Amber Kullanım Kılavuzu

UHeM sitesinden
Atla: kullan, ara

Örnek lsf iş dosyası:

#!/bin/bash
###################################################################
# This LSF submission script was written for submitting Amber11
# jobs on UYBHM HPC Clusters.
# version       : 1.2
###################################################################
#BSUB -P bsldbe                   # project name assigned by uybhm
#BSUB -m karadeniz                # the cluster on which the job will run
#BSUB -n 8                        # number of cores to use this computation
#BSUB -o %J.out                   # output file name
#BSUB -e %J.err                   # error file name
#BSUB -J "Amber11"                # job name that is specified by user
#BSUB -q mid                      # queue name to submit the job
#BSUB -a intelmpi                 # DO NOT TOUCH THIS
 
### DO NOT CHANGE ANY OF THE FOLLOWING LINES
export AMBERHOME=/RS/progs/amber11
export PATH=$PATH:$AMBERHOME/bin
export INTEL_LICENSE_FILE=/RS/progs/intel/licenses
source /RS/progs/intel/composerxe-2011.1.107/bin/compilervars.sh intel64
source /RS/progs/intel/impi/3.1/bin64/mpivars.sh
### END OF NON-DELETE LINES AREA
 
### THE MODIFIABLE LAST LINE
# MUST BE REPLACED WITH AMBER/PMEMD OPTIONS AND INPUT FILES AS USER NEEDS.
# THE "mpirun.lsf" PART MUST NOT BE CHANGED.
mpirun.lsf $AMBERHOME/exe/pmemd.MPI -O -i explicitmin.in -p explicit.top -c explicit.incrd -o explicit.out -r explicit.rst

/RS altındaki kullanıcı dizinindeki .bashrc dosyasına aşağıdaki satırları ilave etmeliyiz:

### for using amber 11 on uybhm clusters
export AMBERHOME=/RS/progs/amber11
export INTEL_LICENSE_FILE=/RS/progs/intel/licenses
source /RS/progs/intel/composerxe-2011.1.107/bin/compilervars.sh intel64
source /RS/progs/intel/impi/3.1/bin64/mpivars.sh
export PATH=$PATH:/RS/progs/amber11/bin
### end of amber 11 bash req. part