Kimik's Quads: Difference between revisions

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go back to [[Main_Page]], [[Computational Resources]], [[Clusters]], [[Local Clusters]], [[kimik2]]
Hardware:
Hardware:


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  NPROC=4
  NPROC=4


''''Submit calculations''''


At the moment, to submit calculations,according to the information that we have, you should do some things:
== '''Submit calculations''' ==
*Add '''%nproc=4''' in the Gaussian input file
 
*Create an script to submit the job
 
  #!/bin/bash
At the moment, to submit calculations:
  #$ -N Test.in
*Add '''%nproc=4''' in the Gaussian input file, if you use the submision script qs it will be added automatically to the in.in file.
  #$ -cwd
*To sumbit the job, type:
  #$ -masterq kimik133.q
  #$ -pe nanYar.quad 1
  export LINDA_PATH=/usr/local/g03.C02/g03/linda7.1
    
    
   export g03root=/usr/local/g03.C02
   qs [number_of_quads]  q  job_type  script_to_submit_or_input_file.in
  . $g03root/g03/bsd/g03.profile
 
 
e.g.
  export PATH=$PATH:$LINDA_PATH/intel-linux2.4/bin
  export LD_LIBRARY_PATH=/usr/local/g03.C02/g03
 
  export GAUSS_SCRDIR=$TMPDIR
 
  CONF_DIR="/usr/local/scriptConf";
  SCREFERENCE="Test.in";
  SCRIPT="Test.in";
  OUTPUT="Test.out";
  GAUSS_PAR_HEAD="/usr/local/scriptConf/gaussParHead";
  g03 < $SCRIPT > $OUTPUT


Where '''Test''' is you input file's name and '''kimik133.q''' is the machine where you are submiting your job. In this case, the name of the script is Test.in.sub
qs 2 q g03 Test.in


To sumbit the job, type
== '''Pseudo-benchmark''' ==
  qsub Test.in.sub


Organometallic system
Stoichiometry C11H17BBrNO3P2Pd
program: G03
functional: b3lyp
# of basis functions: 404
  '''Frequency calculation'''
  --------------------------------------  -------------------
            Time(s)            #cpus    speedup  efficiency
  ---------------------------------------  ------------------       
  4quad      4451 0.29    16     2.8     70%
  2quad      7087 0.47     8      1.8     90%
  1quad    12387 0.82     4      1.0     100%
  -------------------------------------------------------------   
  4nodes(a) 15154 1.00     4      ---      ---
  -------------------------------------------------------------       
(a) large queue
Speedup    = T_1quad/T_#quad
Efficiency = Speedup/#quad


Fullerene
Stoichiometry C60
program: Jaguar
functional: b3lyp
# of basis functions: 900
  '''Frequency calculation'''
  --------------------------------------
            Time(s)            #cpus 
  --------------------------------------       
  1quad      7378 3.16     4           
  2nodes(a)  2333 1.00     2   
  --------------------------------------       
(a) short queue
O_O! #@"! So, don't use Jaguar in the Quadcores.
----
----


Latest revision as of 10:02, 21 September 2011

go back to Main_Page, Computational Resources, Clusters, Local Clusters, kimik2


Hardware: 

Processor: Core 2 Quad 2.40 Ghz
RAM:       4 Gb
scratch:   120 Gb

Queue name: 

nanYar.quad

Nodes availables: 

There are right now 43 nodes available.

Kind of jobs: 

By now, please send ONLY Gaussian's jobs.

Ask for: 

NPROC=4


Submit calculations[edit]

At the moment, to submit calculations:

  • Add %nproc=4 in the Gaussian input file, if you use the submision script qs it will be added automatically to the in.in file.
  • To sumbit the job, type:
 qs [number_of_quads]  q  job_type  script_to_submit_or_input_file.in

e.g. 

qs 2 q g03 Test.in

Pseudo-benchmark[edit]

Organometallic system 
Stoichiometry C11H17BBrNO3P2Pd
program: G03 
functional: b3lyp
# of basis functions: 404 

 Frequency calculation
 --------------------------------------   -------------------
            Time(s)             #cpus     speedup  efficiency
 ---------------------------------------  ------------------        
  4quad      4451	0.29  	   16	    2.8	     70%
  2quad      7087	0.47	    8  	    1.8	     90%
  1quad     12387	0.82	    4       1.0	    100%
 -------------------------------------------------------------     
  4nodes(a) 15154	1.00	    4       ---      ---
 -------------------------------------------------------------        
(a) large queue


Speedup    = T_1quad/T_#quad

Efficiency = Speedup/#quad

Fullerene
Stoichiometry C60
program: Jaguar 
functional: b3lyp
# of basis functions: 900 

 Frequency calculation
 --------------------------------------
            Time(s)             #cpus   
 --------------------------------------        
  1quad      7378	3.16	    4             
  2nodes(a)  2333	1.00	    2     
 --------------------------------------        
(a) short queue

O_O! #@"! So, don't use Jaguar in the Quadcores.

In the future, for more slots ask for multiple of 4. 


If you feel that something its wrong or can be improved please add an entry here or at forums.
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