- A collection of executable scripts for:
- getting the status of the cluster:
cluster-status- node informationgpu-usage- aggregate gpu use informationgpu-usage-by-node- gpu use information per nodefree-gpus- location of free gpus and how manydown-gpus- location of gpus which are down, and full informationwhoson- which users are logged on and running how many jobsclusterspec- print out the name, partition, CPUs, GPUs and RAM of every node.
- information about running jobs:
myjobs- prints all your running jobs (squeue -u ${USER})jobinfo- information per user or node about running jobs
- and aiding your job submission:
interactive&interactive_gpu- gets you an interactive job on one of nodes with or without a gpukillmyjobs- useful for clearing jobs (has facility to exclude some)onallnodes- run a script on all or a selection of nodes (very useful for regular cleaning jobs etc.)sinline- quickly run commands on specified node(s) inline and print output to terminal (as opposed to a log file)
- Templates and a framework for running experiments:
- experiments - template + executable, and README explanation of framework
- simple example - a mock gridsearch requiring no dependencies, a very quick and practical introduction to the framework
- mnist example - conda + pytorch + GPUs 'realistic' gridsearch: can be easiliy edited and used as a basis for your experiments
Make the scripts available in this folder runnable from anywhere by adding the folder containing them to the path. We recommend you do this using git so that you can recieve updates easily.
Follow these commands:
cd ~
mkdir git
cd git
git clone https://github.com/cdt-data-science/cluster-scripts.git
echo 'export PATH=/home/$USER/git/cluster-scripts:$PATH' >> ~/.bashrc
source ~/.bashrc
You should now be able to run the scripts from anywhere when on the cluster. To check that this has worked, go somewhere else, then try some commands. For example:
cd ~
gpu-usage -p
> in_use usable total free
> 69 71 71 2
If you want to have job ID autocompletion for scancel, you need to source the
job-id-completion.sh script:
cd ~
echo "source /home/$USER/git/cluster-scripts/job-id-completion.sh" >> ~/.bashrc
source ~/.bashrc
These examples expect you to have followed the setup.
- Get an interactive session
$ interactive
Doing a --test-only to estimate wait time...
srun: Job 455329 to start at 2019-05-01T14:56:10 using 1 processors on charles12
Running the following command to get you an interactive session:
srun --time=01:00:00 --mem=2000 --cpus-per-task=1 --pty bash
(base) [charles12]s0816700:
- Quickly identify free gpus for use
$ free-gpus
datetime nodename free
21/11/2019 19:39:03 charles01 2
- View whether nodes are down and why
$ down-gpus
datetime nodename in_use usable total
19/04/2019 10:49:12 charles03 0 0 2
Full cluster status:
NODELIST GRES STATE TIMESTAMP REASON FREE_MEM/MEMORY CPU_LOAD
charles01 gpu:2 mixed Unknown none 14101/60000 5.13
charles02 gpu:2 idle Unknown none 18125/60000 0.01
charles03 gpu:2 down* 2019-04-19T10:05:53 forgot to check scratch mount 60915/60000 0.05
charles04 gpu:2 mixed Unknown none 11713/60000 0.15
charles05 gpu:2 mixed Unknown none 29526/60000 0.02
charles06 gpu:2 mixed Unknown none 22375/60000 0.01
charles07 gpu:2 idle Unknown none 11029/60000 0.01
charles08 gpu:2 idle Unknown none 9622/60000 0.01
charles09 gpu:2 idle Unknown none 22869/60000 0.01
charles10 gpu:2 idle Unknown none 22897/60000 0.01
charles11 gpu:4 mixed Unknown none 15546/60000 5.44
charles12 gpu:4 mixed Unknown none 542/60000 5.08
charles13 gpu:3 mixed Unknown none 20867/60000 3.73
charles14 gpu:4 mixed Unknown none 12323/60000 2.94
charles15 gpu:4 mixed Unknown none 5173/64328 5.83
charles16 gpu:4 mixed Unknown none 1550/64328 6.07
charles17 gpu:4 mixed Unknown none 8370/64328 1.38
charles18 gpu:4 mixed Unknown none 3693/64328 3.08
charles19 gpu:4 mixed Unknown none 24555/64328 7.16
- Identify people running jobs currently and their usage
$ whoson
sid name nr_jobs
s1234456 Bob smith 2
s8765423 Joe Bloggs 1
- Get information about jobs running on a node
jobinfo -n charles04
> JobId=452332 JobName=...
> UserId=... GroupId=... MCS_label=N/A
> Priority=1027 Nice=0 Account=... QOS=normal
> JobState=RUNNING Reason=None Dependency=(null)
> Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
> RunTime=9-10:22:17 TimeLimit=UNLIMITED TimeMin=N/A
> SubmitTime=2019-04-17T12:18:35 EligibleTime=2019-04-17T12:18:35
> StartTime=2019-04-17T12:18:35 EndTime=Unknown Deadline=N/A
> PreemptTime=None SuspendTime=None SecsPreSuspend=0
> LastSchedEval=2019-04-17T12:18:35
> Partition=cdtgpucluster AllocNode:Sid=albert:82878
> ReqNodeList=(null) ExcNodeList=(null)
> NodeList=charles04
> BatchHost=charles04
> NumNodes=1 NumCPUs=2 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
> TRES=cpu=2,mem=14000M,node=1,billing=2,gres/gpu=1
> Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
> MinCPUsNode=1 MinMemoryNode=14000M MinTmpDiskNode=0
> Features=(null) DelayBoot=00:00:00
> Gres=gpu:1 Reservation=(null)
> OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
> Command=...
> WorkDir=...
> StdErr=...
> StdIn=/dev/null
> StdOut=...
> Power=
- Kill all your jobs (except 1)
$ # Launch some jobs
$ parallel 'sbatch --nodelist=charles02 --time=05:00 --cpus-per-task=1 --mem=2000 --wrap "sleep 30" --job-name=sleeping{}' ::: {1..10}
Submitted batch job 610800
Submitted batch job 610801
Submitted batch job 610802
Submitted batch job 610803
Submitted batch job 610804
Submitted batch job 610805
Submitted batch job 610806
Submitted batch job 610807
Submitted batch job 610808
Submitted batch job 610809
$ myjobs
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
610800 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
610801 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
610802 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
610803 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
610804 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
610805 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
610806 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
610807 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
610808 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
610809 cdtgpuclu sleeping s0816700 R 0:04 1 charles02
$ # Kill em
$ killmyjobs -e 610809
killing jobs in queue as well as running jobs
excluding 610809
killing 610800 610801 610802 610803 610804 610805 610806 610807 610808
or
$ # Only kill ones running (leave ones in queue alone)
$ killmyjobs -g
not killing jobs in queue
killing 454206 454207 454208 454209
- Run a job on every node in the cluster - useful for something like changing data on scratch spaces
some_script=/mnt/cdtds_cluster_home/s0816700/git/melody_gen/scripts/slurm_diskspace.sh
onallnodes $some_script
- Quickly run commands on nodes inline and return output to console
for ii in {06..08}; do
echo --------
echo damnii$ii
sinline -n damnii$ii \
-c 'du -sh /disk/scratch/* 2>/dev/null | sort -rh' \
-s '--partition=PGR-Standard'
done
> --------
> damnii06
> Submitted batch job 666168
> 108K /disk/scratch/bob
> 4.0K /disk/scratch/greg
> 4.0K /disk/scratch/alice
> --------
> damnii07
> Submitted batch job 666169
> 428K /disk/scratch/bob
> 4.0K /disk/scratch/greg
> 4.0K /disk/scratch/alice
> --------
> damnii08
> Submitted batch job 666170
> 84M /disk/scratch/bob
> 4.0K /disk/scratch/greg
> 4.0K /disk/scratch/veronica
> 4.0K /disk/scratch/alice