Cluster: Difference between revisions
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==== /software/src<br> ==== | ==== /software/src<br> ==== | ||
<br> | Sources of software to install<br> | ||
==== /software/icecube<br> ==== | ==== /software/icecube<br> ==== | ||
Icecube specific tools | Icecube specific tools<br> | ||
===== /software/icecube/i3_ports<br> ===== | ===== /software/icecube/i3_ports<br> ===== | ||
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In order to use it, you must define the environment variable $I3_PORTS<br> | In order to use it, you must define the environment variable $I3_PORTS<br> | ||
<pre>export I3_PORTS="/software/icecube/i3_ports" | <pre>export I3_PORTS="/software/icecube/i3_ports" | ||
</pre> | </pre> | ||
This variable is set only for the current session, in order to not define it everytime, you can add this command to your .bashrc | This variable is set only for the current session, in order to not define it everytime, you can add this command to your .bashrc | ||
===== /software/icecube/offline-software<br> ===== | ===== /software/icecube/offline-software<br> ===== | ||
This folder contains the '''offline-software''' meta-project | |||
To use it, just run the following command (note the point at the beginning of the line) | |||
. /software/icecube/offline-sofware/[VERSION]/env-shell.sh | |||
Available versions : | |||
*V14-02-00<br> | |||
===== /software/icecube/icerec<br> ===== | ===== /software/icecube/icerec<br> ===== | ||
This folder contains the icerec meta-project<br> | This folder contains the '''icerec''' meta-project<br> | ||
To use it, just run the following command (note the point at the beginning of the line)<br> | To use it, just run the following command (note the point at the beginning of the line)<br> | ||
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*V04-05-00 | *V04-05-00 | ||
*V04-05-00-jkunnen<br> | *V04-05-00-jkunnen<br> | ||
===== /software/icecube/simulation<br> ===== | ===== /software/icecube/simulation<br> ===== | ||
<br> | This folder contains the '''simulation''' meta-project | ||
To use it, just run the following command (note the point at the beginning of the line) | |||
<pre>. /software/icecube/simulation/[VERSION]/env-shell.sh</pre> | |||
Available versions : | |||
*V03-03-04 | |||
*V04-00-08 | |||
*V04-00-09<br> | |||
=== /ice3<br> === | === /ice3<br> === | ||
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-l : resources options | -l : resources options | ||
<br> | |||
=== Job management === | === Job management === | ||
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To see all jobs (running / queued), you can use the '''qstat''' command or go to the [http://ganglia.iihe.ac.be/addons/job_monarch/?c=iihe JobMonArch] page | To see all jobs (running / queued), you can use the '''qstat''' command or go to the [http://ganglia.iihe.ac.be/addons/job_monarch/?c=iihe JobMonArch] page | ||
<pre>qstat | <pre>qstat | ||
</pre> | </pre> | ||
''OPTIONS'' | ''OPTIONS'' | ||
-u username : list only jobs submitted by username | -u username : list only jobs submitted by username | ||
-n : show nodes where jobs are running | -n : show nodes where jobs are running | ||
-q : show the job repartition on queues | |||
<br> | |||
== Useful links == | == Useful links == | ||
Revision as of 12:24, 13 February 2014
IIHE local cluster
Overview
The cluster is composed by 4 machine types :
- User Interfaces (UI)
This is the cluster front-end, to use the cluster, you need to log into those machines
Servers : ui01, ui02
- Computing Element (CE)
This server is the core of the batch system : it run submitted jobs on worker nodes
Servers : ce
- Worker Nodes (WN)
This is the power of the cluster : they run jobs and send the status back to the CE
Servers : slave*
- Storage Elements
This is the memory of the cluster : they contains data, software, ...
Servers : datang (/data, /software), lxserv (/user), x4500 (/ice3)
How to connect
To connect to the cluster, you must use your IIHE credentials (same as for wifi)
ssh username@icecube.iihe.ac.be
TIP : icecube.iihe.ac.be points automatically to available UI's (ui01, ui02, ...)
After a successful login, you'll see this message :
========================================== Welcome on the IIHE ULB-VUB cluster Cluster status http://ganglia.iihe.ac.be IT Help support-iihe@ulb.ac.be ========================================== username@uiXX:~$
Your default current working directory is your home folder.
Directory Structure
Here is a description of most useful directories
/user/username
Your home folder
/data
Main data repository
/software
The custom software area
/software/src
Sources of software to install
/software/icecube
Icecube specific tools
/software/icecube/i3_ports
This folder contains the I3 ports used by icecube (meta-)projects
In order to use it, you must define the environment variable $I3_PORTS
export I3_PORTS="/software/icecube/i3_ports"
This variable is set only for the current session, in order to not define it everytime, you can add this command to your .bashrc
/software/icecube/offline-software
This folder contains the offline-software meta-project
To use it, just run the following command (note the point at the beginning of the line)
. /software/icecube/offline-sofware/[VERSION]/env-shell.sh
Available versions :
- V14-02-00
/software/icecube/icerec
This folder contains the icerec meta-project
To use it, just run the following command (note the point at the beginning of the line)
. /software/icecube/icerec/[VERSION]/env-shell.sh
Available versions :
- V04-05-00
- V04-05-00-jkunnen
/software/icecube/simulation
This folder contains the simulation meta-project
To use it, just run the following command (note the point at the beginning of the line)
. /software/icecube/simulation/[VERSION]/env-shell.sh
Available versions :
- V03-03-04
- V04-00-08
- V04-00-09
/ice3
Batch System
Queues
The cluster is decomposed in queues
| any | lowmem | standard | highmem | gpu | |
|---|---|---|---|---|---|
| Description | |||||
| CPU's | |||||
| Walltime default/limit | |||||
| Memory default/limit |
Job submission
To submit a job, you just have to use the qsub command :
qsub myjob.sh
OPTIONS
-q queueName : choose the queue (default: any)
-N jobName : name of the job
-I : pass in interactive mode
-m : mail options
-l : resources options
Job management
To see all jobs (running / queued), you can use the qstat command or go to the JobMonArch page
qstat
OPTIONS
-u username : list only jobs submitted by username
-n : show nodes where jobs are running
-q : show the job repartition on queues
Useful links
Ganglia Monitoring : Servers status
JobMonArch : Jobs overview
