21 Nov 2012 00:51
Re: R: GPU Computing with Flow Cytometry
Manca,
I am not able to compile R 2.15.1 linked to mkl 11.0 on Debian
successfully.
Do I have to compile flowMerge from source as well? Any further
suggestions would be appreciated.
Thanks much, Kevin
Thus far, I have tried...
#get Debian patched source
>apt-get source r-base-core
#edit /r-base-core-12.15.1/debian/rules to read...
217 dh_testdir
218 R_PAPERSIZE=letter \
219 R_BROWSER=xdg-open \
220 PAGER=/usr/bin/pager \
221 PERL=/usr/bin/perl \
222 R_UNZIPCMD=/usr/bin/unzip \
223 R_ZIPCMD=/usr/bin/zip \
224 R_PRINTCMD=/usr/bin/lpr \
225 LIBnn=lib \
226 AWK=/usr/bin/awk \
227 CC=$(compiler) \
228
CXX=${cxxcompiler} \
229 ${fortrancompiler} \
230 FC=${f95compiler} \
231 CFLAGS="$(cflags)" \
232 CXXFLAGS="$(cxxflags)" \
233 FFLAGS="$(fcflags)" \
234 FCFLAGS="$(fcflags)" \
235 CPPFLAGS= \
236
LDFLAGS="-L/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/,
-Bdirect" \
237 SHLIB_LDFLAGS="-lpthread" \
238 MAIN_LDFLAGS="-lpthread" \
239
MKL_LIB_PATH=/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/ \
240 FLIBS= \
241 rsharedir=/usr/share/R/share \
242 rincludedir=/usr/share/R/include \
243 rdocdir=/usr/share/R/doc \
244
LD_LIBRARY_PATH=/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/ \
245 ./configure --prefix=/usr \
246 --with-cairo \
247 --with-jpeglib \
248 --with-readline \
249 --with-tcltk \
250 --with-system-bzlib \
251 --with-system-pcre \
252 --with-system-zlib \
253 --mandir=/usr/share/man \
254 --infodir=/usr/share/info \
255 --datadir=/usr/share/R/share \
256 --includedir=/usr/share/R/include \
257 $(atlas) \
258 $(lapack) \
259 --enable-R-profiling \
260 --enable-R-shlib \
261 --enable-memory-profiling \
262 --with-recommended-packages \
263 --build $(buildarch) \
264
--with-blas="-L/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/ -Wl,
--start-group
/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_gf_lp64.a
\ /opt/intel/composer_xe_2013.1.117/mkl/lib/intel64
/libmkl_gnu_thread.a \
/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/mkl_core.a \
-Wl, --end-group -lgomp -lpthread" \
265 CLFAGS="-O3 -funroll-loops -march=native" \
266 CXXFLAGS="-O3 -funroll-loops -march=native" \
267 FFLAGS="-O3 -funroll-loops -march=native" \
268 FCFLAGS="-O3 -funroll-loops -march=native" \
269 --with-lapack
When I run the flowMerge function pFlowClust (with snowfall) R is
running off BLAS still (evident by giving
>lsof | grep blas
R 6885 seahorse mem REG 8,2
257648 7621081 /usr/lib/libgslcblas.so.0.0.0
R 6885 seahorse mem REG 8,2
655336 7615156 /usr/lib/libblas/libblas.so.3.0
R 6885 23358 seahorse mem REG 8,2
257648 7621081 /usr/lib/libgslcblas.so.0.0.0
R 6885 23358 seahorse mem REG 8,2
655336 7615156 /usr/lib/libblas/libblas.so.3.0
R 23392 seahorse mem REG 8,2
257648 7621081 /usr/lib/libgslcblas.so.0.0.0
R 23392 seahorse mem REG 8,2
655336 7615156 /usr/lib/libblas/libblas.so.3.0
R 23399 seahorse mem REG 8,2
257648 7621081 /usr/lib/libgslcblas.so.0.0.0
R 23399 seahorse mem REG 8,2
655336 7615156 /usr/lib/libblas/libblas.so.3.0
>top | grep 6885
6885 seahorse 20 0 2095m 1.8g 9012 S 0.3 23.8 0:21.35 R
On 11/16/2012 10:33 AM, Tim Triche, Jr. wrote:
> anyone else tried Andrew Cron's GPUmix wrapper from R? I was under
> the impression that both Mike West (who I think is Cron's advisor) and
> Marc Suchard were doing a lot of work applying GPUs to multi-label
> (i.e. 6, 7, 8, 9+ antibodies) FC.
>
> http://www.stat.duke.edu/gpustatsci/software.html
>
> http://www.ficcs.org/wp-content/uploads/downloads/2010/12/ficcs.pdf
>
>
>
>
> On Thu, Nov 15, 2012 at 11:26 PM, Manca Marco (PATH)
> <m.manca@...
> <mailto:m.manca@...>> wrote:
>
> Dear Kevin
>
> I am no expert of the package you are enquiring about, but in
> general you might be interested in substituting the generic BLAS
> on your machine with Intel's MKL (non free, but available with no
> costs for research via Intel) in order to enable native
> parallelization of most of the plausible functions, with no need
> to modify your code. Here are some tests:
> http://planetflux.adamwilson.us/2012/05/compiling-r-with-intels-math-kernel.html
>
> You can get inspiration on the way to install MKL and force its
> use by R, by reading this blog
> http://www.r-bloggers.com/compiling-64-bit-r-2-10-1-with-mkl-in-linux/
>
> The use of your GPU is a completely different issue, and despite
> having a CUDA enabled GPU myself I gave up on it for lack of time
> and frustration... but maybe you are smarter and luckier than me.
> You can start reading from this page and then follow the links:
> http://brainarray.mbni.med.umich.edu/Brainarray/rgpgpu/
>
> I hope this helps. Good luck and best regards,
> Marco
>
>
> --
> Dr Marco Manca
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
>
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
> Visiting address: UNS40 West building - 5th floor Room5.544,
> Universiteit Singel 40, 6229 HX Maastricht
>
> E-mail: m.manca@...
> <mailto:m.manca@...>
> Office telephone: +31(0)433884289 <tel:%2B31%280%29433884289>
> Personal mobile: +31(0)626441205 <tel:%2B31%280%29626441205>
> Twitter: <at> markomanka
>
>
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> ________________________________________
> Da: bioconductor-bounces@...
> <mailto:bioconductor-bounces@...>
> [bioconductor-bounces@...
> <mailto:bioconductor-bounces@...>] per conto di Kevin
> Schiesser [schiesserk@...
> <mailto:schiesserk@...>]
> Inviato: venerdì 16 novembre 2012 0.18
> A: kevin.schiesser@... <mailto:kevin.schiesser@...>
> Cc: bioconductor@... <mailto:bioconductor@...>
> Oggetto: Re: [BioC] GPU Computing with Flow Cytometry
>
> On 11/15/2012 02:52 PM, Kevin Schiesser wrote:
> > Hi y'all,
> >
> > Does Bioconductor support GPU/multi-core computing for flow
> cytometry
> > data analysis?
> >
> > For instance, in the flowMerge package there is a pFlowClust option.
> > When I load the flowMerge library, and call flowClust(), I get the
> > output 'Using the serial version of flowClust'. I have a quad-core
> > processor (Intel(R) Core(TM) i5-3210M CPU <at> 2.50GHz) and a
> geForce GT
> > 650M video card (CUDA enabled) running on Debian Testing
> > 3.2.0-4-amd64. What does pFlowClust look for to choose serial or
> > parallel?
> >
> > I ask because on my lowly laptop the runtime for flowClust(dat,
> > K=1:10) prohibits sound troubleshooting for a flowFrame with 9
> stains.
> > I would like to optimize the hardware I have access to, but I am
> > running out of ideas. Any thoughts?
> >
> > Much thanks,
> > Kevin
> >
> Nevermind... I found
> http://www.findthatdoc.com/search-39323504-hPDF/download-documents-flowclustflowmergeslides-pdf.htm
> to keep me busy for a while... Thanks Greg!
>
> Still, GPU computing would be a very nice option for the
> flowSuiteOfSoftwares. -k
>
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>
>
> --
> /A model is a lie that helps you see the truth./
> /
> /
> Howard Skipper
> <http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>
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