Show pageOld revisionsBacklinksBack to top This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong. CKG Edit ====== BMIR/Khatri lab Cluster ====== ===== Details ===== 9 nodes total (shared with Shah lab) \\ 4 of them are dedicated to Khatri lab \\ - Intel® Xeon® CPU E5-2680 v3 @ 2.50GHz \\ - 24 cores, hyperthreaded \\ - 384 GB of RAM (per node) \\ - 600 GB of disk ( $LOCAL_SCRATCH) \\ ===== How to use it ===== All jobs are sent via khatrilab-dev1.stanford.edu, no need to log into any particular machine. Cluster runs Simple Linux Utility for Resource Management (SLURM) \\ - Scheduler \\ - Compatible with Sherlock cluster \\ - Full control over CPU Memory usage \\ - Job Array support \\ ==== Usage Details: Modules ==== We use environmental module system <code> > module avail > module load R/3.2.0 > module list > module unload R/3.2.0 </code> ==== Usage Details: Commands ==== === srun === Example: <code> srun --partition=khatrilab hostname srun --partition=khatrilab -N 3 hostname srun --partition=khatrilab -N 3 -n 10 hostname </code> === sbatch === Example - full sbatch script to load and run R <code> #!/bin/bash #SBATCH --mail-type=ALL #SBATCH --mail-user=alexskr@stanford.edu #SBATCH --time=0-01:05 # Runtime in D-HH:MM #SBATCH --job-name=sample_R_job #SBATCH --nodes=1 # Ensure that all cores are reserved on one machine #SBATCH -n 20 #number of cores to reserve, default is 1 #SBATCH --mem=4086 # in MegaBytes. default is 8 GB #SBATCH --exclusive # exclusive access to nodes for the job. #SBATCH --partition=khatrilab # Partition allocated for the lab #SBATCH --error=log/job.%J.err #SBATCH --output=result/job.%J.out # Fist we need to enable R module load R/3.2.0 # Run script Rscript rscript_parallel.R </code> === Other commands === <code> scancel squeu sacct sinfo </code> === Interactive Sessions === <code> [alexskr@khatrilab-dev1 ~]$ salloc -N 1 -n 20 -- mem=8066 --partition=khatrilab salloc: Granted job allocation 684 [alexskr@khatrilab-dev1 ~]$ srun --pty bash [alexskr@bmir-ct-1-1 ~]$ </code> lab/bmir_cluster.txt Last modified: 2016/08/18 13:38by alexskr