Linux cluster
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==Parallel computing== | ==Parallel computing== | ||
| + | ===Examples=== | ||
| + | *[http://linuxinfo.physik.hu-berlin.de/pbs.html assigning nodes & cores] | ||
| + | *[http://www.clusterresources.com/products/torque/docs/2.1jobsubmission.shtml qsub examples] | ||
| + | *[http://compbio.korea.ac.kr/wiki/images/c/cb/Parallel_scripts.zip Parallel scripts] | ||
| + | *[http://beowulf.csail.mit.edu/18.337/index.html 18.337/6.338 Parallel Computing @MIT] | ||
| + | |||
===MEME=== | ===MEME=== | ||
*[http://biowulf.nih.gov/apps/meme.html parallel meme] | *[http://biowulf.nih.gov/apps/meme.html parallel meme] | ||
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mpirun -machinefile $PBS_NODEFILE -np $np /home/tools/MEME/bin/meme_p rep21-1.fasta -oc 072909.4 -protein -nmotifs 50 -minsites 2 -minw 8 -p 4 | mpirun -machinefile $PBS_NODEFILE -np $np /home/tools/MEME/bin/meme_p rep21-1.fasta -oc 072909.4 -protein -nmotifs 50 -minsites 2 -minw 8 -p 4 | ||
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==Programs Installed== | ==Programs Installed== | ||
Revision as of 03:57, 30 March 2010
Contents |
Administration
- Change locale (language)
bash shell: export LC_ALL=en_GB.ISO8859-1 export LANG=en_GB.ISO8859-1
Parallel computing
Examples
MEME
qsub -v np=4 -l nodes=node1 memebatch.csh
- CPU time error: add a following option
qsub -q infi
- memebatch.csh:
#!/bin/csh #PBS -N memejobtest setenv PATH /usr/local/mpich/bin:$PATH cd /home/users/igchoi/exp mpirun -machinefile $PBS_NODEFILE -np $np /home/tools/MEME/bin/meme_p rep21-1.fasta -oc 072909.4 -protein -nmotifs 50 -minsites 2 -minw 8 -p 4
Programs Installed
Bin directory (/home/tools)
- Statistical Packages
- R-2.8.1
- RMySQL
- DBI
- R-2.8.1
- Assembly packages
- AMOS
- EMBOSS(/usr/local/share/EMBOSS)
- EULER ( ?? )
- ab initio assembly
- ARACHNE 3.2
- WGS
- de novo
- de Bruijn graphs
- velvet
- abyss 1.0.5
- suffix tree-based approach
- QSRA
- SSAKE
- overlap-layout-consensus
- edena
- ??
- SHARCGS
- de Bruijn graphs
- comparative
- maq 0.7.1
- ETC
- realigner
- SOAPaligner
- Sequence analysis
- manatee(requir setting DIR)
- iprscan
- BLAST
Modules
- Python modules
- biopython
- pyrex
- numpy
- Rpy ( RHOME problem)
- Perl modules
