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..0363a04a1736145b0c2f28fbb524499fca8683c1 --- /dev/null +++ b/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config @@ -0,0 +1,69 @@ +[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] +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 +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