[med-svn] [Git][med-team/libhmsbeagle][master] 3 commits: Upstream is now using proper release tags
Andreas Tille
gitlab at salsa.debian.org
Sat Jun 23 06:14:42 BST 2018
Andreas Tille pushed to branch master at Debian Med / libhmsbeagle
Commits:
d4af106d by Andreas Tille at 2018-06-23T07:13:55+02:00
Upstream is now using proper release tags
- - - - -
16f18654 by Andreas Tille at 2018-06-23T07:14:13+02:00
New upstream version 3.0.2+dfsg
- - - - -
d5eba967 by Andreas Tille at 2018-06-23T07:14:23+02:00
Update upstream source from tag 'upstream/3.0.2+dfsg'
Update to upstream version '3.0.2+dfsg'
with Debian dir 0cefe7ada4e37ef227341b8c18800114fb1c18c6
- - - - -
7 changed files:
- configure.ac
- debian/changelog
- debian/watch
- examples/synthetictest/synthetictest.cpp
- libhmsbeagle/CPU/BeagleCPUImpl.hpp
- libhmsbeagle/GPU/GPUInterfaceCUDA.cpp
- libhmsbeagle/GPU/kernels/Makefile.am
Changes:
=====================================
configure.ac
=====================================
--- a/configure.ac
+++ b/configure.ac
@@ -264,31 +264,6 @@ fi
NVCCFLAGS+=" -Wno-deprecated-gpu-targets"
# ------------------------------------------------------------------------------
-# Setup nvcc ccbin
-# ------------------------------------------------------------------------------
-
-AC_ARG_WITH([nvcc-ccbin],
- [AS_HELP_STRING([--with-nvcc-ccbin=PATH],[path or executable name of host compiler for nvcc @<:@default=auto@:>@])],
- [],
- [with_nvcc_ccbin=auto])
-
-
-if test "x$with_nvcc_ccbin" != "xno"
-then
- if test "x$with_nvcc_ccbin" != "xauto"
- then
- NVCCFLAGS+=" -ccbin $with_nvcc_ccbin"
- else
- case $host_os in
- *darwin*)
- NVCCFLAGS+=" -ccbin /usr/bin/clang"
- ;;
- esac
- fi
-fi
-
-
-# ------------------------------------------------------------------------------
# Setup SSE
# ------------------------------------------------------------------------------
@@ -358,7 +333,7 @@ case $host_os in
then
NVCCFLAGS+=" -m64"
AM_CXXFLAGS="$AM_CXXFLAGS -m64"
- NVCCFLAGS+=" -D_POSIX_C_SOURCE"
+ NVCCFLAGS+=" -D_POSIX_C_SOURCE -ccbin /usr/bin/clang"
CUDA_LIBS+=" -F/Library/Frameworks -framework CUDA"
fi
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-libhmsbeagle (2.1.2+git20180619-1) UNRELEASED; urgency=medium
+libhmsbeagle (3.0.2+dfsg-1) UNRELEASED; urgency=medium
* New upstream version
* Force LC_ALL=C.UTF-8 encoding
=====================================
debian/watch
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1,10 +1,4 @@
version=4
-opts="uversionmangle=s/.*date=(\d{4})-(\d\d)-(\d\d)T.*/2.1.2+git$1$2$3/, \
- filenamemangle=s/.*date=(\d{4})-(\d\d)-(\d\d)T.*/2.1.2+git$1$2$3.tar.gz/, \
- repack,compression=xz" \
- https://qa.debian.org/cgi-bin/fakeupstream.cgi?upstream=github_commits_package_json/beagle-dev/beagle-lib \
- .*/archive/(.*\.tar\.gz?.*)
-
-# Issue asking for release tags:
-# https://github.com/beagle-dev/beagle-lib/issues/115
+opts="uversionmangle=s/_/./g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ https://github.com/beagle-dev/beagle-lib/releases .*/archive/v at ANY_VERSION@@ARCHIVE_EXT@
=====================================
examples/synthetictest/synthetictest.cpp
=====================================
--- a/examples/synthetictest/synthetictest.cpp
+++ b/examples/synthetictest/synthetictest.cpp
@@ -1247,26 +1247,6 @@ void runBeagle(int resource,
sumLogL += siteLogLs[i] * patternWeights[i];
}
fprintf(stdout, "\nsumLogL = %.5f\n", sumLogL);
- if (calcderivs) {
- double* siteSecondDerivs = (double*) malloc(sizeof(double) * nsites);
- beagleGetSiteDerivatives(instance, siteLogLs, siteSecondDerivs);
- sumLogL = 0.0;
- fprintf(stdout, "site first derivs = ");
- for (int i=0; i<nsites; i++) {
- fprintf(stdout, "%.5f \t", siteLogLs[i]);
- sumLogL += siteLogLs[i] * patternWeights[i];
- }
- fprintf(stdout, "\nsumFirstDerivs = %.5f\n", sumLogL);
-
- sumLogL = 0.0;
- fprintf(stdout, "site second derivs = ");
- for (int i=0; i<nsites; i++) {
- fprintf(stdout, "%.5f \t", siteSecondDerivs[i]);
- sumLogL += siteSecondDerivs[i] * patternWeights[i];
- }
- fprintf(stdout, "\nsumSecondDerivs = %.5f\n", sumLogL);
- free(siteSecondDerivs);
- }
free(siteLogLs);
}
=====================================
libhmsbeagle/CPU/BeagleCPUImpl.hpp
=====================================
--- a/libhmsbeagle/CPU/BeagleCPUImpl.hpp
+++ b/libhmsbeagle/CPU/BeagleCPUImpl.hpp
@@ -2551,9 +2551,8 @@ void BeagleCPUImpl<BEAGLE_CPU_GENERIC>::calcEdgeLogLikelihoodsSecondDerivByParti
w += kTransPaddedStateCount;
}
- v += kPartialsPaddedStateCount;
+ v += ((kPatternCount - endPattern) + startPattern) * kPartialsPaddedStateCount;
}
- v += ((kPatternCount - endPattern) + startPattern) * kPartialsPaddedStateCount;
}
} else { // Integrate against a partial at the child
=====================================
libhmsbeagle/GPU/GPUInterfaceCUDA.cpp
=====================================
--- a/libhmsbeagle/GPU/GPUInterfaceCUDA.cpp
+++ b/libhmsbeagle/GPU/GPUInterfaceCUDA.cpp
@@ -203,7 +203,7 @@ int GPUInterface::Initialize() {
SAFE_CUDA(cuDeviceGet(&tmpCudaDevice, i));
SAFE_CUDA(cuDeviceGetAttribute(&capabilityMajor, CU_DEVICE_ATTRIBUTE_COMPUTE_CAPABILITY_MAJOR, tmpCudaDevice));
SAFE_CUDA(cuDeviceGetAttribute(&capabilityMinor, CU_DEVICE_ATTRIBUTE_COMPUTE_CAPABILITY_MINOR, tmpCudaDevice));
- if (capabilityMajor >= 3 && capabilityMinor != 9999) {
+ if ((capabilityMajor > 1 && capabilityMinor != 9999) || (capabilityMajor == 1 && capabilityMinor > 0)) {
resourceMap->insert(std::make_pair(currentDevice++, i));
}
}
=====================================
libhmsbeagle/GPU/kernels/Makefile.am
=====================================
--- a/libhmsbeagle/GPU/kernels/Makefile.am
+++ b/libhmsbeagle/GPU/kernels/Makefile.am
@@ -19,17 +19,17 @@ BeagleCUDA_kernels.h: Makefile kernels4.cu kernelsX.cu kernelsAll.cu ../GPUImplD
#
# Compile 4-state model
$(NVCC) -o BeagleCUDA_kernels.ptx --default-stream per-thread -ptx -DCUDA -DSTATE_COUNT=4 \
- $(srcdir)/kernels4.cu $(NVCCFLAGS) -DHAVE_CONFIG_H $(INCLUDE_DIRS) || { \rm BeagleCUDA_kernels.h; exit; }; \
- echo "#define KERNELS_STRING_SP_4 \"" | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h; \
- cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h; \
+ $(srcdir)/kernels4.cu $(NVCCFLAGS) -DHAVE_CONFIG_H $(INCLUDE_DIRS)
+ echo "#define KERNELS_STRING_SP_4 \"" | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h
+ cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h
echo "\"" >> BeagleCUDA_kernels.h
#
# HERE IS THE LOOP FOR GENERIC KERNELS
#
for s in $(STATE_COUNT_LIST); do \
echo "Making state count = $$s" ; \
- $(NVCC) -o BeagleCUDA_kernels.ptx --default-stream per-thread -ptx -DCUDA -DSTATE_COUNT=$$s \
- $(srcdir)/kernelsX.cu $(NVCCFLAGS) -DHAVE_CONFIG_H $(INCLUDE_DIRS) || { \rm BeagleCUDA_kernels.h; exit; }; \
+ ($(NVCC) -o BeagleCUDA_kernels.ptx --default-stream per-thread -ptx -DCUDA -DSTATE_COUNT=$$s \
+ $(srcdir)/kernelsX.cu $(NVCCFLAGS) -DHAVE_CONFIG_H $(INCLUDE_DIRS)) || exit; \
echo "#define KERNELS_STRING_SP_$$s \"" | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h; \
cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h; \
echo "\"" >> BeagleCUDA_kernels.h; \
@@ -40,17 +40,17 @@ BeagleCUDA_kernels.h: Makefile kernels4.cu kernelsX.cu kernelsAll.cu ../GPUImplD
#
# Compile 4-state model
$(NVCC) -o BeagleCUDA_kernels.ptx --default-stream per-thread -ptx -DCUDA -DSTATE_COUNT=4 -DDOUBLE_PRECISION \
- $(srcdir)/kernels4.cu $(NVCCFLAGS) -DHAVE_CONFIG_H $(INCLUDE_DIRS) || { \rm BeagleCUDA_kernels.h; exit; }; \
- echo "#define KERNELS_STRING_DP_4 \"" | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h; \
- cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h; \
+ $(srcdir)/kernels4.cu $(NVCCFLAGS) -DHAVE_CONFIG_H $(INCLUDE_DIRS)
+ echo "#define KERNELS_STRING_DP_4 \"" | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h
+ cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h
echo "\"" >> BeagleCUDA_kernels.h
#
# HERE IS THE LOOP FOR GENERIC KERNELS
#
for s in $(STATE_COUNT_LIST); do \
echo "Making state count = $$s" ; \
- $(NVCC) -o BeagleCUDA_kernels.ptx --default-stream per-thread -ptx -DCUDA -DSTATE_COUNT=$$s -DDOUBLE_PRECISION \
- $(srcdir)/kernelsX.cu $(NVCCFLAGS) -DHAVE_CONFIG_H $(INCLUDE_DIRS) || { \rm BeagleCUDA_kernels.h; exit; }; \
+ ($(NVCC) -o BeagleCUDA_kernels.ptx --default-stream per-thread -ptx -DCUDA -DSTATE_COUNT=$$s -DDOUBLE_PRECISION \
+ $(srcdir)/kernelsX.cu $(NVCCFLAGS) -DHAVE_CONFIG_H $(INCLUDE_DIRS)) || exit; \
echo "#define KERNELS_STRING_DP_$$s \"" | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h; \
cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$$/\\n\\/' >> BeagleCUDA_kernels.h; \
echo "\"" >> BeagleCUDA_kernels.h; \
View it on GitLab: https://salsa.debian.org/med-team/libhmsbeagle/compare/55d219dafcbbfeccde3af7f7f0a4f9803204a7e9...d5eba9679f4ce62c08cd95b31f899f46926baa93
--
View it on GitLab: https://salsa.debian.org/med-team/libhmsbeagle/compare/55d219dafcbbfeccde3af7f7f0a4f9803204a7e9...d5eba9679f4ce62c08cd95b31f899f46926baa93
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