Infi

11 Dual Intel Xeon processor at 3.06GHz

Access

ssh -X 10.3.30.254

User details

/home is on infi (not in sirius as kimik's and tekla's clusters). Backups are for files size lower than 10 Mb.

There is a quota limit

  20 Gb

Queues

There is a single queues called "n" (without quotes). This queue has 12 nodes (except when some nodes have hardware problems) with 2 processors each. So you ask for slots (NCPUS) and system will allocate for each node 2 slots, p.e. you ask for 8 slots and system will take 4 nodes as it uses 2 slots by node. (can someone write this clearly?, because I can even barely understand it... :)) So you should send jobs asking for even slots (NCPUS).

To send jobs use

     qsub name_of_your_script

We run SGE 6.1, that has many new features, like boolean expressions for hosts, queues, etc. a manual here p.e. to see your jobs

  qstat -u my_username

to see all jobs

  qstat -u *

to see how many slots (quota) are you using and have you available

 qquota -u my_username 

IMPORTANT:

As we still have some problems, to kill or delete jobs please use "qd":

  qd job_id program_name_process

for example, to delete job_id 4000 that runs a adf process (adf.exe) use:

  qd 4000 adf.exe

for DLPOLY:

  qd 4000 DLPOLY.X

Below you can see examples of script for ADF, NWChem, DL_POLY, etc.

---

Avaliable Programs

DLPOLY 2

NWChem

ADF 2006

ADF 2006 Script

#! /bin/bash
# queue system setup:
# pe request
#$ -pe n0 6

#ADF environment
export ADFHOME=/opt/adf2006.01
export ADFBIN=$ADFHOME/bin
export ADFRESOURCES=$ADFHOME/atomicdata
export SCMLICENSE=$ADFHOME/license
export SCM_TMPDIR=$TMPDIR
export SCM_USETMPDIR=yes

#MPI
export MPIDIR=/opt/mpi
export PATH=$MPIDIR:$MPIDIR/bin:$PATH
export LD_LIBRARY_PATH=$MPIDIR/lib
export P4_RSHCOMMAND=rsh
export SCM_MACHINEFILE=$TMPDIR/machines
export SCMWISH=""
export NSCM=6
export P4_GLOBMEMSIZE=32000000
export GFORTRAN_UNBUFFERED_ALL=y

cd /home/pmiro/Water/

$ADFBIN/adf -n $NSCM < aigua.in > aigua.out

DLPOLY Script

#! /bin/bash
# queue system setup:
# pe request
#$ -pe n0 8

export LD_LIBRARY_PATH=$MPIDIR/lib
export DLPOLYPATH=/home/pmiro/dlpoly_MPI/execute
export P4_RSHCOMMAND=rsh
export MACHINEFILE=$TMPDIR/machines
export NCPUS=8

cd /home/pmiro/Bola/SO4Simulation/DownTemp/02/

/opt/mvapich-0.9.9/bin/mpirun -np $NCPUS -machinefile MACHINEFILE $DLPOLYPATH/DLPOLY.X

DLPOLY Scaling

System with 27336 Atoms

      Shared Nodes 
NCPUS    %     Time 1ns (Days)
  1     100         52
  2     203         26
  3     268         19
  4     369         14
  5     428         12
  6     465         11
  7     499         10
  8     557          9
  9     565          9
 10     702          8
 11     732          9

      Non-Shared Nodes 
NCPUS    %     Time 1ns (Days)
  1     100         52
  2     196         26
  4     368         14

NWChem Script

#! /bin/bash
# queue system setup:
# pe request
#$ -pe n0 4

#MPI INTEL
export MPIDIR=/opt/intel/mpi/
export PATH=$MPIDIR:$MPIDIR/bin:$PATH
export LD_LIBRARY_PATH=$MPIDIR/lib
export P4_RSHCOMMAND=rsh
export MACHINEFILE=$TMPDIR/machines
export NCPUS=4

cd /home/abraga/TESTS

/opt/intel/mpi/bin/mpirun -np $NCPUS -machinefile $MACHINEFILE /opt/nwchem/bin/nwchem job.nw >& job.out