LD_LIBRARY_PATH is not generally set, as it is not the "right way" of doing things. http://prefetch.net/articles/linkers.badldlibrary.html
If you need it you can set it by changing it in your shell's .profile equivalent. There are lots of ways to do this depending on your user setup, what shell you use, etc. It looks like your script is running fine, note in this example that that variable holds a file name, not the list of machines itself. http://mitgcm.org/projects/MITGCM_CLUSTER/queues.htm On Mon, Dec 8, 2008 at 2:59 PM, Kist <[EMAIL PROTECTED]> wrote: > The problem is not my $PATH by itself, its the $PATH and the > $LD_LIBRARY_PATH when I run the script with qsub. > > #For example, this is the output of > ###"qsub script3.sh" is: > > /bin:/usr/bin:/opt/pvm3/lib:/opt/pvm3/lib/LINUX:/opt/pvm3/bin/LINUX:/opt/env-switcher/bin:/opt/pbs/bin:/opt/pbs/lib/xpbs/bin:/opt/c3-4/:/home/azaza/bin > . > > . > /var/spool/pbs/aux//107.fedhead.vcluster > > > ###and the output for "sh script3.sh" is: > > /usr/kerberos/sbin:/usr/kerberos/bin:/usr/lib/ccache:/opt/mpich-ch_p4-gcc-1.2.7/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/opt/pbs/bin:/opt/pbs/lib/xpbs/bin:/opt/pvm3/lib:/opt/pvm3/lib/LINUX:/opt/pvm3/bin/LINUX:/opt/env-switcher/bin:/opt/c3-4/:/root/bin > . > > . > > ###where "cat script3.sh" is: > > #!/bin/sh > #PBS -l nodes=2:ppn=1 > #PBS -N func > #PBS -q workq > echo $PATH > echo . > echo $LD_LIBRARY_PATH > echo . > echo $PBS_NODEFILE > > PS: I deletted and added the nodes again, and now the $PATH variable is set, > but I don't know why... > 2008/12/8 Michael Edwards <[EMAIL PROTECTED]> >> >> It is not very likely that OSCAR made your PATH blank. Try this one, >> though you'll have to modify it and take out the stuff that is >> different/irrelevant to your system. >> >> export >> PATH=/opt/csw/gcc4/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/opt/sge/bin/lx26-amd64:/opt/pvm3/lib:/opt/pvm3/lib/LINUX64:/opt/pvm3/bin/LINUX64:/usr/local/share/genesis:/usr/local/matlab/bin:/opt/env-switcher/bin:/opt/lam-7.1.2/bin:/opt/c3-4/:/usr/sbin:/usr/local/starp/2.6.0/bin:/home/edwards/bin >> >> See if it works after setting this path. >> >> On Fri, Dec 5, 2008 at 7:15 PM, Kist <[EMAIL PROTECTED]> wrote: >> > Exactly. >> > >> > echo $PATH >> > echo $LD_LIBRARY_PATH >> > >> > when submiting with qsub returns nothing. >> > >> > And I'm not finding where to fix this. >> > >> > Btw, thanks! >> > >> > 2008/12/5 Michael Edwards <[EMAIL PROTECTED]> >> >> >> >> When you say "It returns nothing." what are you reffering to? >> >> echo $PATH? Then that would be bad and most things will not work. >> >> >> >> On Fri, Dec 5, 2008 at 2:55 PM, Kist <[EMAIL PROTECTED]> wrote: >> >> > It returns nothing. >> >> > Werid. How can the tests run? >> >> > How can I set this up? >> >> > >> >> > 2008/12/1 Greenseid, Joseph M. <[EMAIL PROTECTED]> >> >> >> >> >> >> The command Michael asked was "mpirun," as there's no command called >> >> >> mpi. >> >> >> >> >> >> Can you try submitting a PBS job (via qsub) that runs the commands >> >> >> "echo >> >> >> $PATH" and "echo $LD_LIBRARY_PATH?" >> >> >> >> >> >> ex: >> >> >> >> >> >> #!/bin/sh >> >> >> #PBS -l nodes=1:ppn=1 >> >> >> #PBS -l walltime=00:05:00 >> >> >> echo $PATH >> >> >> echo $LD_LIBRARY_PATH >> >> >> >> >> >> It sounds like your PATH and/or LD_LIBRARY_PATH are somehow getting >> >> >> munged >> >> >> when you submit jobs. >> >> >> >> >> >> Also, with the results of this, can you show what $PATH and >> >> >> $LD_LIBRARY_PATH look like in your normal environment (just run the >> >> >> commands >> >> >> at the command line)? >> >> >> >> >> >> --Joe >> >> >> >> >> >> ________________________________ >> >> >> >> >> >> From: Kist [mailto:[EMAIL PROTECTED] >> >> >> Sent: Mon 12/1/2008 2:08 AM >> >> >> To: oscar-users@lists.sourceforge.net >> >> >> Subject: Re: [Oscar-users] Problem submitting jobs at Fedora 8 >> >> >> withOscar5.1b2 >> >> >> >> >> >> >> >> >> 'which mpi' returns: >> >> >> /usr/bin/which: no mpi in ( ... al lot o directories ...) >> >> >> >> >> >> And if I run it with full path it returns library errors when trying >> >> >> to >> >> >> run my app. >> >> >> >> >> >> >> >> >> 2008/11/28 Michael Edwards <[EMAIL PROTECTED]> >> >> >> >> >> >> >> >> >> Then MPI is working because the tests use it from inside the >> >> >> scheduler. >> >> >> >> >> >> What does "which mpirun" return when you run it on a node? >> >> >> What happens if you run it on a node with the full path? >> >> >> >> >> >> >> >> >> On Fri, Nov 28, 2008 at 3:21 PM, Kist <[EMAIL PROTECTED]> >> >> >> wrote: >> >> >> > Completely. >> >> >> > >> >> >> > 2008/11/22 Michael Edwards <[EMAIL PROTECTED]> >> >> >> >> >> >> >> >> Do the tests in the install wizard run correctly? >> >> >> >> >> >> >> >> On Sat, Nov 22, 2008 at 5:33 PM, Kist <[EMAIL PROTECTED]> >> >> >> wrote: >> >> >> >> > Sorry about just answering this now. >> >> >> >> > I am having some problems submitting jobs using xpbs, >> >> >> because >> >> >> the >> >> >> >> > buttons on >> >> >> >> > the bottom of the xpbs window don't appear with my >> >> >> screen >> >> >> resolution. >> >> >> >> > I am trying to fix it, but I just could not find time to >> >> >> do >> >> >> this yet. >> >> >> >> > >> >> >> >> > Any other idea I can try? >> >> >> >> > >> >> >> >> > Thanks in advance. >> >> >> >> > >> >> >> >> > 2008/11/14 Ali Nazemian <[EMAIL PROTECTED]> >> >> >> >> >> >> >> >> >> >> Hi, >> >> >> >> >> Do u meet same result with using "xpbs" (GUI mode) ?! >> >> >> >> >> >> >> >> >> >> On Fri, Nov 14, 2008 at 8:23 PM, Kist >> >> >> <[EMAIL PROTECTED]> >> >> >> wrote: >> >> >> >> >>> >> >> >> >> >>> I has an Oscar 5.0 over SuSE 10.0 and another over >> >> >> Fedora >> >> >> (6 >> >> >> or 7, I >> >> >> >> >>> can't remember) but they crashed and I installed an >> >> >> Oscar >> >> >> 5.1b2 over >> >> >> >> >>> Fedora >> >> >> >> >>> 8. >> >> >> >> >>> >> >> >> >> >>> All succeeded well in the instalation and testing, but >> >> >> when >> >> >> I tryed to >> >> >> >> >>> submitt a job with qsub (the same way I was doing in >> >> >> the >> >> >> old >> >> >> cluster) >> >> >> >> >>> it >> >> >> >> >>> returned weird errors like: >> >> >> >> >>> "mpirun: Command not found". >> >> >> >> >>> >> >> >> >> >>> Also, when i run, for example, "mpirun -np 2 program" >> >> >> it >> >> >> succeeds, but >> >> >> >> >>> "echo $PBS_NODEFILE" retuns a blank line. >> >> >> >> >>> >> >> >> >> >>> My script works with qsub when I change 'mpiexec' for >> >> >> 'pbsdsh' in the >> >> >> >> >>> execution line, but I got some execution errors when I >> >> >> try >> >> >> to load >> >> >> >> >>> some >> >> >> >> >>> libraries. >> >> >> >> >>> >> >> >> >> >>> Can someone give me a light? >> >> >> >> >>> >> >> >> >> >>> Thanks! >> >> >> >> >>> >> >> >> >> >>> -- >> >> >> >> >>> Raul Kist >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> >> >> >>> This SF.Net email is sponsored by the Moblin Your Move >> >> >> Developer's >> >> >> >> >>> challenge >> >> >> >> >>> Build the coolest Linux based applications with Moblin >> >> >> SDK & >> >> >> win great >> >> >> >> >>> prizes >> >> >> >> >>> Grand prize is a trip for two to an Open Source event >> >> >> anywhere in the >> >> >> >> >>> world >> >> >> >> >>> >> >> >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> >> >> >>> _______________________________________________ >> >> >> >> >>> Oscar-users mailing list >> >> >> >> >>> Oscar-users@lists.sourceforge.net >> >> >> >> >>> >> >> >> https://lists.sourceforge.net/lists/listinfo/oscar-users >> >> >> >> >>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> A.Nazemian >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> >> >> >> This SF.Net email is sponsored by the Moblin Your Move >> >> >> Developer's >> >> >> >> >> challenge >> >> >> >> >> Build the coolest Linux based applications with Moblin >> >> >> SDK >> >> >> & >> >> >> win great >> >> >> >> >> prizes >> >> >> >> >> Grand prize is a trip for two to an Open Source event >> >> >> anywhere in the >> >> >> >> >> world >> >> >> >> >> >> >> >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> >> >> >> _______________________________________________ >> >> >> >> >> Oscar-users mailing list >> >> >> >> >> Oscar-users@lists.sourceforge.net >> >> >> >> >> >> >> >> https://lists.sourceforge.net/lists/listinfo/oscar-users >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> >> >> > This SF.Net email is sponsored by the Moblin Your Move >> >> >> Developer's >> >> >> >> > challenge >> >> >> >> > Build the coolest Linux based applications with Moblin >> >> >> SDK >> >> >> & >> >> >> win great >> >> >> >> > prizes >> >> >> >> > Grand prize is a trip for two to an Open Source event >> >> >> anywhere >> >> >> in the >> >> >> >> > world >> >> >> >> > >> >> >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> >> >> > _______________________________________________ >> >> >> >> > Oscar-users mailing list >> >> >> >> > Oscar-users@lists.sourceforge.net >> >> >> >> > https://lists.sourceforge.net/lists/listinfo/oscar-users >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> >> >> This SF.Net email is sponsored by the Moblin Your Move >> >> >> Developer's >> >> >> >> challenge >> >> >> >> Build the coolest Linux based applications with Moblin SDK >> >> >> & >> >> >> win >> >> >> great >> >> >> >> prizes >> >> >> >> Grand prize is a trip for two to an Open Source event >> >> >> anywhere >> >> >> in the >> >> >> >> world >> >> >> >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> >> >> _______________________________________________ >> >> >> >> Oscar-users mailing list >> >> >> >> Oscar-users@lists.sourceforge.net >> >> >> >> https://lists.sourceforge.net/lists/listinfo/oscar-users >> >> >> > >> >> >> > >> >> >> > >> >> >> > -- >> >> >> > Raul Kist >> >> >> > Microsoft Student Partner >> >> >> > Microsoft Innovation Center - Software Architect >> >> >> > Computer Engineering - UNICAMP - Brazil >> >> >> > [EMAIL PROTECTED] >> >> >> > http://raulkist.spaces.live.com/ >> >> >> > http://www.lms.ic.unicamp.br >> >> >> <http://www.lms.ic.unicamp.br/> >> >> >> > http://www.codeplex.com/LMSU >> >> >> > http://www.codeplex.com/NDOS >> >> >> > >> >> >> > >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> >> > This SF.Net email is sponsored by the Moblin Your Move >> >> >> Developer's challenge >> >> >> > Build the coolest Linux based applications with Moblin SDK >> >> >> & >> >> >> win >> >> >> great >> >> >> > prizes >> >> >> > Grand prize is a trip for two to an Open Source event >> >> >> anywhere >> >> >> in >> >> >> the world >> >> >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> >> > _______________________________________________ >> >> >> > Oscar-users mailing list >> >> >> > Oscar-users@lists.sourceforge.net >> >> >> > https://lists.sourceforge.net/lists/listinfo/oscar-users >> >> >> > >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> >> This SF.Net email is sponsored by the Moblin Your Move >> >> >> Developer's >> >> >> challenge >> >> >> Build the coolest Linux based applications with Moblin SDK & >> >> >> win >> >> >> great prizes >> >> >> Grand prize is a trip for two to an Open Source event >> >> >> anywhere >> >> >> in >> >> >> the world >> >> >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> >> _______________________________________________ >> >> >> Oscar-users mailing list >> >> >> Oscar-users@lists.sourceforge.net >> >> >> https://lists.sourceforge.net/lists/listinfo/oscar-users >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Raul Kist >> >> >> Microsoft Student Partner >> >> >> Microsoft Innovation Center - Software Architect >> >> >> Computer Engineering - UNICAMP - Brazil >> >> >> [EMAIL PROTECTED] >> >> >> http://raulkist.spaces.live.com/ >> >> >> http://www.lms.ic.unicamp.br <http://www.lms.ic.unicamp.br/> >> >> >> http://www.codeplex.com/LMSU >> >> >> http://www.codeplex.com/NDOS >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> >> >> challenge >> >> >> Build the coolest Linux based applications with Moblin SDK & win >> >> >> great >> >> >> prizes >> >> >> Grand prize is a trip for two to an Open Source event anywhere in >> >> >> the >> >> >> world >> >> >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> >> >> _______________________________________________ >> >> >> Oscar-users mailing list >> >> >> Oscar-users@lists.sourceforge.net >> >> >> https://lists.sourceforge.net/lists/listinfo/oscar-users >> >> >> >> >> > >> >> > >> >> > >> >> > -- >> >> > Raul Kist >> >> > Microsoft Student Partner >> >> > Microsoft Innovation Center - Software Architect >> >> > Computer Engineering - UNICAMP - Brazil >> >> > [EMAIL PROTECTED] >> >> > http://raulkist.spaces.live.com/ >> >> > http://www.lms.ic.unicamp.br >> >> > http://www.codeplex.com/LMSU >> >> > http://www.codeplex.com/NDOS >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------------ >> >> > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, >> >> > Nevada. >> >> > The future of the web can't happen without you. Join us at MIX09 to >> >> > help >> >> > pave the way to the Next Web now. Learn more and register at >> >> > >> >> > >> >> > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ >> >> > _______________________________________________ >> >> > Oscar-users mailing list >> >> > Oscar-users@lists.sourceforge.net >> >> > https://lists.sourceforge.net/lists/listinfo/oscar-users >> >> > >> >> > >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, >> >> Nevada. >> >> The future of the web can't happen without you. Join us at MIX09 to >> >> help >> >> pave the way to the Next Web now. Learn more and register at >> >> >> >> >> >> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ >> >> _______________________________________________ >> >> Oscar-users mailing list >> >> Oscar-users@lists.sourceforge.net >> >> https://lists.sourceforge.net/lists/listinfo/oscar-users >> > >> > >> > >> > -- >> > Raul Kist >> > Microsoft Student Partner >> > Microsoft Innovation Center - Software Architect >> > Computer Engineering - UNICAMP - Brazil >> > [EMAIL PROTECTED] >> > http://raulkist.spaces.live.com/ >> > http://www.lms.ic.unicamp.br >> > http://www.codeplex.com/LMSU >> > http://www.codeplex.com/NDOS >> > >> > >> > ------------------------------------------------------------------------------ >> > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, >> > Nevada. >> > The future of the web can't happen without you. Join us at MIX09 to >> > help >> > pave the way to the Next Web now. Learn more and register at >> > >> > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ >> > _______________________________________________ >> > Oscar-users mailing list >> > Oscar-users@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/oscar-users >> > >> > >> >> >> ------------------------------------------------------------------------------ >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, >> Nevada. >> The future of the web can't happen without you. Join us at MIX09 to help >> pave the way to the Next Web now. Learn more and register at >> >> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ >> _______________________________________________ >> Oscar-users mailing list >> Oscar-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/oscar-users > > > > -- > Raul Kist > Microsoft Student Partner > Microsoft Innovation Center - Software Architect > Computer Engineering - UNICAMP - Brazil > [EMAIL PROTECTED] > http://raulkist.spaces.live.com/ > http://www.lms.ic.unicamp.br > http://www.codeplex.com/LMSU > http://www.codeplex.com/NDOS > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Oscar-users mailing list > Oscar-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/oscar-users > > ------------------------------------------------------------------------------ SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ _______________________________________________ Oscar-users mailing list Oscar-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/oscar-users
