Re: [wgs-assembler-users] CA on BlueGene server at Rice University

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Thanks Brian, Serge and Huang,

We've gone through fixing several error messages during the compilation
within the src/ dir from the latest wgs-8.3rc2.tar.bz2 package.
At the end of the day we stopped on "undefined reference" errors on static
libraries (mainly libseq.a, please see make_progs.log file).

The 'gmake install' command within the kmer/ dir ran just fine.

The following indicates BGQ OS type:
[erv3@bgq-fn src]$ uname -a
Linux bgq-fn.rcsg.rice.edu 2.6.32-431.el6.ppc64 #1 SMP Sun Nov 10 22:17:43
EST 2013 ppc64 ppc64 ppc64 GNU/Linux

We also had to edit c_make.as file, adding some -I options (to indicate
paths to libraries) on the CFLAGS fields from the "OSTYPE, Linux" section.

Running "make objs" and "make libs" separately, everything appeared to work
fine (see attached files make_objs.log and make_libs.log).
The above mentioned trouble came up on the "make progs" final command we
ran (make_progs.log file).

Well, just to let you guys know and to see whether some light can be shed.

Thanks a lot,
Cheers,
Elton

PS: I also noticed about the MPI cluster system on BGQ, Brian. So, do you
think it isn't worthwhile keeping the attempt to install CA on BGQ?

2015-06-02 17:15 GMT-03:00 Walenz, Brian <wa...@nb...>:

> Poking around a bit too, it looks like BlueGene/P only supports MPI, which
> the assembler doesn't.  The assembler needs SGE (or PBS or LSF) to run
> independent threaded jobs.
>
> BlueGene/Q has 16 threads and 16 GB per node.  This is a better match to
> assembler workloads.  It'll still need some kind of batch scheduler.
>
> b
>
>
>
> -----Original Message-----
> From: Serge Koren [mailto:ser...@gm...]
> Sent: Tuesday, June 02, 2015 2:48 PM
> To: Brian Walenz
> Cc: wgs...@li...; Elton Vasconcelos
> Subject: Re: [wgs-assembler-users] CA on BlueGene server at Rice University
>
> Looking at the system description, assuming this is the system:
> http://www.rcsg.rice.edu/sharecore/bluegenep-bgp/ <
> http://www.rcsg.rice.edu/sharecore/bluegenep-bgp/>
>
> The cores are 32-bit which would limit your processes to 4GB and wouldn’t
> work well for assembly. Plus, we haven’t compiled/tested the assembler on
> 32-bit platforms in years so I don’t think it’s worth your time to try to
> compile it on there. How big is your genome? A 70X human correction takes
> about 8K cpu hours to generate corrected reads (is that what you mean by
> pre-assemble?) and total runtime (including correct + assemble) is about
> 50K cpu so with 2GHz CPUs you should be closer to a week for a full run not
> 30 days with almost 1000 cores (there is some overhead so not all steps
> would use all your cores). The assembler supports multiple grid systems
> (SGE, LSF, PBS) with a shared filesystem and I see Rice University has some
> clusters available so I’d recommend using one of those rather than
> recompiling.
>
>
> > On Jun 2, 2015, at 11:11 AM, Brian Walenz <th...@gm...> wrote:
> >
> > Nope, not on our mind.  A lack of access is the primary problem,
> followed closely by a lack of time and a lack of demand.
> >
> > There isn't anything fancy or gcc-specific in the code though.  It does
> compile with clang (without thread support, but that's clang's fault).
> Mucking with c_make.as <http://c_make.as/> might be all that is needed.
> To start, try copying the 'Darwin' section, and changing the OSTYPE test to
> whatever 'uname' reports, and the compiler to icc.  Icc will probably
> complain about ARCH_CFLAGS, so might as well get rid of all of those.  -O
> (optimize) is pretty generic.
> >
> > b
> >
> >
> >
> > On Tue, Jun 2, 2015 at 9:41 AM, Elton Vasconcelos <elt...@iq...
> <mailto:elt...@iq...>> wrote:
> > Hello folks,
> >
> > I wonder whether it is on CA developers mind to generate a wgs-assembler
> version that is compatible with IBM compilers, so we could run it on BG/P
> and/or BG/Q supercomputers at Rice University.
> > I am trying to pre-assemble my target genome sequenced by PacBio
> technology. By my calculations, I am gonna need 800 CPUs to run it in 30
> days.
> >
> > Thanks in advance for your attention,
> > Cheers,
> > Elton
> >
> > --
> > Elton Vasconcelos, DVM, PhD
> > Post-doc at Verjovski-Almeida Lab
> > Department of Biochemistry - Institute of Chemistry University of Sao
> > Paulo, Brazil
> >
> >
> > ----------------------------------------------------------------------
> > --------
> >
> > _______________________________________________
> > wgs-assembler-users mailing list
> > wgs...@li...
> > <mailto:wgs...@li...>
> > https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users
> > <https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users>
> >
> >
> > ----------------------------------------------------------------------
> > -------- _______________________________________________
> > wgs-assembler-users mailing list
> > wgs...@li...
> > https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users
>
>

-- 
Elton Vasconcelos, DVM, PhD
Post-doc at Verjovski-Almeida Lab
Department of Biochemistry - Institute of Chemistry
University of Sao Paulo, Brazil