AMBER Archive (2002)

Subject: Re: Problem getting sander started

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Wed Jul 10 2002 - 07:26:39 CDT

The executables should be in idential on all nodes (in terms of directory
hirarchy itself). So, you have to check if amber is installed in identical
directories on all nodes, as well as mpich.
Best of luck,
-Sanjeev

On Wed, 10 Jul 2002, Thomas Steinbrecher wrote:

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