AMBER Archive (2002)

Subject: Problem getting sander started

From: Thomas Steinbrecher (thomas.steinbrecher_at_physchem.uni-freiburg.de)
Date: Wed Jul 10 2002 - 07:24:00 CDT

Greetings,

I have compiled AMBER with MPICH on a cluster of Linux
computers. While running the test suites I noticed that
make test.sander fails in a very strange way. I did the
following:

Testing if mpirun works:

# /usr/local/mpich-1.2.4/bin/mpirun -np 2
/usr/local/mpich-1.2.4/examples/basic/cpi

Process 0 of 2 on pc2-117.physchem.uni-freiburg.de pi is
approximately 3.1415926544231318,
Error is
0.0000000008333387 wall clock time = 0.000680
Process 1 of 2 on node1.cluster

works well. Next is testing if sander works:

# /usr/local/mpich-1.2.4/bin/mpirun -np 2
/usr/local/amber7/exe/sander
bash: /usr/local/amber7/exe/sander: No such file or
directory

I know I shouldn't test it like this, but that is the
command on which the test script fails. sander seems not to
exist. But it is there and readable/executable:

# ls -l /usr/local/amber7/exe/sander
-rwxrwxr-x 1 root root 1743245 Jul 9 15:30
/usr/local/amber7/exe/sander

When I try to run sander without mpirun it works (that is
it starts and searches for some files)

# /usr/local/amber7/exe/sander
Unit 6 Error on OPEN: mdout
[0] MPI Abort by user Aborting program !
[0] Aborting program! p0_5771: p4_error: : 1

The strange thing is, when I copy the sander executable to
another dir, it is executed:

# /usr/local/mpich-1.2.4/bin/mpirun -np 2
/usr/local/mpich-1.2.4/examples/basic/sander
Unit 6 Error on OPEN: mdout
[0] MPI Abort by user Aborting program !
[0] Aborting
program! p0_5868: p4_error: : 1

Though the executable does not differ from the one before:

# ls -l /usr/local/mpich-1.2.4/examples/basic/sander
-rwxr-xr-x 1 root 856 1743245 Jul 10 13:10
/usr/local/mpich-1.2.4/examples/basic/sander

I setup AMBERHOME like that:

# echo $AMBERHOME
/usr/local/amber7

and I do not believe it is a problem with $PATH, because I
supplied the full PATH in my commands. I think its probably
not a problem with amber, but with some of my
Linux-settings.

Has anyone encountered a similar problem before or knows
what I did wrong?

Kind regards,

Thomas