Hi Ross,
For parallel run I type the command as:
mpirun -np 4 $AMBERHOME/exe/sander.MPI -O...
Is it OK to use sander.MPI in the directory $AMBERHOME/exe?
I use the following procedure:
cd $AMBERHOME/AmberTools/src
./configure -mpi gnu
cd ../../src
make clean
make parallel
Then:
cd $AMBERHOME/test
export DO_PARALLEL=’mpirun -np 4’
make test.parallel
Are these OK?
Now I am trying the following:
cd $AMBERHOME/test
unset DO_PARALLEL
unset TESTsander
export DO_PARALLEL='mpirun -np 4'
make test.parallel
Aimin
________________________________________
From: Ross Walker [ross.rosswalker.co.uk]
Sent: Monday, August 01, 2011 11:21 AM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] About running sander parallel
Hi Aimin,
> We have installed Amber11 and AmberTools in the server. And I can run
> the examples of tutorial well. However, when I ran sander parallel by
> putting "mpirun -np 4" in the beginning of the command, the time to
> finish the job is the same as using single cpu.
It looks to me like you are using the executable 'sander' instead of
sander.MPI for running in parallel. For parallel runs you should run as
follows:
mpirun -np 4 $AMBERHOME/bin/sander.MPI -O ...
> I have attached the files by testing parallel version of Amber
> following page 13 of "Amber11 Users' Manual". How can I solve this
> problem so that I can run sander parallel? Thank you in advance.
This does not look correct. Did you test with 'make test.parallel'? since it
looks like it ran the serial '$AMBERHOME/bin/sander' version but with
DO_PARALLEL set. Try the following:
cd $AMBERHOME/test
unset DO_PARALLEL
unset TESTsander
export DO_PARALLEL='mpirun -np 4'
make test.parallel
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
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Received on Mon Aug 01 2011 - 12:00:03 PDT
