Difference between revisions of "Usage policy"

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To be fair to all users of the cluster, please be aware of these resource limits and usage expectations.
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The Storrs HPC cluster is a shared resource available to all researchers on all campuses. Use of the cluster is subject to all applicable university policies, including the [http://policy.uconn.edu/2012/06/21/acceptable-use-information-technology/ Information Technology Acceptable Use] policy. The cluster cannot be used to generate or store data that has been classified as [http://security.uconn.edu/extended-list-of-confidential-data/ Sensitive University Data] or covered by the university's [http://policy.uconn.edu/2015/12/16/export-control-policy/ Export Control Policy]. All data that is stored on the cluster is subject to these restrictions, and data that is not in compliance may be removed. Please familiarize yourself with the data storage guidelines described in the [[Data Storage Guide]].
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Additionally, before using the cluster, please familiarize yourself with the procedures listed below.
  
 
= Scheduled Jobs =
 
= Scheduled Jobs =
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{| class="wikitable sortable"
 
{| class="wikitable sortable"
! Job property    !! Standard QoS Limit || Longrun QoS Limit || Haswell384 QoS Limit
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! Job property    !! Default Partition (<code>general</code>) || <code>serial</code> Partition || <code>parallel</code> Partition || <code>debug</code> Partition
 
|-  
 
|-  
| Run time (hours) || 36                || 72                || 18
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| Run time || 12 hours || 7 days || 6 hours || 30 Minutes
 
|-
 
|-
| Cores / CPUs    ||colspan=2| 48                            || 384
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| Nodes  || 8 || 4 || 16 || 1
 
|-
 
|-
| Jobs            ||colspan=3| 8
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| Concurrent jobs ||colspan=4| 8
 
|}
 
|}
  
 
= Unscheduled programs =
 
= Unscheduled programs =
  
Programs that are running on login node (<code>login.storrs.hpc.uconn.edu</code>) without using the job scheduler, are subject to certain restrictions. Any program that violates these restrictions may be throttled or terminated without notice.
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Programs that are running on a login node (<code>login.storrs.hpc.uconn.edu</code>) without using the job scheduler are subject to certain restrictions. Any program that violates these restrictions may be throttled or terminated without notice.
  
 
{| class="wikitable sortable"
 
{| class="wikitable sortable"
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Below is a list of programs that are allowed on the login node without restrictions:
 
Below is a list of programs that are allowed on the login node without restrictions:
 
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
 
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
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* awk
 +
* basemount
 +
* bash
 
* bzip
 
* bzip
 +
* chgrp
 +
* chmod
 +
* comsollauncher
 
* cp
 
* cp
 
* du
 
* du
 
* emacs
 
* emacs
 +
* find
 
* fort
 
* fort
 
* gcc
 
* gcc
 
* gfortran
 
* gfortran
 +
* grep
 
* gunzip
 
* gunzip
 
* gzip
 
* gzip
 
* icc
 
* icc
 +
* ifort
 +
* jservergo
 +
* less
 +
* ls
 +
* make
 +
* more
 
* mv
 
* mv
 +
* ncftp
 +
* nvcc
 +
* perl
 +
* rm
 +
* rsync
 +
* ruby
 +
* setfacl
 
* sftp
 
* sftp
 
* smbclient
 
* smbclient
 
* ssh
 
* ssh
 +
* tail
 
* tar
 
* tar
 +
* ukbfetch
 
* vim
 
* vim
 
* wget
 
* wget
 +
* x2goagent
 
</div>
 
</div>
 
= HPC Storage (short term) =
 
 
The Storrs HPC cluster has a number of local high performance data storage options available for use during job execution and for the short term storage of job results. None of the cluster storage options listed below should be considered permanent, and should not be used for long term archival of data. Please see the next section below for permanent data storage options that offer greater resiliency.
 
 
{| class="wikitable sortable"
 
! Name          !! Path                          !! Size                  !! Performance !! Persistence  !! Backed up? !! Purpose
 
|-
 
| Scratch          || <code>/scratch/scratch2</code> || 438GB shared    || Fastest        || No, '''2 weeks''' || No        || Fast parallel storage for use during computation
 
|-
 
| Node-local || <code>/work</code>            || 100GB          || Fast          || No, '''5 days'''  || No        || Fast storage local to each compute node, globally accessible from <code>/misc/cnXX</code>
 
|-
 
| Home          || <code>~</code>                || 2GB        || Slow      || Yes    || Yes        || Personal storage, available on every node
 
|-
 
| Group        || <code>/shared</code>          || [[:Category:Help|By request]] || Slow || Yes    || Yes        || Short term group storage for collaborative work
 
|}
 
 
* Data deletion of directories inside the '''scratch2''' folder is based on modification time.  You will get 3 warnings by email before deletion.
 
* If you try to run <code>ls</code> on either the <code>/home</code>, <code>/shared</code>, or <code>/misc/cnXX</code> directories, you might not see them. They are invisible because they are mounted on demand by <code>autofs</code>, when an attempt is made to access a file under the directory, or using <code>cd</code> to enter the directory structure.
 
* You can [[recover deleted files|recover files on your own from our backed up directories]] using snapshots within 2 weeks. Beyond 2 weeks we may be able to help if you [[:Category:Help|contact us]].
 
* You can check on your [[Cannot write to home directory|home directory quota]].
 
 
= Permanent Data Storage (long term) =
 
 
The university has multiple options for long term permanent data storage. Once data is no longer needed for computation, it should be transferred to one of these locations. Data transfer to permanent locations should be done from the <code>login.storrs.hpc.uconn.edu</code> login node.
 
 
{| class="wikitable sortable"
 
! Name !! Path !! Size !! Performance !! Resiliency !! Purpose
 
|-
 
|UITS Research Storage || [[File_transfer_via_SMB|Use smbclient to transfer files]] || [http://uits.uconn.edu/disk-storage-info By request] || Moderate || Data is replicated between two datacenters on Storrs campus || This storage is best used for long term data storage requiring good performance, such as data that will be accessed frequently for post-analysis.
 
|-
 
|Archival cloud storage || <code>/archive</code> || 1.5PB shared || Low || Data is distributed across three datacenter between the Storrs and Farmington campuses || This storage is best for permanent archival of data without frequent access.
 
|-
 
|Departmental/individual storage || [[File_transfer_via_SMB|Use smbclient to transfer files]] || - || - || - || Some departments and/or individual researchers have their own local network storage options. These can be accessed using <code>smbclient</code>
 
|}
 
 
= Shared Read-Only Datasets =
 
Users who need read-only datasets can contact our administrators (hpc@uconn.edu) to request the dataset. For example, people who study bioinformatics often need reference dataset for different organisms. The reference dataset is usually very large so user can only save them in /scratch. But. it is inconvenient to touch the dataset every 15 days to prevent deletion. If you have such kind of dataset, we can store the dataset for you. The dataset must meet the following requirements:
 
* dataset is read-only, cannot be writable or executable
 
* dataset is public (can be used by other users) or is restricted to a group of users
 
The shared dataset is under path: /scratch/scratch2/shareddata/. The data under this directory will be stored permanently. Now we have 4 reference datasets in genome directory: hg19 hg38 mm9 and mm10.
 
 
To make the linking path shorter, you can create a soft link with dataset under your home directory. For example:
 
$ cd
 
$ link -s /scratch/scratch2/shareddata/genome ./genome
 

Latest revision as of 16:08, 12 April 2021

The Storrs HPC cluster is a shared resource available to all researchers on all campuses. Use of the cluster is subject to all applicable university policies, including the Information Technology Acceptable Use policy. The cluster cannot be used to generate or store data that has been classified as Sensitive University Data or covered by the university's Export Control Policy. All data that is stored on the cluster is subject to these restrictions, and data that is not in compliance may be removed. Please familiarize yourself with the data storage guidelines described in the Data Storage Guide.

Additionally, before using the cluster, please familiarize yourself with the procedures listed below.

Scheduled Jobs

All computational jobs need to be submitted to the cluster using the job scheduler. Please read the SLURM Guide for helpful information on using the scheduler. Listed below are the runtime and resource limits for scheduled jobs.

Job property Default Partition (general) serial Partition parallel Partition debug Partition
Run time 12 hours 7 days 6 hours 30 Minutes
Nodes 8 4 16 1
Concurrent jobs 8

Unscheduled programs

Programs that are running on a login node (login.storrs.hpc.uconn.edu) without using the job scheduler are subject to certain restrictions. Any program that violates these restrictions may be throttled or terminated without notice.

Run time (minutes) CPU limit Memory limit
20 5% 5%

Below is a list of programs that are allowed on the login node without restrictions:

  • awk
  • basemount
  • bash
  • bzip
  • chgrp
  • chmod
  • comsollauncher
  • cp
  • du
  • emacs
  • find
  • fort
  • gcc
  • gfortran
  • grep
  • gunzip
  • gzip
  • icc
  • ifort
  • jservergo
  • less
  • ls
  • make
  • more
  • mv
  • ncftp
  • nvcc
  • perl
  • rm
  • rsync
  • ruby
  • setfacl
  • sftp
  • smbclient
  • ssh
  • tail
  • tar
  • ukbfetch
  • vim
  • wget
  • x2goagent