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If you submit many jobs at the same time that are largely identical, you should submit them as array jobs. # Request a whole 28 processor node with at least 512 GB of RAM Below is an example of requesting 512 GB of memory:įor requesting large memory resources using qsub, here is an example qsub script for a job that requires 500 GB of RAM. To request large memory resources in OnDemand, add the appropriate qsub Options from the summary table above to the Extra qsub options text field in the OnDemand form. Request a whole node with 36 cores and at least 1 TB of RAM. Request a whole node with 28 cores and at least 512 GB of RAM. Request a whole node with 28 cores and at least 384 GB of RAM. Request a whole node with 28 cores and at least 256 GB of RAM. Request a whole node with 16 cores and at least 256 GB of RAM. Request a whole node with 28 cores and at least 192 GB of RAM. Request a whole node with 16 cores and at least 128 GB of RAM. Request 8 cores on a machine with at least 128 GB of RAM. See our Allocating Memory for your Job webpage to estimate the amount of memory your job requires. The table below gives suggestions for appropriate qsub options for different ranges of memory your job may need. For more information about available processing and memory resources, visit our Resources Available for your Jobs page. The Technical Summary page describes the configuration of the different types of nodes on the SCC. The qsub options in the table below will schedule your job to a node with enough resources to complete your job.
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Jobs that require more than 64 GB will need to request a whole node. Jobs that require up to 64 GB will share resources on the same node. The SCC has a variety of nodes, each with a different number of cores along with varying amounts of memory. Jobs requiring more than 4 GB of memory should include appropriate qsub options for the amount of memory needed for your job. # Keep track of information related to the current jobĮcho "=" # Combine output and error files into a single file # Send an email when the job finishes or if it is aborted (by default no email is sent). Here is an example of a script with frequently used options: #!/bin/bash -l Python -V Batch Script With Frequently Used Options You can increase this up to 720:00:00 for single processor jobs but your job will take longer to start.
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# The default time, also selected here, is 12 hours. # The job will be aborted if it runs longer than this time. See General job submission directives for a list of other SGE options. If the module command is used in the script the first line should contain the “-l” option to ensure proper command interpretation by the system. The program and its optional input arguments are at the end of the script, preceded by a module statement if needed. All other lines that start with the # symbol are comments that provide details for each option. Lines that start with #$ symbols are used to specify the Sun Grid Engine (SGE) options used by the qsub command. The first line in the script specifies the interpreter – shell. Here is an example of a basic script for the Shared Computing Cluster (SCC). Using the Data Transfer Node to transfer files to the SCC (separate web page).Batch Script With Frequently Used Options.
#BATCH SCRIPT EXAMPLE MANUAL#
NOTE: These scripts are not directly usable to submit jobs, please edit them to meet the requirements of your job submission.ĬPU single node with 20 CPU cores: #!/bin/bashįor more info and additional SBATCH commands, please visit the SLURM SBATCH manual page here. This will submit your job to the SLURM partition/queue you specify in your script. To submit your SBATCH script to SLURM once you are finished, please save the file and start it with the command: ‘$ sbatch. Please see our website here for partition information. We have listed a few sample SBATCH scripts to assist users in building their own scripts to submit jobs. Jobs can be submitted to Koko through two methods, SRUN and SBATCH scripts.