[GE users] ncbi blast on SGE

axinsoft axinsoft at yahoo.com.cn
Tue May 25 14:42:46 BST 2010


murple / reuti,

thank you very much for replying. i am very new to SGE, and just realize array jobs may just same copy of jobs running again and again.

i did not complie anything, just use the default "blastall" in Rocks pack (i am not sure if that is a native one from ncbi).
in Rocks manaul 
http://www.rocksclusters.org/roll-documentation/bio/5.3/blast_usage.html
example is very simple and nothing is mentioned.

regarding OpenMPI, i know there is another package "mpiblast" in Rocks too. is that you are refering to? i hear many people recommending mpiblast.

i am just very curious this article is refered by many people(i sawed somewhere like 16 times refer). and did give me very impressive how Grid Engine is working.
http://developers.sun.com/solaris/articles/integrating_blast.html

it simply use native blast:
${progpath}/blastall -p blastn \
      -d nt     \
      -i ${seqpath}/nt.123 \
      -e 0.1    \
      -o ${outpath}/out.123.blastn
to get the fancy result of:

job-ID prior name       user   state submit/start at    queue master ja-task-ID
------------------------------------------------------------------------------
113    0    blast_5.cs blast   r   05/19/2003 15:57:24 andre.q    MASTER
115    0    blast_7.cs blast   r   05/19/2003 15:57:24 andre.q    MASTER
116    0    blast_8.cs blast   r   05/19/2003 15:57:24 andre.q    MASTER
119    0    blast_11.c blast   r   05/19/2003 15:58:24 andre.q    MASTER
120    0    blast_12.c blast   r   05/19/2003 15:58:54 caesar.q   MASTER
121    0    blast_13.c blast   r   05/19/2003 15:58:55 saqqara.q  MASTER
112    0    blast_4.cs blast   r   05/19/2003 15:57:24 odiche.q   MASTER
117    0    blast_9.cs blast   r   05/19/2003 15:57:25 kaiser.q   MASTER
118    0    blast_10.c blast   r   05/19/2003 15:57:25 kaiser.q   MASTER
122    0    blast_14.c blast   r   05/19/2003 15:59:39 tonylama.q MASTER
123    0    blast_15.c blast   qw  05/19/2003 15:57:14
124    0    blast_16.c blast   qw  05/19/2003 15:57:14

is that article try to tell me: the program could see SGE by default a powerful "virtual" computer?

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