c0 flush_ in /usr/lib32/
> PC: 0x10164d6c amflsh in ../../exe/sander
> PC: 0x1000c150 sander in ../../exe/sander
> PC: 0xace9d74 main in /usr/lib32/

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: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to