Sherlock for IBIIS. William Law Stanford Research Computing
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1 Sherlock for IBIIS William Law Stanford Research Computing
2 Overview How we can help System overview Tech specs Signing on Batch submission Software environment Interactive jobs Next steps
3 We are here to help We run a wide variety of systems We can connect you to resources here and nationally Today I m going to focus on sherlock
4 Why Sherlock? Sherlock is a shared platform for research at Stanford A single node of sherlock is more powerful than your laptop or desktop Sherlock consists of many computers (nodes) which you can run your work on
5 System Overview interconnect ln01 generic nodes ln02 you login nodes specialized nodes filesystems compute nodes
6 Login Nodes Currently two machines use: sherlock.stanford.edu Login nodes = gateway to all other resources
7 Compute Nodes Normal nodes 16 cores in two sockets 64GB RAM 100GB Solid State Disk Infiniband connection 56Gbps (2:1 oversubscribed) GPU nodes (NVIDIA Kepler) Big memory nodes (1.5TB RAM)
8 Storage /home: $HOME (15GB), $PI_HOME (1TB) small amount of space, backed up, small file friendly, accessible across all systems /scratch: $SCRATCH, $PI_SCRATCH large, high performance, not backed up, big file friendly, accessible across all systems /local_scratch: $LOCAL_SCRATCH SSD for duration of the job, local to a node
9 Storage Specs /home NFS IOPS = ~16,200 Bandwidth = 125 MB/s based on connection /scratch Lustre IOPS =~ 54,000 Bandwidth = 6.5 GB/s based on connection total ~20 GB/s read; 13 GB/s write /local_scratch SSD IOPS=100,000 Bandwidth = 500 MB/s read; 400 MB/s write
10 Sign On Setup Kerberos documented here: Logon 2 steps: kinit then ssh
11 Scheduling Jobs Basic concept - tell the scheduler: 1. what you need 2. what it should do Partitions sets of physical machines with comparable hardware QOS sets of limitations (runtime, CPUs per user ) No need to specify QOS or partition in most cases
12 A bit on scheduling Sherlock currently uses fairshare scheduling balances out usage across users and PIs Uses backfill scheduling short jobs can run before larger pending jobs Accurate requirements help the scheduler and you! (shorter wait times) See different partitions/qos at
13 Condo model General partition everybody can run there Owners partitions owners have immediate access to their own nodes they can run on other owners nodes, but could be preempted by the rightful owner s jobs
14 Slurm tools Run salloc srun sbatch scancel Check squeue sstat/sacct sprio sshare reserve nodes run a scheduled command submit a batch script cancel a job check job status and queue check job stats while/after completion view job priority factors view shares (fairshare scheduling)
15 Sample batch file #!/bin/bash #SBATCH --job-name=r-hemisphere #SBATCH --output=hemisphere.out #SBATCH --error=hemisphere.err #SBATCH --mail-type=all #SBATCH #SBATCH --time=20:00 #SBATCH --nodes=1 #SBATCH --mem=4000 #SBATCH --ntasks-per-node=1 module load R srun R --no-save < hemisphere.r
16 Environment Modules Allows to manage software versions module avail shows what is available module load loads a package /share/sw/modules/core R/3.0.2 freesurfer/5.3.0 (D) intelmpi/ openmpi/1.6.5/intel13sp1up1 (D) python/3.3.2 (D) allinea/4.2 fsl/5.0.6-test julia/gcc/0.3.0-pre openmpi/1.7.4/gcc rstudio/ ansys/icemcfd/15.0 fsl/5.0.6 (D) matlab/r2012b openmpi/1.7.4/intel13sp1up1 (D) rstudio/ (D) comsol/43b gcc/4.8.1 matlab/r2013b paraview/4.1.0 sas/9.4 comsol/44 (D) gcta/ matlab/r2014a (D) plink/1.07 stata/12 cuda/5.5 intel/13sp1up1 nag/m24 plink/1.9_b1 (D) stata/13 (D) freesurfer/5.3.0-test intel/13sp (D) openmpi/1.6.5/gcc python/2.7.5 tabix/0.2.6
17 Interactive Jobs for starting Any resource can be interactive A custom tool (sdev) makes interactive jobs easier The dev partition allows jobs to start reasonably quickly You might not be able to run for that long To get a quick debug shell $ sdev To run interactively (not just for debugging) $ srun --pty bash
18 Graphical interfaces Example with Matlab sherlock-ln01$ srun -p dev --qos dev --pty --x11 --time=1: 0:0 --mem=8gb bash sh-5-2$ ml load matlab/r2014a sh-5-2$ matlab
19 Next Steps Request an account - researchcomputing-support@stanford.edu, cc your PI Get started, try submitting some jobs interactive jobs, batch scripts Documentation (WiP)
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