[Bioclusters] openmosix cluster again

[Martín Sarachu]

no, we are using blast from command-line and from a wrapper in EMBOSS

Quoting Hong Zhang <hzhang@research.dfci.harvard.edu>:

> So for blast, are you using blastwww?
> 
> On Tue, 6 Jan 2004, Martín Sarachu wrote:
> 
> > I think Joe is right, we are not saying contradictory things. The only
> patched 
> > tool we use is BLAST.
> > EMBOSS, for example, is the exact same version you would use in a
> non-cluster 
> > environment. EMBOSS jobs are quite variable in its run-times and resources
> they 
> > need. Jobs that requires multiples accesses to a database perform very
> well, and 
> > jobs that do very little (check available databases) don't even migrate.
> > EMBOSS apps are not paralell, so you don't get a reduction in the run-time
> of a 
> > single job (in fact there is some little overhead for the migration), what
> you 
> > get is a reduction on the time it would take to run 20 jobs.
> > There's a nearly-official patch (MASK patch) for openMosix that allows to
> 
> > migrate shared-memory applications (Apache, PostgreSQL).
> > 
> > 
> > Regards,
> > 
> > martin
> > 
> > Joseph Landman wrote:
> > > Hi Hong:
> > > 
> > > I don't think these are contradictory.  Martin has been able to use 
> > > OpenMosix with a variety of tools.  If you note, he used the patched 
> > > version of BLAST (which specifically disables pthreads).  The other 
> > > tools are likely also either patched, or compiled without pthreading. 
> > > Postgres is a database, and you really don't want it migrating from its
> 
> > > data store.  Apache is a web server, and likewise, you don't want it 
> > > migrating (extra latency etc.).
> > > 
> > > Joe
> > > 
> > > hong.zhang@research.dfci.harvard.edu wrote:
> > > 
> > >> Dear Joe and Martin,
> > >>
> > >> Thanks for your instant reply. But it seems you two have contrary 
> > >> opinion.
> > >> I am kinda confused. Would you please give me more explanation?
> > >> I attached both of your answers below.
> > >>
> > >> --------------------------------------------------------------------
> > >> Martin said:
> > >>
> > >> openMosix works great for our site (AR.EMBnet). We have many bio web 
> > >> tools
> > >> (EMBOSS, SMS, WebPhylip) here and all of them (except SRS) work fine
> with
> > >> openMosix. They migrate very well.
> > >> On top of openMosix we use SGE for some jobs users submit by 
> > >> command-line.
> > >> We use the patched version of BLAST to be able to run it (migrate)
> under
> > >> openMosix.
> > >>
> -------------------------------------------------------------------------- 
> > >>
> > >> Joe said
> > >>
> > >>>   Openmosix will not migrate pthreaded jobs.  Postgres and the web
> > >>> interfaces (apache based) are all pthreaded.
> > >>>
> > >>>   What open mosix is as far as bio-clusters are concerned, is a tool
> to
> > >>>
> > >>> do a "semi-automatic" load balance.  Jobs which meet specific
> criteria
> > >>> can be migrated to less busy nodes.  For this to make sense, you
> would
> > >>> need a) the jobs to require long running times (as compared to
> potential
> > >>> migration time), b) sufficiently low IO and other resource
> utilization
> > >>> such that the migration will not generate hot-spots (resource
> > >>> contention, such as network bandwidth for accessing a file over NFS).
> > >>>
> > >>>   It is good for some types of jobs, though in a shared nothing
> > >>> environment (cluster) with limited network bandwidth and relatively
> high
> > >>> latencies, its isn't necessarily better than the queuing systems.
> > >>>
> > >>> Joe
> > >>>
> > >>
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> > >> https://bioinformatics.org/mailman/listinfo/bioclusters
> > > 
> > > 
> > 
> > 
> 
> -- 
> Hong Zhang, MIS
> Bioinformatics Analyst
> Dana Farber Cancer Institute
> Harvard Medical School
> 44 Binney St, D1510A
> Boston MA 02115
> Email: hong.zhang@research.dfci.harvard.edu
> Phone: 617-632-3824
> Fax: 617-632-3351
> 
> 


-- 
Martín Sarachu
mad@biol.unlp.edu.ar
EMBnet Argentina
http://www.ar.embnet.org