Difference between revisions of "User manual cod nodes old"
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The CEES projects are organised as follows: | The CEES projects are organised as follows: | ||
− | /projects/ | + | /projects/cees is the main area. Access is for those in the seq454 unix user group (soon to change name to ceesdata) Please check that files and folders you create have the right permissions: |
<pre>chgrp -R seq454 yourfolder | <pre>chgrp -R seq454 yourfolder | ||
chmod -R 770 yourfolder</pre> | chmod -R 770 yourfolder</pre> | ||
− | It is possible to restrict access to a subgroup of those that are inn the seq454 group, please ask Lex | + | It is possible to restrict access to a subgroup of those that are inn the seq454 group, please ask Lex Nederbragt |
− | Folders in /projects/ | + | Folders in /projects/cees: |
− | projects --> finished projects, data belonging to an (accepted) publication<br>databases --> permanenet files, e.g reference genomes<br>in_progress --> the main working area. Here you store data for unfinished projects<br>bin --> here are programs and | + | projects --> finished projects, data belonging to an (accepted) publication<br>databases --> permanenet files, e.g reference genomes<br>in_progress --> the main working area. Here you store data for unfinished projects<br>bin --> here are programs and scripts located<br>lib --> needed by certain programs<br>src --> source files for some of the programs in the bin folder<br>scripts --> for home-made scripts<br>exchange --> for exchanging files with non-members<br> |
<br> | <br> | ||
− | + | It is recommended to put the /projects/cees/bin folder in your path. Include the following line in your ~/.bash_login file: | |
+ | <pre>export PATH=/projects/cees/bin:$PATH</pre> | ||
− | |||
− | |||
− | |||
− | |||
=== '''Note to SLURM users''' === | === '''Note to SLURM users''' === | ||
Revision as of 12:12, 3 March 2014
This document describes how to use the high-performance compute nodes of the cod group at CEES. We have the following resources available:
cod1 24cpus 128 GB of RAM, ~1 TB disk space --> mainly for mysql databases
cod2 24cpus 128 GB of RAM, ~1.3 TB disk space
cod3 64cpus 512 GB of RAM, ~24 TB disk space
cod4 64cpus 512 GB of RAM, ~24 TB disk space
Contents
Getting access
Provide Lex Nederbragt with your UiO username.
Mailing list
If you're not already on it, get subscribed to the cod-nodes mailing list: https://sympa.uio.no/bio.uio.no/subscribe/cod-nodes. We use this list to distribute information on the use of the CEES cod nodes.
If you intend to use one of the nodes for an extended period of time, please send an email to this list!
Logging in
ssh username@cod1.uio.no
When you are on the UiO network it is enough to write ssh cod1
Check that you are a member of the group 'seq454' by simply typing:
groups
If 'seq454' s not listed, contact Lex.
All nodes have titan and your titan home area mounted to them. So, all the files located in /project are avail be on the cod nodes. In addition, the have local discs, currently:
/data --> for permanent files, e.g input to your program
/work --> working are for your programs
A few important things to note: - reading and writing data to/from /data and /work will be much faster and efficient than to /projects - data on /project is backed up by USIT, but NOT data on /data and /work
This leads to the following strategy for how to choose which disk to use:
- for a quick command, you may use /projects
- for a long running program, or one that generates a lot of data over a long time, use /data and /work
- having your program write a lot over a long time to a file on /projects causes problems for the backup system, as the file may be changed during backup.
TIP: using screen
After starting a long running job, you cannot close the terminal wind, or the job will be cancelled. Instead, run the job from within a 'screen': type
screen
You now stared a 'new' terminal start your job press ctrl-a-d, that is the CTRL key with the 'a' key, followed by the 'd' key Now you're back in the terminal where you started. You can close this terminal, and the one behind the screen still exists and continues To get back into the now hidden one, type
screen -rd
CEES project data
The CEES projects are organised as follows:
/projects/cees is the main area. Access is for those in the seq454 unix user group (soon to change name to ceesdata) Please check that files and folders you create have the right permissions:
chgrp -R seq454 yourfolder chmod -R 770 yourfolder
It is possible to restrict access to a subgroup of those that are inn the seq454 group, please ask Lex Nederbragt
Folders in /projects/cees:
projects --> finished projects, data belonging to an (accepted) publication
databases --> permanenet files, e.g reference genomes
in_progress --> the main working area. Here you store data for unfinished projects
bin --> here are programs and scripts located
lib --> needed by certain programs
src --> source files for some of the programs in the bin folder
scripts --> for home-made scripts
exchange --> for exchanging files with non-members
It is recommended to put the /projects/cees/bin folder in your path. Include the following line in your ~/.bash_login file:
export PATH=/projects/cees/bin:$PATH
Note to SLURM users
If you are used to submit jobs through a slurm script, this will not work on the cod nodes. Here you'll have to give the command directly on the command line.
Job scripts
You can use a job script: collect a bunch of commands and put them in an executable file. Run the command with
source yourcommands.sh
Local services
cod1
- mysql
- the stacks program for analysis of RAD tag data
cod2
- the smrtportal software for secondary analysis of PacBio runs