This is a multi-part message in MIME format. ------=_NextPart_000_0014_01C2949F.76A71ED0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit 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 ! -- ------=_NextPart_000_0014_01C2949F.76A71ED0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <html> <head> <META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; = charset=3Dus-ascii"> <meta name=3DGenerator content=3D"Microsoft Word 10 (filtered)"> <style> <!-- /* Font Definitions */ @font-face {font-family:Gulim; panose-1:2 11 6 0 0 1 1 1 1 1;} @font-face {font-family:Tahoma; panose-1:2 11 6 4 3 5 4 4 2 4;} @font-face {font-family:"\@Gulim"; panose-1:0 0 0 0 0 0 0 0 0 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; margin-bottom:.0001pt; font-size:12.0pt; font-family:Gulim;} a:link, span.MsoHyperlink {color:blue; text-decoration:underline;} a:visited, span.MsoHyperlinkFollowed {color:purple; text-decoration:underline;} p.MsoAutoSig, li.MsoAutoSig, div.MsoAutoSig {margin:0cm; margin-bottom:.0001pt; font-size:12.0pt; font-family:"Times New Roman";} span.EmailStyle17 {font-family:Arial; color:navy;} @page Section1 {size:612.0pt 792.0pt; margin:72.0pt 90.0pt 72.0pt 90.0pt;} div.Section1 {page:Section1;} --> </style> </head> <body bgcolor=3Dwhite lang=3DEN-US link=3Dblue vlink=3Dpurple> <div class=3DSection1> <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> </div> </div> </div> </body> </html> ------=_NextPart_000_0014_01C2949F.76A71ED0--