archive:computer_resources:campusrocks
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archive:computer_resources:campusrocks [2015/04/18 20:35] charles [Sungrid Job scheduler] |
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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| * [[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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| 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 4\\ | + | #$ -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. | Your job goes to a set of nodes with a combined total of a least 4 cores available. | ||
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| #$ -q [Name of specific server queue]\\ | #$ -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' | + | 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 | ||
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| #$ qhost\\ | #$ qhost\\ | ||
| Displays the compute nodes available on the cluster including hardware statistics. | Displays the compute nodes available on the cluster including hardware statistics. | ||
| + | *'j' displays a detailed list of all current jobs running | ||
| #$ qstat\\ | #$ qstat\\ | ||
| - | Displays the status of the jobs submitted to qsub. | + | 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: | Primary job status codes: | ||
| *'r' status indicates that a job is running. | *'r' status indicates that a job is running. | ||
| *'qw' status indicates that a job is waiting to be scheduled/run on a machine. | *'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.1429389343.txt.gz · Last modified: 2015/04/18 20:35 by charles
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