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archive:computer_resources:campusrocks [2010/05/16 01:53]
jstjohn
archive:computer_resources:campusrocks [2015/09/02 16:42] (current)
ceisenhart ↷ Page moved from computer_resources:campusrocks to archive:computer_resources:campusrocks
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 ^Machine ^GB RAM ^CPUs ^Cores ^MHz ^Model ^ ^Machine ^GB RAM ^CPUs ^Cores ^MHz ^Model ^
-|campusrocks.local(head node?)|30 ||1 |1000 |Dual-Core AMD Opteron(tm) Processor 2218 HE| +|campusrocks.local(head node?)|30 ||1 |2600 |Dual-Core AMD Opteron(tm) Processor 2218 HE| 
-|campusrocks-0-2(through 30).local |15 |4 |2 |1800 |Dual-Core AMD Opteron(tmProcessor 2218 HE|+|campusrocks-0-2(through 30).local |15 |4 |2 |2664 Intel(R) Xeon(R) CPU 5150 | 
 +|campusrocks-0-(31,32).local |15 |8 |2 | 3192 | Intel(R) Xeon(TM) CPU|
 |campusrocks-1-0(through 31).local |15 |2 |1 |2592 |Dual-Core AMD Opteron(tm) Processor 2218 HE| |campusrocks-1-0(through 31).local |15 |2 |1 |2592 |Dual-Core AMD Opteron(tm) Processor 2218 HE|
 +|campusrocks-2-(0,​1).local |192 | 48|  |  |  |
  
 campusrocks-0-6.local exceptionally has 30 GB RAM campusrocks-0-6.local exceptionally has 30 GB RAM
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    * [[Creating an account|Create a new account]]    * [[Creating an account|Create a new account]]
-   * [[http://​campusrocks.soe.ucsc.edu/​roll-documentation/​sge/​5.2/​|Documentation]] (works only on campus or when connected via [[http://​vpn.soe.ucsc.edu |VPN]].)+   * [[http://​campusrocks.soe.ucsc.edu/​roll-documentation/​sge/​5.2/​|SGE Documentation]] (works only on campus or when connected via [[http://​vpn.soe.ucsc.edu |VPN]].) 
 +   * {{:​computer_resources:​roll-sge-usersguide.pdf| SGE User's Guide (no VPN needed)}}
    * [[http://​campusrocks.soe.ucsc.edu/​ganglia/​|Status page]]    * [[http://​campusrocks.soe.ucsc.edu/​ganglia/​|Status page]]
    * [[Installed Software|Software]]    * [[Installed Software|Software]]
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 They threaten to kill jobs found running on the head node. They threaten to kill jobs found running on the head node.
  
-There is [[http://campusrocks.soe.ucsc.edu/roll-documentation/​sge/5.2/|Online ​documentation]] of how to use sungrid to submit jobs on the cluster. ​ The main commands are+There is [[http://www.rocksclusters.org/rocks-documentation/​4.1/|online ​documentation]] of how to use sungrid to submit jobs on the cluster. ​ The main commands are
   * qsub: Submits a job (create a shell script, then run "qsub -cwd shellscript"​)   * qsub: Submits a job (create a shell script, then run "qsub -cwd shellscript"​)
   * qdel: Delete a job   * qdel: Delete a job
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 #$ -l mem_free=15g\\ #$ -l mem_free=15g\\
 Your job goes to a node with at least 15g of free memory. There is probably something like '-l mem_avail'​ that works if you would like to schedule your job on a node with a certain amount of max memory available, even if some of it is currently in use. Your job goes to a node with at least 15g of free memory. There is probably something like '-l mem_avail'​ that works if you would like to schedule your job on a node with a certain amount of max memory available, even if some of it is currently in use.
 +
 +#$ -pe mpi [number of desired cores to use]\\
 +Your job goes to a set of nodes with a combined total of a least 4 cores available.
 +
 +#$ -cwd\\
 +Your job will be launched at the directory where the qsub command was given. Useful for setting predictable bash commands. Though not recommended for portability as other users of the script would need to also know where to launch the qsub command.
 +
 +#$ -q [Name of specific server queue]\\
 +Used to specify which set of servers you would like the sungrid scheduler to schedule/​run your jobs in. Names on campus rocks include '​all.q'​ and '​small.q'​. Default: '​all.q'​
 +
 +#$ -M ADolichophallus@ucsc.edu\\
 +#$ -m e\\
 +Used to have campus rocks email you at the end of your job.
 +
 +#$ -j y\\
 +Used to combine stderr & stdout into stdout.
 +
 +Example qsub commands:
 +  * qsub -N skewer_adapter_removal -cwd -V -pe mpi 20 -l mem_free=50g /​campusdata/​BME235/​S15_assemblies/​SOAPdenovo2/​adapterRemovalTask/​skewer_run/​run_skewer_adapter_removal.sh
 +
 +
 +Useful commands for viewing currently run jobs:
 +
 +#$ qhost\\
 +Displays the compute nodes available on the cluster including hardware statistics.
 +  *'​j'​ displays a detailed list of all current jobs running
 +
 +#$ qstat\\
 +Displays the status of the jobs submitted to qsub.\\
 +  *flag '​-f'​ displays more hardware usage information on each node. The '​resv/​used/​tot.'​ column displays number of processing cores reserved, used, and the total number of cores for a node respectively.
 +Primary job status codes:
 +  *'​r'​ status indicates that a job is running.
 +  *'​qw'​ status indicates that a job is waiting to be scheduled/​run on a machine.
 +
 +#$ qacct -j [job id]\\
 +Displays resource usage and runtime statistics for a job that has run to completion.\\
 +Very useful for determining optimal resource allocation for tasks.
 +
  
  
archive/computer_resources/campusrocks.1273974813.txt.gz · Last modified: 2010/05/16 01:53 by jstjohn