[Bioclusters] Re: [GE users] submit a job
bioinfo Gu
bioclusters@bioinformatics.org
Thu, 21 Nov 2002 07:33:43 -0800 (PST)
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Hi Chris:
Thank you very much for your reply. Now I have installed blast program on NFS disk and make symbolic links. But when I run qsub blast.script, it still does not work.
******athena is matser and execution host, apollo is execution host. *****
when I run "qsub -q athena.q blast.script", it will give me errors:
/usr/local/bin/blastall.REAL: Exec format error. Binary file not executable.
Even I run :
athena.wistar.upenn.edu> blastall.REAL
/usr/local/bin/blastall: Exec format error. Binary file not executable.
when I login as root: the error is :
/db5/apollo/programs/blast/blastall: syntax error at line 2: `(' unexpected
***But when I run the same program on apollo, everything is fine.
I am new to blast program, Thank you very much for your help.
Grace
chris dagdigian <dag@sonsorol.org> wrote:
Grace,
Your life will be easier if your gridengine ncbi-blast system had the
same path to the blastall binary on all your execution hosts. Can you
set this up for instance with a symbolic links? It makes writing your
scripts much easier. If all else fails you can put the blastall binary
into an NFS share, presumably you already have at least one NFS share
going for the sge stuff.
It would also be helpful to us if you posted the output of the blastall
error message you are seeing-- believe it or not they actually do try to
tell you what is going wrong. From memory I seem to recall that if you
do not use the .ncbirc config file you need to set at least two
environment variables: $BLASTDB points to the sequence databases and
$BLASTMAT points to the directory that holds all of the scoring matrices.
Since you can't directly qsub calls to binaries with gridengine what you
need to do is create a perl or shell script that will run the blast
query for you. You should prove that this script will work when run
individually from any execution node before you try sending it to
gridengine via qsub.
I'd suggest following up with a reply strictly to the
bioclusters@bioinformatics.org mailing list as this is starting to get
off-topic for the sge-users list. The bioclusters folks deal with blast
farms all the time.
Regards,
Chris
bioteam.net
bioinfo Gu wrote:
> Hi,
>
> I have installed the gridengine on two machines. Here is my structure:
> one(athena) is master node(not execution node), another(apollo) is
> execution node. I have submit the simple.sh and sleeper.sh, both of
> them work fine. But I want to run my own jobs on gridengine. I
> have installed 'blastall' on both machine,
>
> athena: /path/to/blastprogram/blastall
>
> apollo: /path/to/blastprogram/blastall
>
> these two paths are different.
>
> I have checked the environmental variable for blastall program on
> execution node, it should be all right, but when I 'qsub
> blastall_script', it always give me some error about blastall program.
> so I doubt my environmental variable is not right under gridengine.
>
> My question is when I run 'qsub blastall' on athena(master), which
> program should be invoke, blastall will take agvantage of the
> resource of each execution node, is it right? Suppose that I have
> more than one execution nodes, how can I explain the environmental
> variables(or other resources). I found somewhere, but now I can not
> remember.
>
> Thank you very much.
>
> Grace
>
>
--
Chris Dagdigian,
Bioteam.net - Independent Bio-IT & Informatics consulting
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net
_______________________________________________
Bioclusters maillist - Bioclusters@bioinformatics.org
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<P>Hi Chris:
<P>Thank you very much for your reply. Now I have installed blast program on NFS disk and make symbolic links. But when I run qsub blast.script, it still does not work.
<P>******athena is matser and execution host, apollo is execution host. *****
<P>when I run "qsub -q athena.q blast.script", it will give me errors:
<P>/usr/local/bin/blastall.REAL: Exec format error. Binary file not executable.
<P>Even I run : </P>
<P>athena.wistar.upenn.edu> blastall.REAL<BR>/usr/local/bin/blastall: Exec format error. Binary file not executable.<BR></P>
<P>when I login as root: the error is :</P>
<P>/db5/apollo/programs/blast/blastall: syntax error at line 2: `(' unexpected</P>
<P>***But when I run the same program on apollo, everything is fine.
<P>I am new to blast program, Thank you very much for your help.
<P>Grace
<P> <STRONG><EM>chris dagdigian <dag@sonsorol.org></EM></STRONG> wrote:
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">
<P><BR>Grace,<BR><BR>Your life will be easier if your gridengine ncbi-blast system had the <BR>same path to the blastall binary on all your execution hosts. Can you <BR>set this up for instance with a symbolic links? It makes writing your <BR>scripts much easier. If all else fails you can put the blastall binary <BR>into an NFS share, presumably you already have at least one NFS share <BR>going for the sge stuff.<BR><BR>It would also be helpful to us if you posted the output of the blastall <BR>error message you are seeing-- believe it or not they actually do try to <BR>tell you what is going wrong. From memory I seem to recall that if you <BR>do not use the .ncbirc config file you need to set at least two <BR>environment variables: $BLASTDB points to the sequence databases and <BR>$BLASTMAT points to the directory that holds all of the scoring matrices.<BR><BR>Since you can't directly qsub calls to binaries with gridengine what you <BR>need to do is create a perl or shell sc
ript that will run the blast <BR>query for you. You should prove that this script will work when run <BR>individually from any execution node before you try sending it to <BR>gridengine via qsub.<BR><BR>I'd suggest following up with a reply strictly to the <BR>bioclusters@bioinformatics.org mailing list as this is starting to get <BR>off-topic for the sge-users list. The bioclusters folks deal with blast <BR>farms all the time.<BR><BR>Regards,<BR>Chris<BR>bioteam.net<BR><BR><BR>bioinfo Gu wrote:<BR><BR>> Hi,<BR>><BR>> I have installed the gridengine on two machines. Here is my structure: <BR>> one(athena) is master node(not execution node), another(apollo) is <BR>> execution node. I have submit the simple.sh and sleeper.sh, both of <BR>> them work fine. But I want to run my own jobs on gridengine. I <BR>> have installed 'blastall' on both machine,<BR>><BR>> athena: /path/to/blastprogram/blastall<BR>><BR>> apollo: /path/to/blastprogram/blastal
l<BR>><BR>> these two paths are different.<BR>><BR>> I have checked the environmental variable for blastall program on <BR>> execution node, it should be all right, but when I 'qsub <BR>> blastall_script', it always give me some error about blastall program. <BR>> so I doubt my environmental variable is not right under gridengine.<BR>><BR>> My question is when I run 'qsub blastall' on athena(master), which <BR>> program should be invoke, blastall will take agvantage of the <BR>> resource of each execution node, is it right? Suppose that I have <BR>> more than one execution nodes, how can I explain the environmental <BR>> variables(or other resources). I found somewhere, but now I can not <BR>> remember.<BR>><BR>> Thank you very much.<BR>><BR>> Grace <BR>><BR>><BR><BR>-- <BR>Chris Dagdigian, <DAG@SONSOROL.ORG><BR>Bioteam.net - Independent Bio-IT & Informatics consulting<BR>Office: 617-666-6454, Mobile: 617-877-54
98, Fax: 425-699-0193<BR>PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net <BR><BR><BR><BR><BR>_______________________________________________<BR>Bioclusters maillist - Bioclusters@bioinformatics.org<BR>https://bioinformatics.org/mailman/listinfo/bioclusters</P></BLOCKQUOTE><p><br><hr size=1>Do you Yahoo!?<br>
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