Editing Infi

go back to [[Main Page]], [[Computational Resources]], [[Clusters]], [[Local Clusters]]


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. Because each node has two processors, you should ideally ask for an even number of CPU to optimize the performance. :-)

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.
[http://docs.sun.com/app/docs/doc/820-0699?l=en&q=sge+6.1 a manual here]
e.g. to see your jobs

   qstat -u my_username
to see all jobs
 
   qstat -u *

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

  qquota -u my_username

=='''IMPORTANT:'''==

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

   '''qd job_id program'''
   while "program" could be: adf nwchem dlpoly

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

   '''qd 4000 adf'''

for DLPOLY:
   '''qd 4000 dlpoly'''


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


----

== Avaliable Programs ==

[http://aliga.iciq.es/wiki/index.php/DL_POLY_2 DLPOLY 2]
 
[http://aliga.iciq.es/wiki/index.php/NWCHEM NWChem]
 
[http://aliga.iciq.es/wiki/index.php/ADF_2006 ADF 2007]

[http://aliga.iciq.es/wiki/index.php/ADF_2006 ADF 2006]

== ADF 2006 Script ==

 #! /bin/bash
 # queue system setup:
 # pe request
 #$ -pe n 4
 #
 #MPI stuff
 export MPIDIR=/opt/mpi
 export PATH=$MPIDIR:$MPIDIR/bin:$PATH
 export LD_LIBRARY_PATH=$MPIDIR/lib
 export P4_RSHCOMMAND=rsh
 export SCM_MACHINEFILE=$TMPDIR/machines
 export SCMWISH=""
 export NSCM=4
 export P4_GLOBMEMSIZE=16000000
 export GFORTRAN_UNBUFFERED_ALL=y
 export TMPDIR=/scratch
 #
 # ADF Stuff
 export TMPDIR=/scratch
 export ADFHOME=/opt/adf2006.01
 export ADFBIN=$ADFHOME/bin
 export ADFRESOURCES=$ADFHOME/atomicdata
 export SCMLICENSE=$ADFHOME/license
 export SCM_TMPDIR=$TMPDIR
 export SCM_USETMPDIR=yes
 #
 cd /home/ezuidema/test
 #
 $ADFBIN/adf -n $NSCM <  test.in  > test.out
 #
 mv TAPE21 test.t21

== ADF 2006 Scaling ==

== 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 n 4
 
 #MPI INTEL
 export MPIDIR=/opt/mpi/
 export PATH=$MPIDIR:$MPIDIR/bin:$PATH
 export LD_LIBRARY_PATH=$MPIDIR/lib
 export P4_RSHCOMMAND=rsh
 export MACHINEFILE=$TMPDIR/machines
 export NCPUS=4
 export NWCHEM_BASIS_LIBRARY=/opt/nwchem/data/libraries/
 
 cd /home/abraga/TESTS
 
 /opt/intel/mpi/bin/mpirun -np $NCPUS -machinefile $MACHINEFILE /opt/nwchem/bin/nwchem job.nw >& job.out