Hi Purvesh,
clearly some bottleneck exists in the system, however it's difficult to
say what's going on based on your description alone. Can you post
1) the mpiBLAST command-line used
2) the stderr output produced when running that command with the --debug
argument added
3) the amount of memory consumed by mpiblast processes on the active node
4) the amount of physical memory in the active node
If (2) is > 5kb, please send it directly to me instead of posting it to
the list.
At startup mpiBLAST computes the effective search space for all query
sequences. In the process, a low-complexity filter is applied to the
sequences which can take non-trivial compute resources. It may be
helpful to disable the filter using the -F F command line argument and
see whether the job runs faster.
-Aaron
Purvesh Khatri wrote:
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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