This is all about how to compute on coyote.
Gaining access:
I'm pretty sure that [greg] still helps out with this, you would probably need to ask him for access
What is available:
matlab (7.8.0.347 (R2009a) 64-bit (glnxa64))
?
?
Interactive computing:
I'm not sure how to work interactively. I've was able to get onto a node with:
qsub -I -l nodes=1
But when I tried to use matlab with (module add matlab) it didn't work (although it did work upon ssh'ing)
Submitting multiple jobs:
From Mark and Chris-
I've been using a script chris wrote which works pretty well:/home/csmillie/bin/ssub
What it does
It streamlines job submission. If you give it a list of commands, it will (1) create scripts for them, and (2) submit them as a job array. You can give it the list of commands as command line arguments or through a pipe.
Quick examples
1. Submit a single command to the clusterssub "python /path/to/script.py > /path/to/output.txt"
2. Submit multiple commands to the cluster (use semicolon separator)ssub "python /path/to/script1.py; python /path/to/script2.py"
3. Submit a list of commands to the cluster (newline separator)cat /list/of/commands.txt | ssub
Detailed example/home/csmillie/alm/mam/aln/95
In this directory, I have 12,352 fasta files I want to align. I can do this on 100 nodes quite easily:
1. First, I create a list of commands:for x in `ls *fst`; do y=$
; echo muscle -in $x -out $y.aln; done > commands.txt
The output looks like this:
...
muscle -in O95_9990.fst -out O95_9990.aln
muscle -in O95_9991.fst -out O95_9991.aln
muscle -in O95_9992.fst -out O95_9992.aln
muscle -in O95_9993.fst -out O95_9993.aln
...
2. Then I submit these commands as a job array:cat commands.txt | ssub
How to configure it
Copy it to your ~/bin (or wherever). Then edit the top of the script:uname = your usernametmpdir = directory where scripts are createdmax_size = number of nodes you want to use
Other thingsIt automatically creates random filenames for your scripts and job arrays. These files are created in the directory specified by "tmpdir" It can also submit individual scripts instead of a job array.