Commit 16f18654 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 3.0.2+dfsg

parent a64c706d

configure.ac

+1 −26
Original line number Diff line number Diff line
@@ -263,31 +263,6 @@ fi 
# do not warn about deprecated GPU architectures

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

examples/synthetictest/synthetictest.cpp

+0 −20
Original line number Diff line number Diff line
@@ -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

+1 −2
Original line number Diff line number Diff line
@@ -2551,10 +2551,9 @@ void BeagleCPUImpl<BEAGLE_CPU_GENERIC>::calcEdgeLogLikelihoodsSecondDerivByParti 


                        w += kTransPaddedStateCount;

                    }

                    v += kPartialsPaddedStateCount;

                }

                    v += ((kPatternCount - endPattern) + startPattern) * kPartialsPaddedStateCount;

                }

            }



        } else { // Integrate against a partial at the child

libhmsbeagle/GPU/GPUInterfaceCUDA.cpp

+1 −1
Original line number Diff line number Diff line
@@ -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

+10 −10
Original line number Diff line number Diff line
@@ -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; \