Hi,
I am running mpiBLAST on a 7 node cluster, where each node has 4
processors (2 dual-core AMD processors). I am running mpiBLAST with -n
30 using MPICH2. I use 30 since the mpiBLAST documentation says that add
2 more processes for scheduling and output.
Before submitting my job to the cluster, I benchmarked the cluster and
found that I can blast 125 sequences in less than 4 minutes. However,
when I submitted a job with 40,000 mRNA sequences (with the same
parameters and against the same database as benchmarks) with -n 30 I
find that all of the time mpiBLAST processes are sleeping, except on the
master node. On the master node all 4 processes are either running or in
uninterruptible sleep mode. In the first 12 hours, after submitting the
request, only 14 sequences were alinged. Also, in the last 12 hours not
a single sequence has been aligned. Based on my benchmarks I was
expecting at least a few thousands of sequences to have been aligned
already.
Can anyone help me please?
Thank you for your help,
Purvesh Khatri
--
Purvesh Khatri
Dept. of Computer Science
Wayne State University
Detroit, MI 48202
Phone: 313 577 5070
Fax: 313 577 6868
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