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

[Elton V. <elt...@iq...>]

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
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...>:

> 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...>
> 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 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?
>>
>>
>>


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