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

[Serge K. <ser...@gm...>]

Yes, the latest CA 8.3 release can assemble D. melanogaster in < 700CPU hours. You can see the updated timings here:
http://wgs-assembler.sourceforge.net/wiki/index.php/Version_8.3_Release_Notes <http://wgs-assembler.sourceforge.net/wiki/index.php/Version_8.3_Release_Notes>

I’ve routinely run D. melanogaster on a 16-core, 32GB machine in less than a day (I haven’t timed it exactly) so for your genome you’re looking at 3-4K cpu hours. You should be able to run it on a single 16-core 32GB machine in a couple of days so I think it’s easiest to run it on a single largish machine you have access to.

Sergey

> On Jun 2, 2015, at 9:12 PM, Brian Walenz <th...@gm...> wrote:
> 
> That's an old page.  The most recent page, linked from http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page <http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page>, is:
> 
> http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR <http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR>
> 
> (look for 'self correction')
> 
> I've run drosophilia on my 12-core development machine in a few hours to overnight (I haven't timed it).  Sergey replaced blasr with a much much faster algorithm, and that was where most of the time was spent.
> 
> b
> 
> 
> On Tue, Jun 2, 2015 at 9:02 PM, Elton Vasconcelos <elt...@iq... <mailto:elt...@iq...>> wrote:
> Thanks for the hints, Brian!
> 
> We'll try everything you suggested tomorrow, back in the lab.
> Then I'll tell you what we got.
> For now, I only wanna say that our main concern, instead of running runCA itself, is gonna be with the pre-assembly (correction) step, running PacBiotoCA and PBcR pipeline that are embedded in the wgs package.
> Please take a look at the following strategy to assemble the Drosophila genome sequenced by PacBio technology (which presents a high error rate on the base calling, ~15%)  at CBCB in Maryland :
> http://cbcb.umd.edu/software/PBcR/dmel.html <http://cbcb.umd.edu/software/PBcR/dmel.html>
> They mentioned 621K CPU hours to correct that genome of ~122 Mb.
> Our organism genome is something like 380 Mb long. Three times Drosophila's one.
> Well, just to let you know again! ;-)
> 
> Talk to you later,
> Thanks again.
> Good night!
> Elton
> 
> 2015-06-02 20:19 GMT-03:00 Brian Walenz <th...@gm... <mailto:th...@gm...>>:
> For the link problems - all those symbols come out of the kmer package.  Check that the flags and compilers and whatnot are compatible with those in wgs-assembler.
> 
> The kmer configuration is a bit awkward.  A shell script (configure.sh) dumps a config to Make.compilers, which is read by the main Makefile.  'gmake real-clean' will remove the previous build AND the Make.compilers file.  'gmake' by itself will first build a Make.compilers by calling configure.sh, then continue on with the build.  The proper way to modify this is:
> 
> edit configure.sh
> gmake real-clean
> gmake install
> repeat until it works
> 
> In configure.sh, there is a block of flags for Linux-amd64.  I think it'll be easy to apply the same changes made for wgs-assembler.
> 
> After rebuilding kmer, the wgs-assembler build should need to just link -- in other words, remove just wgs-assembler/Linux-amd64/bin -- don't do 'gmake clean' here!  You might need to remove the dependency directory 'dep' too.
> 
> 
> For running - the assembler will emit an SGE submit command to run a single shell script on tens-to-hundreds-to-thousands of jobs.  Each job will be 8-32gb (tunable) and 1-32 cores (nothing special here: more is faster, fewer is slower).  If you can figure out how to run jobs of the form "command.sh 1", "command.sh 2", "command.sh 3", ..., "command.sh N" on on BG/Q you're most of the way to running CA.  To make it output such a submit command, supply "useGrid=1 scriptOnGrid=0" to runCA.
> 
> The other half of the assembler will be either large I/O or large memory.  If you've got access to a machine with 256gb and 32 cores you should be fine.  I don't know what a minimum usable machine size would be.
> 
> So, the flow of the computer will be:
> 
> On the 256gb machine:  runCA useGrid=1 scriptOnGrid=0 ....
> Wait for it to emit a submit command
> Launch those jobs on BG/Q
> Wait for those to finish
> Relaunch runCA on the 256gb machine.  It'll check that the job outputs are complete, and continue processing, probably emitting another submit command, so repeat.
> 
> Historical note: back when runCA was first developed, we had a DEC Alpha Tru64 machine with 4 CPUs and 32gb of RAM, and a grid of a few hundred 2 CPU, 2gb, 32-bit Linux machines.  The Alpha wasn't in the grid, and a different architecture anyway, so we had to run CA this way.  It was a real chore.  We're all spoiled with our 4 core 8gb laptops now...
> 
> b
> 
> 
> 
> 
> 
> 
> On Tue, Jun 2, 2015 at 5:49 PM, Elton Vasconcelos <elt...@iq... <mailto:elt...@iq...>> wrote:
> 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 <http://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 <http://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? 
> 
> 
> 
> 
> 
> -- 
> Elton Vasconcelos, DVM, PhD
> Post-doc at Verjovski-Almeida Lab
> Department of Biochemistry - Institute of Chemistry
> University of Sao Paulo, Brazil
> 
>