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source code for GPU-enabled K-Score implementation - gives proper answers but no faster due to memory bandwidth bottleneck

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test
test
 
 
.gitignore
.gitignore
 
 
Makefile
Makefile
 
 
Makefile-orig-07-07-01-2
Makefile-orig-07-07-01-2
 
 
README-MAPREDUCE
README-MAPREDUCE
 
 
README.markdown
README.markdown
 
 
base64.cpp
base64.cpp
 
 
base64.h
base64.h
 
 
expat.h
expat.h
 
 
expat_external.h
expat_external.h
 
 
expat_external_old.h
expat_external_old.h
 
 
expat_old.h
expat_old.h
 
 
loadmspectrum.cpp
loadmspectrum.cpp
 
 
loadmspectrum.h
loadmspectrum.h
 
 
mapreducehandler.cpp
mapreducehandler.cpp
 
 
mapreducehelper.cpp
mapreducehelper.cpp
 
 
mapreducehelper.h
mapreducehelper.h
 
 
mapreducehelper_bangbang.cpp
mapreducehelper_bangbang.cpp
 
 
masscalc.cpp
masscalc.cpp
 
 
masscalc.h
masscalc.h
 
 
mbiomlreport.cpp
mbiomlreport.cpp
 
 
mbiomlreport.h
mbiomlreport.h
 
 
mcleave.h
mcleave.h
 
 
mdomains.h
mdomains.h
 
 
mhistogram.h
mhistogram.h
 
 
mmotif.h
mmotif.h
 
 
mpam.cpp
mpam.cpp
 
 
mpam.h
mpam.h
 
 
mplugin.cpp
mplugin.cpp
 
 
mplugin.h
mplugin.h
 
 
mpmods.cpp
mpmods.cpp
 
 
mpmods.h
mpmods.h
 
 
mprocess.cpp
mprocess.cpp
 
 
mprocess.h
mprocess.h
 
 
mrefine.cpp
mrefine.cpp
 
 
mrefine.h
mrefine.h
 
 
mreport.cpp
mreport.cpp
 
 
mreport.h
mreport.h
 
 
mscore.cpp
mscore.cpp
 
 
mscore.h
mscore.h
 
 
mscore_c.cpp
mscore_c.cpp
 
 
mscore_c.h
mscore_c.h
 
 
mscore_hrk.cpp
mscore_hrk.cpp
 
 
mscore_hrk.h
mscore_hrk.h
 
 
mscore_k.cpp
mscore_k.cpp
 
 
mscore_k.h
mscore_k.h
 
 
mscore_kgpu.cpp
mscore_kgpu.cpp
 
 
mscore_kgpu.h
mscore_kgpu.h
 
 
mscore_kgpu_thrust.cu
mscore_kgpu_thrust.cu
 
 
mscore_kgpu_thrust.h
mscore_kgpu_thrust.h
 
 
mscore_tandem.cpp
mscore_tandem.cpp
 
 
mscore_tandem.h
mscore_tandem.h
 
 
mscorepam.h
mscorepam.h
 
 
mscorestate.h
mscorestate.h
 
 
msemistate.h
msemistate.h
 
 
msequence.h
msequence.h
 
 
msequencecollection.cpp
msequencecollection.cpp
 
 
msequencecollection.h
msequencecollection.h
 
 
msequenceserver.cpp
msequenceserver.cpp
 
 
msequenceserver.h
msequenceserver.h
 
 
msequtilities.cpp
msequtilities.cpp
 
 
msequtilities.h
msequtilities.h
 
 
mspectrum.h
mspectrum.h
 
 
mspectrumcondition.cpp
mspectrumcondition.cpp
 
 
mspectrumcondition.h
mspectrumcondition.h
 
 
mtermmods.cpp
mtermmods.cpp
 
 
mtermmods.h
mtermmods.h
 
 
mxxcleavage.cpp
mxxcleavage.cpp
 
 
mxxcleavage.h
mxxcleavage.h
 
 
p3.cpp
p3.cpp
 
 
p3mprocess.cpp
p3mprocess.cpp
 
 
p3mprocess.h
p3mprocess.h
 
 
p3msequenceserver.cpp
p3msequenceserver.cpp
 
 
p3msequenceserver.h
p3msequenceserver.h
 
 
release_notes.html
release_notes.html
 
 
saxbiomlhandler.cpp
saxbiomlhandler.cpp
 
 
saxbiomlhandler.h
saxbiomlhandler.h
 
 
saxgamlhandler.cpp
saxgamlhandler.cpp
 
 
saxgamlhandler.h
saxgamlhandler.h
 
 
saxhandler.cpp
saxhandler.cpp
 
 
saxhandler.h
saxhandler.h
 
 
saxmodhandler.cpp
saxmodhandler.cpp
 
 
saxmodhandler.h
saxmodhandler.h
 
 
saxmzdatahandler.cpp
saxmzdatahandler.cpp
 
 
saxmzdatahandler.h
saxmzdatahandler.h
 
 
saxmzxmlhandler.cpp
saxmzxmlhandler.cpp
 
 
saxmzxmlhandler.h
saxmzxmlhandler.h
 
 
saxsaphandler.cpp
saxsaphandler.cpp
 
 
saxsaphandler.h
saxsaphandler.h
 
 
saxtandeminputhandler.cpp
saxtandeminputhandler.cpp
 
 
saxtandeminputhandler.h
saxtandeminputhandler.h
 
 
saxtaxhandler.cpp
saxtaxhandler.cpp
 
 
saxtaxhandler.h
saxtaxhandler.h
 
 
serialize.cpp
serialize.cpp
 
 
serialize.h
serialize.h
 
 
stdafx.cpp
stdafx.cpp
 
 
stdafx.h
stdafx.h
 
 
tandem.cpp
tandem.cpp
 
 
timer.cpp
timer.cpp
 
 
timer.h
timer.h
 
 

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xtandem-g

Private development for adding GPGPU support to xtandem.

Note, this code is not standalone and is meant to drop into an existing TPP svn checkout under extern/xtandem/src-g (or whatever alternate src directory name you choose.)

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source code for GPU-enabled K-Score implementation - gives proper answers but no faster due to memory bandwidth bottleneck

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