[Bioclusters] how can I know jobs over ?
Wim Glassee
bioclusters@bioinformatics.org
Mon, 25 Nov 2002 16:26:52 +0100
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Hi,
I run SGE, but I believe the options are very similar to the openPBS
ones.
In SGE you can use the -hold_jid option of qsub to have a job wait for
the termination of other jobs.
qsub itself returns the jobid.
So, run your qsubs and store the jobids in a comma-separated list, then:
qsub -hold_jid $mylist merge.sh
Hope this helps,
Wim
Wim Glassee - BioInformatics Unit - Molecular Genetics Group -
Department of BioChemistry - University of Antwerp - BELGIUM - email:
wim.glassee@ua.ac.be
-----Original Message-----
From: bioclusters-admin@bioinformatics.org
[mailto:bioclusters-admin@bioinformatics.org] On Behalf Of zzar
Sent: maandag 25 november 2002 3:04
To: bioclusters@bioinformatics.org
Subject: [Bioclusters] how can I know jobs over ?
I using openPBS.
I want make many output file merge script ,after all job is over..
ex)
------------------------------
#!/bin/sh
qsub test.one.job
qsub test.two.job
qsub test.three.job
XXXXX if < all job over > XXXXXX
cat test.one.job >> all.job
cat test.two.job >> all.job
cat test.three.job >> all.job
--------------------------
output : test.one.job.o1 (2.3)
how can I know all job over ?
and I read qsub man page , -bb or -be option but error message =>
qsub: invalid option -- b
thank you !
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<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Hi,</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>I run SGE, but I believe the =
options are
very similar to the openPBS ones.</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>In SGE you can use the =
–hold_jid
option of qsub to have a job wait for the termination of other =
jobs.</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>qsub itself returns the =
jobid.</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>So, run your qsubs and store the =
jobids in
a comma-separated list, then:</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>qsub –hold_jid $mylist =
merge.sh</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Hope this helps,</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Wim</span></font></p>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<div>
<p class=3DMsoAutoSig><font size=3D3 color=3Dnavy face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:navy'>Wim Glassee - BioInformatics Unit =
-
Molecular Genetics Group - Department of BioChemistry - =
</span></font><font
color=3Dnavy><span style=3D'color:navy'>University</span></font><font =
color=3Dnavy><span
style=3D'color:navy'> of </span></font><font color=3Dnavy><span =
style=3D'color:navy'>Antwerp</span></font><font
color=3Dnavy><span style=3D'color:navy'> - </span></font><font =
color=3Dnavy><span
style=3D'color:navy'>BELGIUM</span></font><font color=3Dnavy><span
style=3D'color:navy'> - email: wim.glassee@ua.ac.be</span></font></p>
</div>
<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<div style=3D'border:none;border-left:solid blue 1.5pt;padding:0cm 0cm =
0cm 4.0pt'>
<p class=3DMsoNormal><font size=3D2 face=3DTahoma><span =
style=3D'font-size:10.0pt;
font-family:Tahoma'>-----Original Message-----<br>
<b><span style=3D'font-weight:bold'>From:</span></b>
bioclusters-admin@bioinformatics.org
[mailto:bioclusters-admin@bioinformatics.org] <b><span =
style=3D'font-weight:bold'>On
Behalf Of </span></b>zzar<br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> maandag 25 november =
2002
3:04<br>
<b><span style=3D'font-weight:bold'>To:</span></b> =
bioclusters@bioinformatics.org<br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> [Bioclusters] =
how can I
know jobs over ?</span></font></p>
<p class=3DMsoNormal><font size=3D3 face=3DGulim><span =
style=3D'font-size:12.0pt'> </span></font></p>
<div>
<p class=3DMsoNormal><font size=3D2 face=3DGulim><span =
style=3D'font-size:10.0pt'>I
using openPBS.</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3DGulim><span =
style=3D'font-size:10.0pt'>I
want make</span></font><font size=3D2 face=3D"Times New Roman"><span
style=3D'font-size:10.0pt;font-family:"Times New =
Roman"'> </span></font><font
size=3D2><span style=3D'font-size:10.0pt'>many output file merge script =
,after all
job is over..</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3DGulim><span =
style=3D'font-size:10.0pt'>ex)</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>------------------------------</span></font></=
p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'> #!/bin/sh</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>qsub test.one.job</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>qsub test.two.job</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>qsub test.three.job</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3DGulim><span =
style=3D'font-size:10.0pt'>XXXXX
if < all job over > XXXXXX</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>cat test.one.job >> =
all.job</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>cat test.two.job >></span></font><font =
size=3D2
face=3D"Times New Roman"><span =
style=3D'font-size:10.0pt;font-family:"Times New =
Roman"'> </span></font><font
size=3D2><span style=3D'font-size:10.0pt'> all.job</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>cat test.three.job >> =
all.job</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>--------------------------</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>output : test.one.job.o1 =
(2.3)</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3DGulim><span =
style=3D'font-size:10.0pt'>how
can</span></font><font size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:
10.0pt;font-family:"Times New Roman"'> </span></font><font =
size=3D2><span
style=3D'font-size:10.0pt'>I know all job over ?</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3DGulim><span =
style=3D'font-size:10.0pt'>and</span></font><font
size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:10.0pt;font-family:"Times New =
Roman"'> </span></font><font
size=3D2><span style=3D'font-size:10.0pt'>I read qsub man =
page</span></font><font
size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:10.0pt;font-family:"Times New =
Roman"'> </span></font><font
size=3D2><span style=3D'font-size:10.0pt'>,</span></font><font size=3D2
face=3D"Times New Roman"><span =
style=3D'font-size:10.0pt;font-family:"Times New =
Roman"'> </span></font><font
size=3D2><span style=3D'font-size:10.0pt'>-bb or -be =
option</span></font><font
size=3D2 face=3D"Times New Roman"><span =
style=3D'font-size:10.0pt;font-family:"Times New =
Roman"'> </span></font><font
size=3D2><span style=3D'font-size:10.0pt'> </span></font><font size=3D2
face=3D"Times New Roman"><span =
style=3D'font-size:10.0pt;font-family:"Times New =
Roman"'> </span></font><font
size=3D2><span style=3D'font-size:10.0pt'>but error message =3D> =
qsub: invalid
option -- b</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3DGulim><span =
style=3D'font-size:10.0pt'>thank
you !</span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt;font-family:"Times New Roman"'> </span></font></p>
</div>
<div>
<p class=3DMsoNormal><font size=3D2 face=3DGulim><span =
style=3D'font-size:10.0pt'>--</span></font></p>
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