AMBER: Sander is changing directories

From: Andreas Kerzmann <>
Date: Wed, 08 Jun 2005 11:37:58 +0200

Hi all,

I have a strange problem. I use AMBER 7 here and until now I only used
it on i386 platforms. I compiled it with g77 (several versions) without
MPI and never had any problems.

Now I am migrating to an Opteron cluster system and astonishingly,
sander does not work properly anymore. It did compile perfectly (gcc
3.2.2 on an RHEL 3 machine) and it can be started, but it seemingly
changes direcories at some point so that it cannot access the
computation files anymore.

What I get is an error message stating that the crd file cannot be
opened. After some debugging I used strace in order to find out what was
going wrong. Here is a part of the log:

11287 rt_sigaction(SIGFPE, {0x4eb33e, [FPE], SA_RESTART|0x4000000},
NULL, 8) = 0
11287 chdir("/share/opt/x86_64_rhel3/amber7/exe") = 0
11287 mmap(NULL, 196608, PROT_READ|PROT_WRITE,
 = 0x2a95c82000

This chdir command is most annoying, because sander does not change back
to the directory where it was started. This AMBER version was compiled
with mpich support while the other (working) one was not. Can this cause
the error? I'm puzzled. Does anyone have an idea?

Best Regards,

  Andreas Kerzmann

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Received on Wed Jun 08 2005 - 10:53:00 PDT
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