Difference between revisions of "User manual cod nodes old"
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cod1 24cpus 128 GB of RAM, ~1 TB disk space --> mainly for mysql databases<br>cod2 24cpus 128 GB of RAM, ~1.3 TB disk space<br> cod3 64cpus 512 GB of RAM, ~24 TB disk space<br> cod4 64cpus 512 GB of RAM, ~24 TB disk space | cod1 24cpus 128 GB of RAM, ~1 TB disk space --> mainly for mysql databases<br>cod2 24cpus 128 GB of RAM, ~1.3 TB disk space<br> cod3 64cpus 512 GB of RAM, ~24 TB disk space<br> cod4 64cpus 512 GB of RAM, ~24 TB disk space | ||
| − | == <br> '''General use''' == | + | == <br> '''General use''' == |
=== '''Getting access''' === | === '''Getting access''' === | ||
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Check that you are a member of the group 'seq454' by simply typing: | Check that you are a member of the group 'seq454' by simply typing: | ||
<pre>groups</pre> | <pre>groups</pre> | ||
| − | If 'seq454' s not listed, please contact Lex Nederbragt. | + | If 'seq454' s not listed, please contact Lex Nederbragt.<br> |
| − | + | === '''TIP: using screen''' === | |
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| − | === | ||
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 | 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 | ||
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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 | 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 | ||
<pre>screen -rd</pre> | <pre>screen -rd</pre> | ||
| − | == '''Data and software''' == | + | == '''Data and software''' == |
| + | |||
| + | === Disks === | ||
| + | |||
| + | All nodes have 'abel' (the UiO supercomputer cluster) disks, and your abel home area mounted to them. So, all the files located in /projects are available on the cod nodes, see below. In addition, the nodes have local discs, currently:<br>/data --> for permanent files, e.g input to your program<br>/work --> working are for your programs | ||
=== '''CEES project data''' === | === '''CEES project data''' === | ||
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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> | 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> | ||
| + | |||
| + | === Choosing where to work with and store your data === | ||
| + | |||
| + | *reading and writing data to and from /data and /work will be much faster and efficient than to /projects/cees | ||
| + | *data on /projects/cees is backed up by USIT, but NOT data on /data and /work<br> | ||
| + | |||
| + | This leads to the following strategy for how to choose which disk to use: | ||
| + | |||
| + | *for something short and quick, you can use /projects | ||
| + | *for a long running program, or one that generates a lot of data over a long time, use /data and /work | ||
| + | *once the long running job is done, you can move the data you want to keep to /projects/cees | ||
| + | *NOTE having your program write a lot over a long time to a file on /projects/cees causes problems for the backup system, as the file may be changed during backup | ||
| + | *for long-term storage of data you do not need regular access to, please use the norstore allocation (ask Lex Nederbragt) | ||
=== Software === | === Software === | ||
| − | * | + | *locally installed programs are in /projects/cees/bin |
*much software is available through the 'module' system, see [https://www.uio.no/english/services/it/research/hpc/abel/help/user-guide/modules.html this manual]. | *much software is available through the 'module' system, see [https://www.uio.no/english/services/it/research/hpc/abel/help/user-guide/modules.html this manual]. | ||
*we can make our own modules, see the instructions (forthcoming) | *we can make our own modules, see the instructions (forthcoming) | ||
Revision as of 12:29, 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
General use
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, please contact Lex Nederbragt.
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
Data and software
Disks
All nodes have 'abel' (the UiO supercomputer cluster) disks, and your abel home area mounted to them. So, all the files located in /projects are available on the cod nodes, see below. In addition, the nodes have local discs, currently:
/data --> for permanent files, e.g input to your program
/work --> working are for your programs
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
Choosing where to work with and store your data
- reading and writing data to and from /data and /work will be much faster and efficient than to /projects/cees
- data on /projects/cees 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 something short and quick, you can use /projects
- for a long running program, or one that generates a lot of data over a long time, use /data and /work
- once the long running job is done, you can move the data you want to keep to /projects/cees
- NOTE having your program write a lot over a long time to a file on /projects/cees causes problems for the backup system, as the file may be changed during backup
- for long-term storage of data you do not need regular access to, please use the norstore allocation (ask Lex Nederbragt)
Software
- locally installed programs are in /projects/cees/bin
- much software is available through the 'module' system, see this manual.
- we can make our own modules, see the instructions (forthcoming)
- to use our local modules, see below under 'setting up your environment'
- we can add our own local python and perl modules, please ask
Setting up your environment
- to have access to the commonly used programs and scripts, add the /projects/cees/bin folder in your path
- to automaticilly set permissions to new files and folders, use 'umask 0002' command
- to use our own modules (see elsewhere for 'modules'), add the path to local modules
In order to achieve all this, include the following lines in your ~/.bash_login file (please create the file if it doesn't already exist):
export PATH=/projects/cees/bin:$PATH umask 0002 module use /projects/cees/bin/modules
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
