Amber 8

Amber 8 is installed on the Anfinsen Cluster. Amber was built with the intel c compiler 8.1 and intel fortran compiler 8.1 (/usr/local/intel/). It also takes advantage of the Intel Math Kernel Library 7.2 (/usr/local/intel/mkl72/). Amber has been configured for parallel work with mpich-1.2.4 (/usr/local/mpich-1.2.4.intel_condor). Mpich-1.2.4 was chosen, because it is compatible with Condor.

Environment Setup

You will need to make sure that your environment is setup as follows:

• PATH contains /usr/local/amber8.ifort_mpich-1.2.4_condor/exe and /usr/local/condor/bin
• remove references to amber 7
• AMBERHOME is set to /usr/local/amber8.ifort_mpich-1.2.4_condor

Running Parallel Sander jobs

Sander jobs need to be submitted through Condor rather than directly through mpich.

The following is an example of a condor submit file for one sander job. This is just one job, a condor submit file can actually contain entries for multiple jobs.

# MPI AMBER8 to CONDOR test
universe = MPI
initialdir = /home/tsg/users/loughlin/amber8_test
executable = /usr/local/amber8.ifort_mpich-1.2.4_condor/exe/sander
arguments =-O -i /home/tsg/users/loughlin/amber8_test/min0.in -p /home/tsg/users/loughlin/amber8_test/1ucs.top -c 
/home/tsg/users/loughlin/amber8_test/1ucs.crd -r /home/tsg/users/loughlin/amber8_test/rst1.rst -o 
/home/tsg/users/loughlin/amber8_test/min0.out
log = /home/tsg/users/loughlin/amber8_test/logfile
output = /home/tsg/users/loughlin/amber8_test/outfile.$(NODE)
error = /home/tsg/users/loughlin/amber8_test/errfile.$(NODE)
machine_count = 4
queue  

Once you have constructed a submit file, use the condor_submit command on the Anfinsen master node to submit your job.

-- DanielLoughlin? - 09 Mar 2005