Using PBS in SPIDER to replace pubsub

• Only multiref alignment in spide rhas been optimised in spider mpi -- other commands are not accelerated
• Additionally, only a subset of commands are mp aware in spider
• Can use pbs to speed up loops on non-mp aware processes
• example of a spider script to speed up a non-linear filter

;========================input
fr l
[tomo]tomo1_crop.spd
;=========output=================
fr l
[filt]filt
;=========params==============
x90=60          ; cycles
x91=0.1         ; delta t
x92=0           ; sigma
;x93=0.05       ; lambda

;=============================
;---------- following set of commands sets the main qsub script for the cluster, one script per loop event
vm
echo "#!/bin/sh" > qsub-header.txt
vm
echo "#PBS -l select=ncpus=1:mem=6GB " >> qsub-header.txt
vm
echo "#PBS -l place=scatter" >> qsub-header.txt
vm
echo "cd /usr/data/asiebert/30_04_08_Rbs/tomo1" >> qsub-header.txt

;-----------------------------------------------

do lb1 x10=1,10                 ; this loop only makes the scripts using a "slave" script as template

  RR x93             ; adjust lambda according to the following sequence
  0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10                               ;  a nice log sequence

   vm
   echo "x93={**X93}" > filtscript{**x10}.$PRJEXT
   vm
   echo "x10={**X10}" >> filtscript{**x10}.$PRJEXT
   vm
   cat spider_script_filt1_clu_slave.$PRJEXT >> filtscript{**x10}.$PRJEXT
   vm
   cp qsub-header.txt qsub-script{**x10}.txt
   vm
   echo "/usr/apps/spidermp $PRJEXT/$DATEXT @filtscript{**x10}" >> qsub-script{**x10}.txt
   vm
   qsub qsub-script{**x10}.txt
lb1

en      ; end the main script                                                                  
 

• The script which actually does the work:

;========================input
fr l
[tomo]tomo1_crop.spd
;=========output=================
fr l
[filt]filt
;=========params==============
x90=60          ; cycles
x91=0.1         ; delta t
x92=0           ; sigma
;x93=0.05       ; lambda

;=============================

   ce ad
   [tomo]
   [filt]{***x10}
   HEG
   x90
   x91
   x92,x93
en d