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11 Dual Intel Xeon processor at 3.06GHz
go back to [[Main Page]], [[Computational Resources]], [[Clusters]], [[Local Clusters]]




11 Dual Intel Xeon processor at 3.06GHz


== Access ==
== Access ==
Line 18: Line 19:
== Queues ==
== 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... :))
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. :-)
So you should send jobs asking for even slots (NCPUS).


To send jobs use  
To send jobs use  
Line 29: Line 29:
We run SGE 6.1, that has many new features, like boolean expressions for hosts, queues, etc.
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]
[http://docs.sun.com/app/docs/doc/820-0699?l=en&q=sge+6.1 a manual here]
p.e. to see your jobs
e.g. to see your jobs


   qstat -u my_username
   qstat -u my_username
Line 36: Line 36:
   qstat -u *
   qstat -u *


to see how many slots (quota) are you using and have you available
to see how many slots (quota) you are using and how many you have available
 
  qquota -u my_username


  qquota -u my_username
=='''IMPORTANT:'''==
=='''IMPORTANT:'''==


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


Line 75: Line 77:
  # queue system setup:
  # queue system setup:
  # pe request
  # pe request
  #$ -pe n0 6
  #$ -pe n 4
  #
  #ADF environment
  #MPI stuff
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 MPIDIR=/opt/mpi
  export PATH=$MPIDIR:$MPIDIR/bin:$PATH
  export PATH=$MPIDIR:$MPIDIR/bin:$PATH
Line 92: Line 86:
  export SCM_MACHINEFILE=$TMPDIR/machines
  export SCM_MACHINEFILE=$TMPDIR/machines
  export SCMWISH=""
  export SCMWISH=""
  export NSCM=6
  export NSCM=4
  export P4_GLOBMEMSIZE=32000000
  export P4_GLOBMEMSIZE=16000000
  export GFORTRAN_UNBUFFERED_ALL=y
  export GFORTRAN_UNBUFFERED_ALL=y
   
  export TMPDIR=/scratch
  cd /home/pmiro/Water/
#
   
# ADF Stuff
  $ADFBIN/adf -n $NSCM < aigua.in > aigua.out
export TMPDIR=/scratch
export ADFHOME=/opt/adf2006.01
export ADFBIN=$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 ==
== ADF 2006 Scaling ==
Line 148: Line 154:
  # queue system setup:
  # queue system setup:
  # pe request
  # pe request
  #$ -pe n0 4
  #$ -pe n 4
   
   
  #MPI INTEL
  #MPI INTEL
  export MPIDIR=/opt/intel/mpi/
  export MPIDIR=/opt/mpi/
  export PATH=$MPIDIR:$MPIDIR/bin:$PATH
  export PATH=$MPIDIR:$MPIDIR/bin:$PATH
  export LD_LIBRARY_PATH=$MPIDIR/lib
  export LD_LIBRARY_PATH=$MPIDIR/lib
Line 157: Line 163:
  export MACHINEFILE=$TMPDIR/machines
  export MACHINEFILE=$TMPDIR/machines
  export NCPUS=4
  export NCPUS=4
export NWCHEM_BASIS_LIBRARY=/opt/nwchem/data/libraries/
   
   
  cd /home/abraga/TESTS
  cd /home/abraga/TESTS
   
   
  /opt/intel/mpi/bin/mpirun -np $NCPUS -machinefile $MACHINEFILE /opt/nwchem/bin/nwchem job.nw >& job.out
  /opt/intel/mpi/bin/mpirun -np $NCPUS -machinefile $MACHINEFILE /opt/nwchem/bin/nwchem job.nw >& job.out

Latest revision as of 10:33, 3 August 2009

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


11 Dual Intel Xeon processor at 3.06GHz

Access[edit]

ssh -X 10.3.30.254

User details[edit]

/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[edit]

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. 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:[edit]

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[edit]

DLPOLY 2

NWChem

ADF 2007

ADF 2006

ADF 2006 Script[edit]

#! /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[edit]

DLPOLY Script[edit]

#! /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[edit]

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[edit]

#! /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
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