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Amber 10 on Sequoia at MCSR
Amber 10 is installed on Sequoia in /usr/local/apps/MPTamber10/amber10. You should set the AMBERHOME environment variable to /usr/local/apps/MPTamber10/amber10. The executables are in $AMBERHOME/exe, and the examples are in $AMBERHOME/examples. You may browse this directory and copy example files into your own working directory for execution. You should ensure that the $AMBERHOME/exe/ directory is in your PATH environment variable.
Amber10 example
To run a parallel Amber10 program, use mpiexec, and specify the number of CPUs/processes to run on with the -np option to mpiexec. For example, to run the Amber "cytosine" program using the sample "in.md" input file supplied in the /usr/local/apps/MPTamber10/amber10/tutorial directory
- Ensure the following environment variables are set:
export AMBERHOME=/usr/local/apps/MPTamber10/amber10
export MPI_HOME=/usr/lib64
export MKL_HOME=/mnt/data/apps/intel/ict/mkl/10.0.3.020
export NETCDF_HOME=/usr/local/apps/MPTamber10/amber10/src/netcdf
module load intel-compilers-em64t-10.1.017
- Ensure the PATH environment variable includes $AMBERHOME/exe/
export PATH=$PATH:$AMBERHOME/exe
- Copy the following file to your working directory.
/usr/local/apps/MPTamber10/amber10/tutorial/in.md
/usr/local/apps/MPTamber10/amber10/tutorial/crd.md.23
/usr/local/apps/MPTamber10/amber10/tutorial/prmtop
- Decide which executable to use and set it as TESTsander_pmemd. The executables of SANDER and PMEMD are as follows:
export TESTsander_pmemd=/usr/local/apps/MPTamber10/amber10/exe/sander
export TESTsander_pmemd=/usr/local/apps/MPTamber10/amber10/exe/sander.MPT
export TESTsander_pmemd=/usr/local/apps/MPTamber10/amber10/exe/sander.LES
export TESTsander_pmemd=/usr/local/apps/MPTamber10/amber10/exe/sander.LES.MPT
export TESTsander_pmemd=/usr/local/apps/MPTamber10/amber10/exe/pmemd.SERIAL
export TESTsander_pmemd=/usr/local/apps/MPTamber10/amber10/exe/pmemd.MPT
- You should use PBS to submit your Amber jobs. For Amber we have a separate queue and hence it has to be specified in the PBS script. Here is a sample PBS script.
#PBS -S /bin/bash
#PBS -l walltime=1000:000:00
#PBS -l ncpus=8
#PBS -l mem=1gb
#PBS -N JobName
#PBS -q SPIDEY
. /usr/local/apps/intel/fce/10.1.017/bin/ifortvars.sh
. /usr/local/apps/intel/cce/10.1.017/bin/iccvars.sh
export OMP_NUM_THREADS=1
export AMBERHOME==/usr/local/apps/MPTamber10/amber10
export MPI_HOME=/usr/lib64
export MKL_HOME=/mnt/data/apps/intel/ict/mkl/10.0.3.020
export NETCDF_HOME=/usr/local/apps/MPTamber10/amber10/src/netcdf
export TESTsander_pmemd=/usr/local/apps/MPTamber10/amber10/exe/sander.MPT
export DO_PARALLEL="mpiexec -n 16"
cd /ptmp/$USER/
$DO_PARALLEL $TESTsander_pmemd -O -i in.md -c crd.md.23 -o cytosine.out
- To run the PBS script
qsub pbs_script_name
- Make sure it created a new cytosine.out
- Verify results in cytosine.out
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