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Joshua Newman

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Joshua Newman last won the day on November 3 2015

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  1. Cannot run bwa with multiple nodes

    Hello TungXP, PBS Pro assigns the resources, but it's up to the job script to set up any parallelism. You can refer to the $PBS_NODEFILE variable to determine what you've been assigned. The job script will only run on the primary execution host, so typically MPI is used to spawn processes on other nodes assigned to the job. I'm not very familiar with bwa, but if you're using bio-bwa as it appears, it is not MPI aware and will not execute tasks on multiple nodes. The parallel fork pbwa does, but it doesn't look like it supports the mem command you're using. Josh
  2. How to move PBS server and schedular to new server?

    Hello Roland, There are a couple of factors involved based on whether or not you're running Windows, what version of PBS you are running, whether you need to upgrade PBS when you migrate to the new server (i.e. the older PBS version doesn't support the newer OS version, or you simply want to upgrade), and whether or not you want to keep your jobs running during the move. You'll also need to make sure that your license server is relocated to the new server if it is running on the server you are retiring. In a perfect world, where you are not running Windows, the license server is on a separate system, the PBS versions are identical, the operating system versions are identical, and jobs are no longer running, you can copy things over and be able to start PBS back up on the new server without changes. If you are not living in this perfect world, please let us know: - The OS and version of the server you are retiring - The OS and version of the server you are migrating to - Where your license server resides - What version of PBS you are currently running - What version of PBS Pro you wish to run on the new server - Do you need to keep jobs running during the move? If you are living in the perfect world I described and wish to use the copy method: 1) on the old server and all execution nodes, /etc/init.d/pbs stop 2) make backup copies of /etc/pbs.conf, $PBS_EXEC (/opt/pbs/default by default), and $PBS_HOME (/var/spool/PBS by default) 3) copy /etc/pbs.conf to the new server. 4) modify the PBS_SERVER line in /etc/pbs.conf on the new server to reflect the new server hostname. 5) modify the PBS_SERVER line in /etc/pbs.conf on each execution node to reflect the new server hostname. 6) modify all $clienthost lines in $PBS_HOME/mom_priv/config on each execution host to reflect the new server hostname. 7) copy $PBS_HOME to the same location on the new server 8) copy $PBS_EXEC to the same location on the new server 9) copy /etc/init.d/pbs to the new server 10) on the new server, chkconfig pbs on 11) on the new server and all execution hosts, /etc/init.d/pbs start
  3. PBS not allocating available CPU's

    We'll work with you offline to see if we can get to the bottom of this. Thanks! Josh
  4. PBS pro 12.1.1 how to configure email content

    Hello, The emails you see are sent from the server host and the content is not configurable. I am curious, however, whether you are running the mailx command on the PBS_SERVER or another host versus the job's execution host. Since your job script runs on an execution host, the results you get from executing the mailx command could be different during job execution than outside of it. You can typically test things like this by submitting an interactive job with "qsub -I" (that's a capital i as in India) and running the same command. Try that first, but beyond that there are a few other system-wide options you have as an administrator via an epilogue or hooks. Check the PBS Pro 12.1 Admin Guide section 12.4 for the epilogue and chapter 6 for hooks. You'll need to follow section 6.16 to import smtplib for use with a hook. Josh
  5. Reservation handling with override

    Hello Tomtom, In order to confirm a reservation, it cannot conflict with currently running jobs, other confirmed reservations or dedicated time, and the resources must be available for the reservation. Since scheduler functions are needed to fulfill these requirements, a reservation cannot be confirmed when scheduling is turned off. As you have noticed with pbs_rsub and pbs_rstat, many of PBS Pro's functions and commands are unsupportable when used without PBS Pro's scheduler. Unless your alternative scheduler is a drop-in replacement, you will be unable to do many tasks (including confirming reservations) using PBS Pro commands. May I ask what are you trying to achieve with your own scheduler?
  6. Hook error: No module named socket

    Also, It appears you meant to use e.reject instead of e.eject as your last line.
  7. Hook error: No module named socket

    Hello TomTom, Currently there are two separate library paths for the python distributed with PBS Professional, one for running things outside the server context and one for running things inside the server context (i.e. server hooks). In order to import socket, you will need to add the external PBS python library paths to the hook's sys.path. Beware, however, that you should be careful what you do with these modules, as every server hook is blocking by design. You would not, for instance, want to create some kind of service layer inside a hook as it will need to complete all processing before control is released back to the server. Caveat aside, to add the external PBS python paths to a hook, you can follow the PBS Pro Admin Guide 12.2, section 6.16 "Python Modules and PBS" For your benefit, assuming $PBS_EXEC is /opt/pbs/default: import sys my_paths = ['/opt/pbs/default/python/lib/python25.zip', '/opt/pbs/default/python/lib/python2.5', '/opt/pbs/default/python/lib/python2.5/plat-linux2', '/opt/pbs/default/python/lib/python2.5/lib-tk', '/opt/pbs/default/python/lib/python2.5/lib-dynload', '/opt/pbs/default/python/lib/python2.5/site-packages'] for my_path in my_paths: if my_path not in sys.path: sys.path.append(my_path) Be sure to check for existence of the path in sys.path first, as the python process does not get reloaded for every server hook execution as it does for mom hooks. EDIT: corrected my_paths