Commit e4b0fabf authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.1.2+git20180307

parent eb955c6a

.gitignore

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# /

/beagle-lib-1.0.pc

/configure

/Makefile.in

/config.log

/INSTALL

/COPYING

/Makefile

/.config

/config.status

/libtool

/autom4te.cache

/aclocal.m4

/hmsbeagle-1.0.pc

/doc

/.idea

/Beagle-lib.iml

/hmsbeagle-1.pc



# /examples/

/examples/Makefile.in

/examples/Makefile

/examples/extensivetest



# /examples/complextest/

/examples/complextest/Makefile.in

/examples/complextest/Makefile

/examples/complextest/complextest

/examples/complextest/.deps



# /examples/fourtaxon/

/examples/fourtaxon/check_lnL_using_paup.nex

/examples/fourtaxon/fourtaxon.o

/examples/fourtaxon/fourtaxon

/examples/fourtaxon/Makefile.in

/examples/fourtaxon/.deps

/examples/fourtaxon/Makefile

/examples/fourtaxon/fourtaxonrun.sh



# /examples/genomictest/

/examples/genomictest/Makefile.in

/examples/genomictest/.deps

/examples/genomictest/Makefile

/examples/genomictest/genomictest

/examples/genomictest/genomictest.sh



# /examples/matrixtest/

/examples/matrixtest/Makefile.in

/examples/matrixtest/matrixtest

/examples/matrixtest/.deps

/examples/matrixtest/Makefile



# /examples/oddstatetest/

/examples/oddstatetest/Makefile.in

/examples/oddstatetest/.deps

/examples/oddstatetest/Makefile

/examples/oddstatetest/oddstatetest



# /examples/tinytest/

/examples/tinytest/Makefile.in

/examples/tinytest/.deps

/examples/tinytest/Makefile

/examples/tinytest/tinytest



# /libhmsbeagle/

/libhmsbeagle/config.h.in

/libhmsbeagle/Makefile.in

/libhmsbeagle/.deps

/libhmsbeagle/stamp-h1

/libhmsbeagle/config.h

/libhmsbeagle/Makefile



# /libhmsbeagle/CPU/

/libhmsbeagle/CPU/Makefile.in

/libhmsbeagle/CPU/.deps

/libhmsbeagle/CPU/Makefile



# /libhmsbeagle/GPU/

/libhmsbeagle/GPU/Makefile.in

/libhmsbeagle/GPU/PeelingFunctions.linkinfo

/libhmsbeagle/GPU/.deps

/libhmsbeagle/GPU/TransitionFunctions.linkinfo

/libhmsbeagle/GPU/Makefile

/libhmsbeagle/GPU/BeagleCUDA_kernels.h

/libhmsbeagle/GPU/BeagleCUDA_kernels.ptx



# /libhmsbeagle/GPU/kernels/

/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_64.ptx

/libhmsbeagle/GPU/kernels/Makefile.in

/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_48.ptx

/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels.h

/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels.ptx

/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_4.ptx

/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_32.ptx

/libhmsbeagle/GPU/kernels/Makefile

/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_xcode.h

/libhmsbeagle/GPU/kernels/BeagleCUDA_kernels_xcode.ptx



# /libhmsbeagle/JNI/

/libhmsbeagle/JNI/Makefile.in

/libhmsbeagle/JNI/.deps

/libhmsbeagle/JNI/Makefile



# /libhmsbeagle/plugin/

/libhmsbeagle/plugin/Makefile.in

/libhmsbeagle/plugin/.deps

/libhmsbeagle/plugin/Makefile



# /m4/

/m4/libtool.m4

/m4/lt~obsolete.m4

/m4/ltsugar.m4

/m4/ltversion.m4

/m4/ltoptions.m4



# /project/beagle-xcode/

/project/beagle-xcode/build



# /project/beagle-xcode/beagle-xcode.xcodeproj/

/project/beagle-xcode/beagle-xcode.xcodeproj/*.pbxuser

/project/beagle-xcode/beagle-xcode.xcodeproj/*.perspectivev3

/project/beagle-xcode/beagle-xcode.xcodeproj/xcuserdata

/project/beagle-xcode/beagle-xcode.xcodeproj/project.xcworkspace



# other

.DS_Store

installed/

libhmsbeagle/.libs/

libhmsbeagle/CPU/.libs/

libhmsbeagle/CPU/libhmsbeagle-cpu-sse.la

libhmsbeagle/CPU/libhmsbeagle-cpu.la

libhmsbeagle/CPU/libhmsbeagle_cpu_la-BeagleCPUPlugin.lo

libhmsbeagle/CPU/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo

libhmsbeagle/GPU/.libs/

libhmsbeagle/GPU/libhmsbeagle-cuda.la

libhmsbeagle/GPU/libhmsbeagle_cuda_la-CUDAPlugin.lo

libhmsbeagle/GPU/libhmsbeagle_cuda_la-GPUImplHelper.lo

libhmsbeagle/GPU/libhmsbeagle_cuda_la-GPUInterfaceCUDA.lo

libhmsbeagle/GPU/libhmsbeagle_cuda_la-KernelLauncher.lo

libhmsbeagle/GPU/libhmsbeagle_cuda_la-KernelResource.lo

libhmsbeagle/libhmsbeagle-jni.la

libhmsbeagle/libhmsbeagle.la

libhmsbeagle/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo

libhmsbeagle/libhmsbeagle_la-beagle.lo

libhmsbeagle/plugin/.libs/

libhmsbeagle/plugin/libplugin.la

libhmsbeagle/plugin/libplugin_la-Plugin.lo

libhmsbeagle/plugin/libplugin_la-UnixSharedLibrary.lo

project/.DS_Store

project/beagle-xcode/.DS_Store

project/beagle-xcode/BEAGLEv1.0.pkg

examples/complextest/.libs/

examples/complextest/complextest.o

examples/fourtaxon/.libs/

examples/genomictest/.libs/

examples/genomictest/genomictest.o

examples/genomictest/linalg.o

examples/matrixtest/.libs/

examples/matrixtest/matrixtest.o

examples/oddstatetest/.libs/

examples/oddstatetest/oddstatetest.o

examples/tinytest/.libs/

examples/tinytest/tinytest.o

libhmsbeagle/GPU/kernels/BeagleOpenCL_kernels.h

libhmsbeagle/GPU/kernels/BeagleOpenCL_kernels_xcode.h

libhmsbeagle/GPU/libhmsbeagle-opencl.la

libhmsbeagle/GPU/libhmsbeagle_opencl_la-GPUImplHelper.lo

libhmsbeagle/GPU/libhmsbeagle_opencl_la-GPUInterfaceOpenCL.lo

libhmsbeagle/GPU/libhmsbeagle_opencl_la-KernelLauncher.lo

libhmsbeagle/GPU/libhmsbeagle_opencl_la-KernelResource.lo

libhmsbeagle/GPU/libhmsbeagle_opencl_la-OpenCLPlugin.lo

libhmsbeagle/config.h.in~

project/beagle-xcode/BEAGLE-1.0.pkg

.travis.yml

+18 −17
Original line number Diff line number Diff line
@@ -12,6 +12,7 @@ matrix: 
          packages:

            - gdb

            - apport

            - nvidia-opencl-dev



#cache:

#  directories:

.travis/amd_sdk.sh

+48 −39
Original line number Diff line number Diff line
@@ -2,8 +2,13 @@ 


# Original script from https://github.com/gregvw/amd_sdk/



export OPENCL_VENDOR_PATH=${AMDAPPSDKROOT}/etc/OpenCL/vendors

export LD_LIBRARY_PATH=${AMDAPPSDKROOT}/lib/x86_64:${LD_LIBRARY_PATH}

export CMAKE_LIBRARY_PATH=${AMDAPPSDKROOT}/lib/x86_64



if [ ! -e ${AMDAPPSDKROOT}/bin/x86_64/clinfo ]; then

    # Location from which get nonce and file name from

URL="http://developer.amd.com/tools-and-sdks/opencl-zone/opencl-tools-sdks/amd-accelerated-parallel-processing-app-sdk/"

    URL="http://developer.amd.com/amd-accelerated-parallel-processing-app-sdk/"

    URLDOWN="http://developer.amd.com/amd-license-agreement-appsdk/"



    NONCE1_STRING='name="amd_developer_central_downloads_page_nonce"'
@@ -11,15 +16,9 @@ FILE_STRING='name="f"' 
    POSTID_STRING='name="post_id"'

    NONCE2_STRING='name="amd_developer_central_nonce"'



#AMD APP SDK v3.0:

if [[ $1 == "300" ]]; then

  echo "AMD APP SDK v3.0"

  FORM=`wget -qO - $URL | sed -n '/download-2/,/64-bit/p'`

else

#AMD APP SDK v2.9.1:

  echo "AMD APP SDK v2.9.1"

    # This gets the second latest (2.9.1 ATM, latest is 3.0)

    # For newest: FORM=`wget -qO - $URL | sed -n '/download-2/,/64-bit/p'`

    FORM=`wget -qO - $URL | sed -n '/download-5/,/64-bit/p'`

fi



    # Get nonce from form

    NONCE1=`echo $FORM | awk -F ${NONCE1_STRING} '{print $2}'`
@@ -43,3 +42,13 @@ NONCE2=`echo $NONCE2 | awk -F'"' '{print $2}'` 
    echo $NONCE2



    wget --content-disposition --trust-server-names $URLDOWN --post-data "amd_developer_central_nonce=${NONCE2}&f=${FILE}" -O AMD-SDK.tar.bz2;



    # Unpack and install

    tar -xjf AMD-SDK.tar.bz2;

    mkdir -p ${OPENCL_VENDOR_PATH};

    sh AMD-APP-SDK*.sh --tar -xf -C ${AMDAPPSDKROOT};

    echo libamdocl64.so > ${OPENCL_VENDOR_PATH}/amdocl64.icd;

    chmod +x ${AMDAPPSDKROOT}/bin/x86_64/clinfo;

fi



${AMDAPPSDKROOT}/bin/x86_64/clinfo

configure.ac

+20 −19
Original line number Diff line number Diff line
@@ -332,6 +332,7 @@ jnilibext=no 


if test "x$with_jdk" != "xno"

then

	JAVAC=javac

    AC_PROG_JAVAC

    if test "x$JAVAC" != "x"

    then

examples/standalone/epochtest/.config/depcomp

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