diff --git a/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config b/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config new file mode 100644 index 0000000000000000000000000000000000000000..52d94b96bbe4b442796d8a740445f8dd1d21d6d6 --- /dev/null +++ b/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config @@ -0,0 +1,71 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +abyss/2.2.4 https://github.com/bcgsc/abyss/archive/2.2.4.tar.gz abyss-2.2.4.tar.gz +test-data https://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz test-data.tar.gz + +[DEPENDENCY] +set -e +set -x +yum install -y vim tar git wget automake autoconf libtool make cmake +./jarvis -install bisheng/4.1.0 com +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` +./jarvis -install hmpi/2.4.2 clang +module use ./software/moduledeps/bisheng4.1.0 +module load hmpi/2.4.2 +./jarvis -install boost/1.72.0/clang bisheng +module load boost-clang/1.72.0 +yum install libomp -y +tar -vzxf ${JARVIS_DOWNLOAD}/abyss-2.2.4.tar.gz +mkdir -p ABYSS +tar xvf ${JARVIS_DOWNLOAD}/test-data.tar.gz + +[ENV] +yum install -y vim tar git wget automake autoconf libtool make cmake +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module use ./software/moduledeps/bisheng4.1.0 +module load hmpi/2.4.2 +yum install libomp -y +export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` +module use ./software/moduledeps/bisheng4.1.0 +module load boost-clang/1.72.0 + +[APP] +app_name = abyss +build_dir = ${JARVIS_ROOT}/abyss-2.2.4/ +binary_dir = ${JARVIS_ROOT}/ABYSS/bin +case_dir = ${JARVIS_ROOT}/test-data/ + +[BUILD] +./autogen.sh +export CURRENT_MPI_PATH=`which mpirun | sed 's/\/bin\/mpirun//g'` +./configure --prefix=${JARVIS_ROOT}/ABYSS --with-boost=${BOOST_PATH} --without-sparsehash --with-mpi=$CURRENT_MPI_PATH +make -j 32 AM_CXXFLAGS=-Wall +make install AM_CXXFLAGS=-Wall +sed -i '543s/\$(mpirun)/\$(mpirun) --allow-run-as-root -mca coll_hcoll_enable 0/' "${JARVIS_ROOT}/ABYSS/bin/abyss-pe" +sed -i '551s/\$(mpirun)/\$(mpirun) --allow-run-as-root -mca coll_hcoll_enable 0/' "${JARVIS_ROOT}/ABYSS/bin/abyss-pe" + + + +[CLEAN] +make clean + +[RUN] +run = +binary = abyss-pe k=25 name=test in="reads1.fastq reads2.fastq" +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all diff --git a/templates/code_aster/14.6.0/code_aster.arm.cpu.kgcc.hmpi.config b/templates/code_aster/14.6.0/code_aster.arm.cpu.kgcc.hmpi.config new file mode 100644 index 0000000000000000000000000000000000000000..059e320dd0d18ca5f77f020c06a6a8eab49d2067 --- /dev/null +++ b/templates/code_aster/14.6.0/code_aster.arm.cpu.kgcc.hmpi.config @@ -0,0 +1,87 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +code_aster/14.6.0 https://www.code-aster.org/FICHIERS/aster-full-src-14.6.0-1.noarch.tar.gz aster-full-src-14.6.0-1.noarch.tar.gz + +[DEPENDENCY] +set -e +set -x + +yum install -y vim tar git wget automake autoconf libtool make cmake +./jarvis -install hpckit/2024.12.30 any +source software/utils/hpckit/2024.12.30/HPCKit/latest/setvars.sh --use-bisheng --force +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` +yum -y install zlib* lapack* blas* python3.aarch64 python3-devel.aarch64 cmake3 boost-python* boost boost-devel numpy* python-numpy flex bison tcl tk +yum install -y lapack lapack-devel +yum install -y openblas openblas-devel +yum install -y glibc-devel +pip install -i https://pypi.tuna.tsinghua.edu.cn/simple numpy==1.24.4 +tar -xvf ${JARVIS_DOWNLOAD}/aster-full-src-14.6.0-1.noarch.tar.gz +mkdir -p CODE-ASTER + +[ENV] +yum install -y vim tar git wget automake autoconf libtool make cmake +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` +yum -y install zlib* lapack* blas* python3.aarch64 python3-devel.aarch64 cmake3 boost-python* boost boost-devel numpy* python-numpy flex bison tcl tk +yum install -y lapack lapack-devel +yum install -y openblas openblas-devel + +[APP] +app_name = code_aster +build_dir = ${JARVIS_ROOT}/aster-full-src-14.6.0/ +binary_dir = ${JARVIS_ROOT}/CODE-ASTER/bin/ +case_dir = ${JARVIS_ROOT}/CODE-ASTER/bin/ + +[BUILD] +sed -i "354s/'ppc64'/'ppc64', 'aarch64'/" setup.py +sed -i "518c\ if cc is None and ftools.check_compiler_name(cc, 'GCC'):" setup.py +sed -i '1538i\ '\''aarch64'\'': '\''shell|script|aarch64'\'',' as_setup.py +sed -i "94i CC='$CC'\nCXX='$CXX'\nF90='$FC'\nLD=F90\nCXXFLAGS=\"-std=c++11\"\nF90FLAGS='-fallow-argument-mismatch'\nLIBDIR=['$HOME/anaconda3/envs/aster/lib', ]" setup.cfg +sed -i '187s|^.*$| conf_cmd = ("export F77=$F90; "|' products.py +cd SRC +tar xvf aster-14.6.0.tgz +sed -i '103s|^.*$| if self.env.DEST_CPU == '\''x86_64'\'' or self.env.DEST_CPU == '\''aarch64'\'':|' aster-14.6.0/bibfor/wscript +sed -i '224c\ curr_idmess = idmess.split("\\0")\n x = curr_idmess.split("_")' aster-14.6.0/bibpyt/Utilitai/Utmess.py +tar cvzf aster-14.6.0.tgz aster-14.6.0 +rm -rf aster-14.6.0 +tar -xvf tfel-3.2.1-1.tar.gz +sed -i '19i #include ' tfel-3.2.1/mfront/src/NewtonRaphsonSolvers.cxx +sed -i '19i #include ' tfel-3.2.1/mfront/src/NewtonRaphsonSolvers.cxx +sed -i '18i #include ' tfel-3.2.1/mfront/src/BroydenSolvers.cxx +sed -i '18i #include ' tfel-3.2.1/mfront/src/SecondBroydenSolver.cxx +sed -i '18i #include ' tfel-3.2.1/mfront/src/LevenbergMarquardtSolvers.cxx +sed -i '21i #include ' tfel-3.2.1/mfront/include/MFront/MFrontLogStream.hxx +tar -czvf tfel-3.2.1.tar.gz tfel-3.2.1 +export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH +export LIBRARY_PATH=/usr/lib64:$LIBRARY_PATH +sudo ln -sf /usr/lib64/libutil.so.1 /usr/lib64/libutil.so +sudo ln -sf /usr/lib64/libutil.a /usr/lib64/libutil.a +sudo ln -sf /usr/lib64/libdl.so.2 /usr/lib64/libdl.so +sudo ldconfig # 更新动态库缓存:ml-citation{ref="6,7" data="citationList"} + +cd .. +echo y | python3 setup.py --prefix=${JARVIS_ROOT}/CODE-ASTER + +[CLEAN] +make clean + +[RUN] +run = +binary = as_run --version +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all diff --git a/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config b/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config new file mode 100644 index 0000000000000000000000000000000000000000..921f09ab5992e13aee3d95c69b9c7a9cdc4b3133 --- /dev/null +++ b/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config @@ -0,0 +1,83 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +tensorflow/2.4.1 https://github.com/tensorflow/tensorflow/archive/refs/tags/v2.4.1.tar.gz tensorflow-2.4.1.tar.gz + +[DEPENDENCY] +set -e +set -x + +yum install -y vim tar git wget +module purge +./jarvis -install package/anaconda3/2023.3 any +source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh +./jarvis -install kgcc/10.3.1 com +module use software/modulefiles +module load kgcc/10.3.1 +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` +sudo yum install -y glibc-devel +pip install cython +tar -xzvf ${JARVIS_DOWNLOAD}/tensorflow-2.4.1.tar.gz +mkdir -p tensorflow + +[ENV] +yum install -y vim tar git wget +module purge +source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh +module use software/modulefiles +module load kgcc/10.3.1 +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` +sudo yum install -y glibc-devel +pip install cython + +[APP] +app_name = tensorflow +build_dir = ${JARVIS_ROOT}/tensorflow-2.4.1/ +binary_dir = +case_dir = ${JARVIS_ROOT}/tensorflow-2.4.1/tensorflow/examples/speech_commands/ + + +[BUILD] +#conda env remove -n tensorflow-2.4.1 +conda create -n tensorflow-2.4.1 bazel=3.7 python=3.7.11 -y +conda activate tensorflow-2.4.1 +conda install -c conda-forge keras-preprocessing=1.1.2 numpy=1.18.5 -y + +yes '' | python configure.py +bazel build //tensorflow/tools/pip_package:build_pip_package +bazel-bin/tensorflow/tools/pip_package/build_pip_package ${JARVIS_ROOT}/tensorflow +cd ${JARVIS_ROOT}/tensorflow +pip install tensorflow-2.4.1-cp37-cp37m-linux_aarch64.whl --no-deps +conda install -c anaconda absl-py -y +pip install google-api-python-client +pip install protobuf==3.20.1 # 选择一个 3.20.x 的版本 +conda install -c conda-forge wrapt -y +conda install -c conda-forge typing_extensions -y +conda install -c conda-forge opt_einsum -y +pip install gast==0.4.0 +pip install astunparse==1.6.3 +pip install --force-reinstall termcolor +pip install flatbuffers==23.5.9 + + +[CLEAN] +make clean + +[RUN] +run = conda activate tensorflow-2.4.1 && time python train.py +binary = +nodes = 1 + +[JOB] +conda activate tensorflow-2.4.1 + +[PERF] +perf= +nsys= +ncu=--target-processes all +