[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 
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.

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?


To unsubscribe from this discussion, e-mail: [users-unsubscribe at gridengine.sunsource.net].

More information about the gridengine-users mailing list