Difference between revisions of "User manual cod nodes old"
(First version) |
(Formatting) |
||
| Line 1: | Line 1: | ||
| − | This document describes how to use the high-performance compute nodes of the cod group at CEES. | + | This document describes how to use the high-performance compute nodes of the cod group at CEES. We have the following resources available: |
| − | We have the following resources available: | ||
| − | cod1 | + | cod1 24cpus 128 GB of RAM, ~1 TB disk space<br>cod2 24cpus 128 GB of RAM, ~1.3 TB disk space<br> cod3 64cpus 512 GB of RAM, ~4 TB disk space<br> cod4 64cpus 512 GB of RAM, ~4 TB disk space |
| − | cod2 | ||
| − | cod3 | ||
| − | cod4 | ||
| − | '''Getting access | + | <br> '''Getting access''' |
| − | Ask Lex or Karin | + | Ask Lex or Karin |
| − | '''Mailing list''' | + | <br> '''Mailing list''' |
| − | If you're not already on it, get subscribed to the cees-hpc mailing list: | + | If you're not already on it, get subscribed to the cees-hpc mailing list: https://sympa.uio.no/bio.uio.no/subscribe/cees-hpc |
| − | https://sympa.uio.no/bio.uio.no/subscribe/cees-hpc | ||
| − | If you intend to use one of the nodes for an extended period of time, please send an email to this list | + | If you intend to use one of the nodes for an extended period of time, please send an email to this list |
| − | '''Logging in''' | + | <br> '''Logging in''' |
| + | <pre>ssh username@cod1.titan.uio.no</pre> | ||
| + | When you are on the UiO network it is enough to write ssh cod1 | ||
| − | + | 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 | |
| − | /work -- | ||
| − | A few important things to note: | + | 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 |
| − | - 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. | |
| − | + | <br> '''TIP: using screen''' | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | screen -rd | + | 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 |
| + | <pre>screen</pre> | ||
| + | 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> | ||
| + | '''CEES project data''' | ||
| − | + | The CEES projects are organised as follows: | |
| − | + | /projects/454data is the main area (at some point this will change names). 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: | |
| − | /projects/454data is the main area (at some point this will change names) | + | <pre>chgrp -R seq454 yourfolder |
| − | Access is for those in the seq454 unix user group (soon to change name to ceesdata) | + | chmod -R 770 yourfolder</pre> |
| − | Please check that files and folders you create have the right permissions: | + | It is possible to restrict access to a subgroup of those that are inn the seq454 group, please ask Lex/Karin |
| − | chgrp -R seq454 yourfolder | ||
| − | chmod -R 770 | ||
| − | + | Folders in /projects/454data: | |
| − | + | 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 script located<br>lib --> needed by certain programs<br>src --> source files for some of the programs in the bin folder<br>exchange --> for exchanging files with non-members<br> | |
| − | projects -- | ||
| − | databases -- | ||
| − | in_progress -- | ||
| − | bin -- | ||
| − | lib -- | ||
| − | src -- | ||
| − | exchange -- | ||
| − | + | <br> | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | Other folders:<br>bioportal --> used by the NSC<br>cees --> will be removed at a later date<br>scripts --> to be removed (empty)<br>utsp --> to be removed<br>www_docs_old --> to be removed<br>runs --> to be removed | |
| − | |||
| − | '''Note to SLURM users''' | + | <br> |
| + | |||
| + | It is recommended to put the /projects/454data/bin folder in your path. Include the following line in your ~/.bash_login file: | ||
| + | <pre>export PATH=/projects/454data/bin:$PATH</pre> | ||
| + | '''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. | 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''' | + | <br> '''Job scripts''' |
| − | You can use a job script: collect a bunch of commands and put them in an executable file. Run the command with | + | 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 | + | <pre>source yourcommands.sh</pre> |
Revision as of 09:59, 15 June 2012
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
cod2 24cpus 128 GB of RAM, ~1.3 TB disk space
cod3 64cpus 512 GB of RAM, ~4 TB disk space
cod4 64cpus 512 GB of RAM, ~4 TB disk space
Getting access
Ask Lex or Karin
Mailing list
If you're not already on it, get subscribed to the cees-hpc mailing list: https://sympa.uio.no/bio.uio.no/subscribe/cees-hpc
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.titan.uio.no
When you are on the UiO network it is enough to write ssh cod1
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/454data is the main area (at some point this will change names). 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/Karin
Folders in /projects/454data:
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 script located
lib --> needed by certain programs
src --> source files for some of the programs in the bin folder
exchange --> for exchanging files with non-members
Other folders:
bioportal --> used by the NSC
cees --> will be removed at a later date
scripts --> to be removed (empty)
utsp --> to be removed
www_docs_old --> to be removed
runs --> to be removed
It is recommended to put the /projects/454data/bin folder in your path. Include the following line in your ~/.bash_login file:
export PATH=/projects/454data/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
