embossIntel

EMBOSS GPU

1. ssh into the GPU cluster using the following: ssh –X username@gpu.chpc.ac.za.
2. In your user home directory: create a file named: .embossrc.
3. Insert the following line in the file named .embossrc: INCLUDE /GPU/opt/emboss-
intel/EMBOSS-6.3.1/test/.embossrc.
4. From then, export the following path in the user environment (.bashrc or .profile
file):

export LD_LIBRARY_PATH=/GPU/opt/emboss-intel-new/lib:$LD_LIBRARY_PATH
export PATH=/GPU/opt/emboss-intel-new/bin:$PATH

5. To test/lists EMBOSS and Embassy sub-packages, type the command: wossname -
auto –alpha and the command will display more than 200 programs as follows:
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[username@hn.gpu~]$ wossname –auto –alpha
ALPHABETIC LIST OF PROGRAMS
aaindexextract Extract amino acid property data from AAINDEX
abiview Test an application ACD file
:
:
:
Yank Add a sequence reference (a full USA) to a list file
[smabakane@hn.gpu ~]$
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6. To search information about specific program, type the command: tfm –program
programname.
7. To list database names, type the command: showdb and it will display the following:
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Display information on configured databases
Name
Type
ID
Qry All
Comment
qapblast
Protein
OK
OK OK
Blast swissnew
:
:
tgenbank Nucleotide OK
OK OK
GenBank in native...
[username@hn.gpu ~]$
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8. Create the below example script and name the file: emboss.moab:
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###These lines are for Moab
#MSUB -l nodes=1:ppn=8:gpus=4 partition=c1060
#MSUB -l walltime=168:00:00
#MSUB -m be
#MSUB -V
#MSUB -o /GPU/home/username/embosstest/out
#MSUB -e /GPU/home/username/embosstest/err
#MSUB -d /GPU/home/username/embosstest
#MSUB -mb
##### Running commands
needle tembl:z11115 tembl:z11115 -out all.needle –auto
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Note: the below script submit a job that will read 11115 records in the database.
9. Submit the job using the command: msub emboss.moab.
10. An output file named: all.needle is then generated in the following directory:
/GPU/home/username/embosstest.
11. To check the status of the job, type: showq.
12. To check status of the nodes, type: pbsnodes.
Caution: Users should not attempt to read database in the login node as the processes
hangs the login node and disallow users to login to the cluster.
For more information about EMBOSS; you may visit: http://emboss.sourceforge.net/.