MOLCAS script to launch MVAPICH/NoPBS job

This script will launch molcas on N cpus (depending on the variable $CPUS)  using the MVAPICH/parallel paradigm.
Used to test molcas installation in a totally occupied cluster!!

*************************************************************************
#!/bin/bash
MOLCAS=/data1/aldo/Source-Code/molcas/molcas74
export MOLCAS

#crates the temporary output files inside the working directory
MOLCAS_WORKDIR=
export MOLCAS_WORKDIR

#How many CPUS do you want for the calculation?
CPUS=2
export CPUS

# As I'm not using the PBS queue system at this time I've to write a file with
# the name of the hosts which will be used for the calculation (nodelist)
# and put it inside the working area, so molcas can find it !
PBS_NODEFILE=/data1/aldo/molcas/test-ch4/nodelist
export PBS_NODEFILE

#Execute the application by calling the driver script, here specifying the whole path
# because is not in a user wide available location...yet !

/data1/aldo/Source-Code/molcas/molcas74/sbin/molcas.driver molcas-input

# Ready to rock !!
***************************************************************

MOLCAS command line " molcas help basis XX"

** type  molcas help basis A  to list basis set for the element A
*********************************************************************
$> molcas help basis Pd
Recommended basis sets for  Pd
Pd.ANO-RCC-MB                            Pd.ANO-RCC...5s4p2d.                   
Pd.ANO-RCC-VDZ                           Pd.ANO-RCC...6s5p3d.                   
Pd.ANO-RCC-VDZP                          Pd.ANO-RCC...6s5p3d1f.                 
Pd.ANO-RCC-VTZP                          Pd.ANO-RCC...7s6p4d2f1g.               
Pd.ANO-RCC-VQZP                          Pd.ANO-RCC...8s7p5d3f2g1h.               

 Other basis sets for  Pd
Pd.ECP.HW.5s6p4d.3s3p2d.18e-LANL2DZ.
Pd.ANO-DK3.Tsuchiya.23s19p12d.4s3p2d.
Pd.ano-rcc.Roos.21s18p13d6f4g2h.10s9p9d6f4g2h.
Pd.ECP.Dolg.8s7p6d.6s5p3d.18e-MWB.                                                    
Pd.ECP.Barandiaran.11s8p7d.1s2p2d.16e-CG-AIMP.                                
Pd.ECP.Barandiaran.11s8p7d3f.1s2p2d1f.16e-CG-AIMP.                            
Pd.ECP.Barandiaran.11s8p7d.1s2p2d.16e-NR-AIMP.                                
Pd.ECP.Rakowitz.11s8p7d3f.5s4p4d1f.18e-NP-AIMP.                               
Pd.ECP.Stoll.8s7p6d.6s5p3d.18e-MWB.
Pd.Raf-r.Wahlgren.17s13p9d2f.7s6p4d2f.                                   
Pd.ECP.Hay-Wadt.5s6p4d.3s3p2d.18e-LANL2DZ.
*******************************************************************

MOLCAS command line " molcas help"

Useful Commands
******************************************************************
$> molcas help
Welcome to molcas help!

type  molcas help module  to get the list of keywords
type  molcas help module keyword  to get the description of keyword
type  molcas help -t text  to locate text
type  molcas help ENVIRONMENT  to list ENV variables
type  molcas help EMIL  to list EMIL commands
type  molcas help basis A  to list basis set for the element A

Installed modules:
ALASKA CASPT2 CASVB CCSDT CHCC CHECK CHT3 CIISCMNG CPF EMIL ESPF ESPF
EXPBAS FFPT GATEWAY GENANO GRID_IT GUESSORB GUGA LOCALISATION LOPROP M2SO
MBPT2 MCKINLEY MCLR MOTRA MRCI MULA NUMERICAL_GRADIENT PARALLELTEST RASSCF
RASSI SCF SEWARD SLAPAF VIBROT

Utilities:
edit verify installpkg help find copy install timing defdoc snooper revert
getpatch uninstallpkg checksum uninstall gv
*********************************************************************

Copy single file to multiple directories

Parent_Directoy
Filename1
Child_Directory1
Child_Directory2
Child_Directory3
Child_Directory4
....
So I need to copy Filename1 to all of the Child_Directories.

<!--ntstart--><b>find <parent directory> -type d -exec cp <parent directory>/<Filename1> {}/ \;</b><!--ntend-->

or in a bourne/shell script :
If you have other junk in the parent dir but a pattern that matches all subdirs (eg Child_Directory*), you can do this (bourne/ksh/bash):

<!--ntstart--><b>for subdir in <parent directory>/<pattern> ; do cp <parent directory>/<Filename1> ${subdir}/ ; done</b><!--ntend-->

Delete Multiple Jobs

* Delete jobs with qdel*

>qdel 1908.titan.physics.umass.edu

or do it with a qselect to pick all of your jobs

> qdel `qselect -u bbrau`

Changing Node State (Torque)

A common task is to prevent jobs from running on a particular node by marking it offline with pbsnodes -o nodename. Once a node has been marked offline, the scheduler will no longer consider it available for new jobs. Simply use pbsnodes -c nodename when the node is returned to service.

Also useful is pbsnodes -l which lists all nodes with an interesting state, such as down, unknown, or offline. This provides a quick glance at nodes that migth be having a problem.

http://www.clusterresources.com/torquedocs21/3.3nodestate.shtml

Generador de enlaces a librerias en linea!!!

Generador de enlaces a librerias!

http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/