Changes between Version 32 and Version 33 of FAQ

Timestamp:

08/08/24 09:53:03 (5 months ago)

Author:

gbell

Comment:

--

FAQ

@@ -13 +13 @@
 1. How can I '''[#tracks download data/tracks from UCSC]'''?[[br]] [[br]]
 1. How can I '''[#barctools access BaRC Tools]''' or know what tools are available?[[br]] [[br]]
-1. How can I '''[#LSF submit a job to the LSF cluster]'''?[[br]] [[br]]
+1. How can I '''[#slurm submit a job to the slurm cluster]'''?[[br]] [[br]]
 1. How can I find out what '''[#perlR Perl modules or R packages]''' are installed? Which version is currently installed in the server?[[br]] [[br]]
 1. How can I '''[#xwindow connect to fry]'''?[[br]] [[br]]
@@ -95 +95 @@
 1. [=#barctools How can I '''access BaRC Tools''' or know what tools are available?] [[br]] [[br]]
   * BaRC Tools can be found on [http://bioinfo.wi.mit.edu/bio/tools/ BaRC Tools].  Available tools are summarized in [http://bioinfo.wi.mit.edu/bio/education/hot_topics/barc_tools/barcTools-summary.pdf Summary] [[br]] [[br]] 
-1. [=#LSF How can I '''submit a job to the LSF cluster'''?] [[br]] [[br]]
-   * Usually you just need to preface your usual command with 'bsub'
-   * See [http://bioinfo.wi.mit.edu/bio/bioinfo/docs/LSF_help.php Whitehead Linux cluster - LSF help] for sample commands and links to more documentation 
-   * In addition, see the tutorial created by IT called [http://wi-inside.wi.mit.edu/departments/it/services/scientificcomputing/scitutorials Getting Started with the LSF Cluster][[br]] [[br]]
+1. [=#slurm How can I '''submit a job to the slurm cluster'''?] [[br]] [[br]]
+   * Usually you just need to wrap your usual command with syntax like 
+
+{{{
+sbatch --partition=20 --job-name=MY_JOB --mem=32G --wrap "MY COMMAND"
+}}}
+ 
+where 
+   * 'sbatch' is the main command
+   * 'partition' indicates that you want to use Ubuntu 20 servers (with the most up-to-date software)
+   * 'job-name' is any short one-word name so you can more easily monitor its progress
+   * 'mem' is a required parameter requesting a specific amount of memory, and 
+   * 'wrap' means that 'sbatch will wrap the specified command string in a simple "sh" shell script, and submit that script to the slurm controller'.
+
+   * See [https://clusterguide.wi.mit.edu/using-the-slurm-cluster/ IT's Using the slurm cluster] for sample commands, changes in the environment (compared to the older LSF cluster) and links to more documentation 
+   [[br]] [[br]]
 1. [=#perlR How can I find out what '''Perl modules or R packages''' are installed?] Which version is currently installed in the server? [[br]] [[br]]
   * There are links on [https://trac.wi.mit.edu/wiki the home page] of Trac, our Tak tracking system to [http://tak/trac/wiki/Packages installed packaged software], [http://tak/trac/wiki/Perl installed Perl modules], [http://tak/trac/wiki/Python installed Python modules], and [http://tak/trac/wiki/R installed R modules]. [[br]] [[br]]