Hi,
I've been able to successful run I-Tasser on multiple servers with out issue but when I went to run it in parallel mode I've been discovering qsub errors and the runI-Tasser.pl script is not progressing.
First I'm running it like this (I deleted my username and a few other things):
I-TASSERmod/runI-TASSER.pl -libdir `pwd`/database -seqname QH3N209 -datadir ~/myseq/ -java_home /my/path/to/jre -runstyle parallel -usrname myuser -pkgdir `pwd`
Your setting for I-TASSER is:
-pkgdir =/home/myuser/I-TASSER3.0
-libdir =/home/myuser/I-TASSER3.0/database
-seqname =myseq
-datadir =/home/myuser/myseq/
-usrname =myuser
-runstyle =parallel
-homoflag =real
-idcut =1
-ntemp =20
-nmodel =5
-LBS =false
-EC =false
-GO =false
1. make seq.txt and rmsinp
2.1 run Psi-blast
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
submit threading jobs first and run pair during threading
3.1 do threading
start parallel threading PPAS
Unable to run job: unknown resource "walltime".
Exiting.
start parallel threading dPPAS
Unable to run job: unknown resource "walltime".
Exiting.
start parallel threading dPPAS2
Unable to run job: unknown resource "walltime".
Exiting.
start parallel threading Env-PPAS
Unable to run job: unknown resource "walltime".
Exiting.
start parallel threading MUSTER
Unable to run job: unknown resource "walltime".
Exiting.
start parallel threading wPPAS
Unable to run job: unknown resource "walltime".
Exiting.
start parallel threading wdPPAS
Unable to run job: unknown resource "walltime".
Exiting.
start parallel threading wMUSTER
Unable to run job: unknown resource "walltime".
Exiting.
running pair now ................
So I went and looked at the runI-Tasser.pl script and replaced the line:
$bsub=`qsub -e $errfile -o $outfile -l $walltime -N $tag $jobname`; with:
$bsub=`qsub -e $errfile -o $outfile -l mem_free=16G,h_vmem=17G,h_stack=256M,h_cpu=72:00:00,s_rt=50:00:00,h_rt=72:00:00 -N $tag $jobname`;
This gave me the output: I again ran the same $I-TASSERmod/runI-TASSER.pl -libdir `pwd`/database -seqname QH3N209 -datadir ~/myseq/ -java_home /my/path/to/jre -runstyle parallel -usrname myuser -pkgdir `pwd`
Your setting for I-TASSER is:
-pkgdir =/home/myuser/I-TASSER3.0
-libdir =/home/myuser/I-TASSER3.0/database
-seqname =myseq
-datadir =/home/myuser/myseq/
-usrname =myuser
-runstyle =parallel
-homoflag =real
-idcut =1
-ntemp =20
-nmodel =5
-LBS =false
-EC =false
-GO =false
1. make seq.txt and rmsinp
2.1 run Psi-blast
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
submit threading jobs first and run pair during threading
3.1 do threading
start parallel threading PPAS
start parallel threading dPPAS
start parallel threading dPPAS2
start parallel threading Env-PPAS
start parallel threading MUSTER
start parallel threading wPPAS
start parallel threading wdPPAS
start parallel threading wMUSTER
running pair now ................
Which looked better... and I even saw the jobs in the queue (using qstat)
However I noticed the jobs disappeared from the queue very quickly and I had error files for each job, that contained:
err_dPPAS2_myseq:
use: Command not found.
ENV: Undefined variable.
Each job had a file like this. Any thoughts on what is causing this error and what I can do to fix it? It seems pretty clear that its like a simple problem with the way that qsub is being invoked but I don't really know enough about it to troubleshoot whats happening and my searching (this forum and Google) has been successful so far.