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CAML Cluster

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Contents

CAML Cluster

camlload.png camlram.png


Updated hourly - see full cluster status at the CAML Grid Status page

Changes With Upgrade

There are only three queues now:

  • govasp.q - the GoVasp nodes
  • all.q - every non-IB node (4 and 8 core together)
  • ib1.q - the IB nodes, as before.

Medea submits to all.q now.

The locations of mpiexec/mpirun have changed:

  • /cluster/caml/mpich2-intel/bin/ (for non-IB MPI)
  • /cluster/caml/mvapich2-intel/bin (for IB MPI (THIS IS NOT THERE YET))

These are the Parallel Environments in SGE:

  • ib-hydra - use this for MPI jobs, whether or not they are IB or Gigabit
  • linda4p - For Gaussian jobs.
  • linda_ib - For IB Gaussian jobs (NOT WORKING YET)
  • mpich2_intelmpd - The same as ib-hydra
  • namd - for namd jobs, IB or non-IB.



About

Applications

CPMD

Installation

LAMMPS

Installation

The SGE script is:

#!/bin/sh
#

#$ -q 4core
#$ -N lammpstest
#$ -pe mpich2_psmp 8
#$ -cwd 
#$ -v SMPD_OPTION_NO_DYNAMIC_HOSTS=1

# This line defines the MPI communications port, do not change.
@ smpdport = $JOB_ID % 5000 + 20000

/cluster/caml/mpi-pgi/bin/mpiexec -n $NSLOTS -machinefile $TMPDIR/machines -port $smpdport -phrase $smpdport /cluster/caml/lammps/lmp_pg < /research-projects/partita/mark/lammps/in.min


exit 0

NAMD

SGE script is:

 #!/bin/csh -f

 # The name of our actual namd analysis script from the commandline
 set NAMD_SCRIPT = $1
 set OUTPUT_FILE = results.txt
 
 # The name of the job (NAMD_test) ...
 #$ -N NAMD_test

 # The parallel environment (namd) and number of processors (5) ...
 #$ -pe namd 5 

 # Execute from the current working directory 
 #$ -cwd


 echo " ## DEBUG ## This NAMD program got $NSLOTS slots across $NHOSTS machines..."
 echo "My customized namd-machines file has contents of:"
 cat $TMPDIR/namd-machines
 echo ""

 /cluster/caml/namd/charmrun /cluster/caml/namd/namd2 ++nodelist $TMPDIR/namd-machines +p $NSLOTS $NAMD_SCRIPT > $OUTPUT_FILE


Installation

Source Installation (2011)

VASP

Installation

Requires GotoBLAS.

See: CAML-VASP-Install

VMD

Installation

Using the binary distribution from http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD, follow the readme.

Usage

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