Re: [Condor-users] Blast on Windows

["Dr Ian C. Smith" <i.c.smith@xxxxxxxxxxxxxxx>]

Does each individual search take over an hour. That seems a huge
amount of time even for something like the whole of EMBL.
I have had big problems with fragmentation on XP for files over
2 GB and blast basically ran forever. I'd try splitting the
blast databases into smaller volumes (100 MB max seemed a
decent compromise). The blast indexing program from NCBI
will do this for you.

-ian.

-----------------------------------
Dr Ian C. Smith,
e-Science team,
University of Liverpool
Computing Services Department,
Room 4.09, Chadwick Tower
Tel: ++44 (0)151 794 3745
e-mail: i.c.smith@xxxxxxxxxxxxxxx

--On 11 April 2006 23:20 -0400 Jess Cannata <jac67@xxxxxxxxxxxxxx> wrote:

> I am having problems running Blast (non-parallel) jobs on Windows XP
> using Condor 6.6.10. Blast jobs that take less than an hour finish
> without error. Jobs that take more than hour never terminate even though
> the job has "finished," meaning the job no longer uses any CPU time.
> They continue to run forever and continue to allocate RAM. I've included
> a log file of one of the non-terminating jobs which should have finished
> after an hour and a half.
>
> I have run the same jobs on the same machines without Condor and these
> jobs finish without any problem. Other types of jobs (non-Blast) run
> longer than one hour without incident. Has anyone seen this problem
> before? Would any Blast on Windows users be willing to share their
> Condor submission files?
>
> Thanks in advance.
>
> Jess
> 000 (276.000.000) 04/09 00:32:38 Job submitted from host:
> <141.161.x.2:9664> ...
> 001 (276.000.000) 04/09 00:32:44 Job executing on host:
> <141.161.x.38:1227> ...
> 006 (276.000.000) 04/09 00:32:52 Image size of job updated: 88744
> ...
> 006 (276.000.000) 04/09 00:52:52 Image size of job updated: 881472
> ...
> 006 (276.000.000) 04/09 01:12:52 Image size of job updated: 881660
> ...
> 010 (276.000.000) 04/09 12:18:48 Job was suspended.
>         Number of processes actually suspended: 2
> ...
> 011 (276.000.000) 04/09 12:28:50 Job was unsuspended.
> ...
> 004 (276.000.000) 04/09 12:28:50 Job was evicted.
>         (0) Job was not checkpointed.
>                 Usr 0 00:28:45, Sys 0 00:00:33  -  Run Remote Usage
>                 Usr 0 00:00:00, Sys 0 00:00:00  -  Run Local Usage
>         0  -  Run Bytes Sent By Job
>         2190680  -  Run Bytes Received By Job
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