Changes between Initial Version and Version 1 of qcg-simple-examples

Timestamp:

08/08/13 16:52:10 (12 years ago)

Author:

piontek

Comment:

--

qcg-simple-examples

@@ +1 @@
+[[PageOutline]]
+
+'''IMPORTANT:''' All descriptions presented on this page are only examples and there is no guaranty that they can be executed without prior modifications especially as almost all of them require input files to be present in specific locations.
+
+= Popular legacy applications =
+
+== Abaqus ==
+{{{
+#QCG host=nova
+#wymaganie pamieci w mb
+#QCG memory=2000
+#liczba wezlow/rdzeni
+#QCG nodes=1:4
+ 
+#QCG application=abaqus
+#QCG argument=design.inp
+#QCG stage-in-file=design.inp
+ 
+#QCG stage-out-dir= . -> abaqus-results-${JOB_ID}
+#QCG output=output.${JOB_ID}
+#QCG error=error.${JOB_ID}
+}}}
+ 
+== Abinit ==
+{{{
+#QCG queue=plgrid-long
+#QCG note=4QLsTi+Ni_h3
+#QCG output=myjob.log
+#QCG error=myjob.error
+#QCG stage-in-file=Bi2Se3.in
+#QCG stage-in-file=Bi2Se3x.files
+#QCG stage-in-file=34se.6.hgh
+#QCG stage-in-file=83bi.5.hgh
+#QCG stage-in-file=22ti.4.hgh
+#QCG stage-in-file=28ni.10.hgh
+#QCG stage-out-dir=. -> results-${JOB_ID}
+#QCG nodes=1:8
+#QCG memory=12000
+#QCG host=hydra
+#QCG walltime=P7D
+#QCG application=abinit
+#QCG argument=Bi2Se3x.files
+#QCG grant=moj_grant
+}}}
+ 
+== Gamess ==
+{{{
+ #!/bin/bash
+  
+#QCG queue=plgrid-long
+#QCG walltime=P4D
+#QCG note=nano3_3+hcl-gms-mp2-accd_F00_galera
+#QCG output=outputs/nano3_3+hcl-gms-mp2-accd_F00_galera.output
+#QCG error=outputs/nano3_3+hcl-gms-mp2-accd_F00_galera.error
+#QCG stage-in-file=nano3_3+hcl-gms-mp2-accd_F00_galera.inp -> nano3_3+hcl-gms-mp2-accd_F00_galera.inp
+#QCG stage-out-file=nano3_3+hcl-gms-mp2-accd_F00_galera.log -> outputs/nano3_3+hcl-gms-mp2-accd_F00_galera.log
+#QCG nodes=2:12
+#QCG memory=16000
+#QCG host=galera
+#QCG application=gamess
+#QCG argument=nano3_3+hcl-gms-mp2-accd_F00_galera.inp
+}}}
+ 
+
+== Gaussian ==
+{{{
+#QCG queue=plgrid-long
+#QCG name=etanal
+#QCG note=etanal Gaussian
+#QCG output=${JOB_ID}.output
+#QCG error=${JOB_ID}.error
+#QCG stage-in-file=etanal.gjf -> etanal.gjf
+#QCG stage-out-file=wynik.tar -> ${JOB_ID}.tar
+#QCG nodes=1:12
+#QCG host=galera.task.gda.pl
+#QCG walltime=P7D
+#QCG notify=mailto:piontek@man.poznan.pl
+#QCG memory=15360
+ 
+#QCG preprocess=echo START
+#QCG application=g09
+#QCG argument=etanal.gjf
+#QCG postprocess=tar cvf wynik.tar *
+}}}
+ 
+
+== NAMD ==
+{{{
+#QCG note=NAMD apoa1
+#QCG name=ex_1                                                           
+#QCG host=hydra.icm.edu.pl                                               
+#QCG walltime=PT10M                                                      
+#QCG queue=plgrid                                                        
+#QCG nodes=1:12:12                                                                                                     
+#QCG output=apoa1.output                                                 
+#QCG error=apoa1.error                                                   
+#QCG application=NAMD                                                    
+#QCG argument=apoa1/apoa1.namd                                           
+#QCG stage-in-file=apoa1.zip                                             
+#QCG preprocess=unzip apoa1.zip                                          
+#QCG stage-out-dir=. -> results                                       
+#QCG notify=xmpp:tomasz.piontek@plgrid.pl 
+#QCG watch-output=mailto:tp@mail,20,ENERGY
+}}}
+
+== R ==
+{{{
+#QCG host=zeus
+#QCG queue=plgrid
+#QCG walltime=PT5M
+#QCG application=R
+  
+#QCG output=${JOB_ID}.output
+#QCG error=${JOB_ID}.error
+#QCG argument=PoDA-example.R
+#QCG stage-in-file=PoDA-example.R
+#QCG stage-in-file=PoDA.R
+#QCG stage-in-file=PoDA-example-data.RData
+#QCG stage-out-file=Rplots.pdf
+}}}
+ 
+== Some useful examples ==
+
+== Text file conversion ==
+{{{
+#!/bin/bash
+  
+#QCG host=zeus
+#QCG queue=plgrid
+#QCG walltime=PT5M
+  
+#QCG output=${JOB_ID}.output
+#QCG error=${JOB_ID}.error
+  
+#QCG stage-in-file=input.txt -> lower.txt
+  
+cat lower.txt | tr "[:lower:]" "[:upper:]" > upper.txt
+echo "Liczba znakow: " `wc -m upper.txt`
+sleep 120
+echo "Koniec: " `date`
+  
+#QCG stage-out-file=upper.txt -> ${JOB_ID}.upper
+}}}
+
+
+== MPI application ==
+{{{
+#QCG note=CPminV04_mpi1024
+#QCG host=galera.task.gda.pl
+#QCG nodes=4:12:2
+#QCG queue=plgrid
+#QCG stage-in-dir=.->.
+#QCG stage-in-file=../minV04
+#QCG stage-out-dir=outdata
+#QCG stage-out-file=log
+module load openmpi
+mpirun -machinefile $QCG_NODEFILE --cpus-per-proc 6 --bysocket  ./minV04 > log
+}}}