RE: AMBER: RE:Amber 8 with lam compilation problem

From: Ross Walker <>
Date: Tue, 22 Feb 2005 23:20:54 -0800

> It compile without any errors but i have only 2 files sander and
> sand.LES when i test my amber make test.sander i have no errors .
> Is it normal that i have only 2 files ??

For a parallel compilation yes it is correct. Only these two modules run in
parallel. Because of this you ideally want to build two copies of amber in
different directories. One without any mpi and one with mpi. Note, pmemd
also works in parallel but you have to build this seperately. I would make
sure you can run sander properly before trying pmemd.

> When i test sander my amber use only one processor , how i must
> run amber to use 2 or more processors ?

You need to use mpirun. You also need to configure and run lamboot. E.g.
create a lamdef file.

Node1 cpu=1
Node2 cpu=1
Node3 cpu=1
Node4 cpu=1

Etc for each of your nodes (check the lam docs for more info)

Then run lamboot

>lamboot lamdef

Then run sander with mpirun. For 4 cpus you would do:

mirun -np 4 $AMBERHOME/sander -O -i mdin -o ...........

Note for running the test cases there is an environment variable you can set
that tells it what mpi command to use.


cd $AMBERHOME/test
export DO_PARALLEL="mpirun -np 4 "

Assuming lamboot is up and running this should run on the first 4 cpu;s
specified in the lamdef file you used with lamboot. You an check how many
cpus are being used in a sander run by looking in the output file. If it is
running in parallel it will tell you on how many cpus and also give you the
atom division between cpus.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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Received on Wed Feb 23 2005 - 07:53:00 PST
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