Silver Quickstart Guide

Login Procedure

Like most MSI resources, access to Silver requires that you connect through login.msi.umn.edu or nx.msi.umn.edu. Please see MSI's interactive connections FAQ, and use silver.msi.umn.edu as the hostname.

How to compile

IBM's native compilers (xlf and xlc) and GNU compilers are available on silver. OpenMPI libraries are available for MPI jobs. One can type:

module avail

to find out which version of the compilers and libraries are installed on silver.

Compiling on Silver

 

Compiling Serial Programs

FORTRAN [IBM XL compilers]:

module load xlf

xlf -O3 -qtune=pwr6 -qarch=pwr6 prog.f

xlf90 -O3 -qtune=pwr6 -qarch=pwr6 prog.f90

xlf95 -O3 -qtune=pwr6 -qarch=pwr6 prog.f95

C and C++ [IBM XL compilers]:

module load xlc

xlc -O3 -qtune=pwr6 -qarch=pwr6 prog.c

xlC -O3 -qtune=pwr6 -qarch=pwr6 prog.cpp

FORTRAN [GNU compilers]:

module load gcc/4.4.0

gfortran -O3 prog.f

C and C++ [IBM XL compilers]:

module load gcc/4.4.0

gcc -O3 prog.c

Compiling OpenMP or multi-threading Programs with IBM XL compilers:

FORTRAN [IBM XL compilers]:

xlf_r -O3 -qsmp=omp -qtune=pwr6 -qarch=pwr6 prog.f

C and C++[IBM XL compilers]:

xlc_r -O3 -qsmp=omp prog.c

xlC_r -O3 -qsmp=omp prog.cpp

Compiling MPI Programs with IBM XL Compilers

module load xlf /12.1

FORTRAN [IBM XL compilers]:

mpfort -O3 myMPIcode.f

C and C++[IBM XL compilers]:

module load xlc/10.1

mpcc -O3 myMPIcode.c

mpcxx -O3 myMPIcode.cpp

Compiling MPI programs with GNU Compilers

module load ompi/gnu-4.4.0

FORTRAN [IBM XL compilers]:

mpfort -O3 myMPIcode.f

C and C++[IBM XL compilers]:

module load ompi/gnu-4.4.0

mpicc -O3 myMPIcode.c

mpicxx -O3 myMPIcode.cpp

How to run jobs interactively

Serial jobs

cd working_directory

./a.out

OpenMP or multi-threading jobs

export OMP_NUM_THREADS=2

cd OpenMp_directory

./a.out

MPI jobs

cd mpi_directory

mpirun -np 2 ./a.out

How to submit batch jobs to the queue

We use PBS to ensure the machine is being used to its full potential and is fair to every user. To submit jobs to the queue using PBS, all you need to do is create a script file and use the command qsub to submit. Following are examples of submission scripts for a serial, OpenMP, and MPI jobs. Example of PBS script to submit a serial batch job

#!/bin/bash -l
#PBS -l mem=50mb,nodes=1:ppn=1,walltime=3:00:00
#PBS -m abe
cd /home/s1/user_name/TESTS
./a.out

The above example will submit a single processor job that uses 50 MB of memory. The job can run for up to 3 hours. Because of the -m switch, PBS will send email to you if the job is aborted (a), when the job begins running (b), and when the job terminates (e). The lines with #PBS lines are the lines that start this job. Example of PBS script to submit an OpenMP or multi-threading batch job The following is a 4-processor OpenMP job that will run up to 4 hours.

#!/bin/bash -l
#PBS -l nodes=1:ppn=4,mem=1gb,walltime=4:00:00
#PBS -m abe
cd /home/s1/user_name/TESTS
export OMP_NUM_THREADS=4
./a.out

Example of PBS script to submit a parallel MPI batch job The following is a 4-processor MPI job that will run up to 4 hours.

#!/bin/bash -l
#PBS -l nodes=1:ppn=4,mem=1gb,walltime=4:00:00
#PBS -m abe
module load gcc ompi
cd /home/s1/user_name/TESTS
mpirun -np 4 ./a.out

Useful PBS Commands

Submitting a job:

qsub myscript

Monitoring job's status:

qstat

Canceling a job:

qdel

Useful Scripts :

Script to run Amber on Silver

#!/bin/bash -l
#PBS -l walltime=24:0:0
#PBS -l mem=4GB
#PBS -l nodes=1:ppn=4
module load amber/10
export MP_HOSTFILE=$PBS_NODEFILE
export MP_PROCS=4
export MP_SHARED_MEMORY=yes
export MP_EAGER_LIMIT=65536
export MP_BUFFER_MEM=67108864
export MEMORY_AFFINITY=MCM
export MP_WAIT_MODE=poll

cd $PBS_O_WORKDIR

poe sander.MPI -O -i mdin -o mdout -p prmtop -c inpcrd 

Script to Run NAMD on Silver

#!/bin/bash -l
#PBS -l walltime=24:0:0
#PBS -l mem=12GB
#PBS -l nodes=3:ppn=4
module load namd/2.7b1
export MP_HOSTFILE=$PBS_NODEFILE
export MP_PROCS=12
export MP_SHARED_MEMORY=yes
export MP_EAGER_LIMIT=65536
export MP_BUFFER_MEM=67108864
export MEMORY_AFFINITY=MCM
export MP_WAIT_MODE=poll
cd $PBS_O_WORKDIR
poe namd2.7 apoa1.namd &> myoutput.out 

Script to run GROMACS on Silver

#!/bin/bash -l
#PBS -l walltime=24:0:0
#PBS -l mem=16GB
#PBS -l nodes=3:ppn=4
module load gromacs/4.0.5-xl-ompi
cd $PBS_O_WORKDIR

mpirun mdrun -s topol &> myoutput.out

AutoDock

soft/autodock/tools-1.5.4> module load autodock/4.2.3

soft/autodock/tools-1.5.4> autodock4
usage: AutoDock
-p parameter_filename
-l log_filename
-k (Keep original residue numbers)
-i (Ignore header-checking)
-t (Parse the PDBQT file to check torsions, then
stop.)
-d (Increment debug level)
-C (Print copyright notice)
--version (Print autodock version)
--help (Display this message)

AutoGrid

soft/autodock/tools-1.5.4> autogrid4

usage: AutoGrid
-p parameter_filename
-l log_filename
-d (increment debug level)
-h (display this message)
--version (print version information, copyright,
and license)

Please contact MSI support staff for technical questions or additional help by e-mail: help@msi.umn.edu or phone: 612-624-8858.