From 83fc2aaa23ee7aeca144405eb511ac3f99de6d6e Mon Sep 17 00:00:00 2001 From: wanghanwen <1564586847@qq.com> Date: Mon, 11 Apr 2022 17:49:05 +0800 Subject: [PATCH] =?UTF-8?q?=E6=96=B0=E5=A2=9Ebwa=E3=80=81grads=E3=80=81hdf?= =?UTF-8?q?5=E3=80=81jasper=E8=84=9A=E6=9C=AC?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- package/bwa/0.7.17/install.sh | 21 ++++++++++ package/grads/2.0.a4/install.sh | 13 +++++++ package/hdf5/1.10.1/install.sh | 13 +++++++ package/jasper/1.900.2/install.sh | 13 +++++++ templates/bwa/0.7.17/data.bwa.arm.cpu.config | 33 ++++++++++++++++ .../grads/2.0.a4/data.grads.arm.cpu.config | 32 ++++++++++++++++ .../hdf5/1.10.1/data.hdf5.arm.cpu.config | 38 +++++++++++++++++++ .../jasper/1.900.2/data.jasper.arm.cpu.config | 31 +++++++++++++++ 8 files changed, 194 insertions(+) create mode 100644 package/bwa/0.7.17/install.sh create mode 100644 package/grads/2.0.a4/install.sh create mode 100644 package/hdf5/1.10.1/install.sh create mode 100644 package/jasper/1.900.2/install.sh create mode 100644 templates/bwa/0.7.17/data.bwa.arm.cpu.config create mode 100644 templates/grads/2.0.a4/data.grads.arm.cpu.config create mode 100644 templates/hdf5/1.10.1/data.hdf5.arm.cpu.config create mode 100644 templates/jasper/1.900.2/data.jasper.arm.cpu.config diff --git a/package/bwa/0.7.17/install.sh b/package/bwa/0.7.17/install.sh new file mode 100644 index 0000000..f71c6a0 --- /dev/null +++ b/package/bwa/0.7.17/install.sh @@ -0,0 +1,21 @@ +#download from https://github.com/jratcliff63367/sse2neon https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 +#module load bisheng2/2.1.0 +#!/bin/bash +set -x +set -e +cd ${JARVIS_TMP} +rm -rf bwa-0.7.17 sse2neon-master +tar -xvf ${JARVIS_DOWNLOAD}/bwa-0.7.17.tar.bz2 +unzip ${JARVIS_DOWNLOAD}/sse2neon.zip +cd bwa-0.7.17 +bisheng_includedir=`which clang` +bisheng_includedir=${bisheng_includedir%/*/*}/include +cp ${JARVIS_TMP}/sse2neon-master/SSE2NEON.h ${bisheng_includedir} +sed -i "1s/gcc/clang/g" Makefile +sed -i "14s%$%-I${bisheng_includedir}%g" Makefile +sed -i "29s///g" ksw.c +sed -i "33s%^%//%g" rle.h +make +mkdir -p $1/bin +cp -r ../bwa-0.7.17/* $1/bin +rm -rf ${bisheng_includedir}/SSE2NEON.h diff --git a/package/grads/2.0.a4/install.sh b/package/grads/2.0.a4/install.sh new file mode 100644 index 0000000..5d01ebf --- /dev/null +++ b/package/grads/2.0.a4/install.sh @@ -0,0 +1,13 @@ +#download from https://sourceforge.net/projects/opengrads/files/grads2/2.0.a4-1/grads-2.0.a4.oga.1-src.tar.gz +#!/bin/bash +set -x +set -e + +cd ${JARVIS_TMP} +rm -rf grads-2.0.a4.oga.1-src.tar.gz +tar -xvf ${JARVIS_DOWNLOAD}/grads-2.0.a4.oga.1-src.tar.gz +cd grads-2.0.a4.oga.1 +#CC=clang CXX=clang++ +./configure --prefix=$1 --build=aarch64-unknown-linux-gnu +make -j +make install diff --git a/package/hdf5/1.10.1/install.sh b/package/hdf5/1.10.1/install.sh new file mode 100644 index 0000000..7387371 --- /dev/null +++ b/package/hdf5/1.10.1/install.sh @@ -0,0 +1,13 @@ +#download from https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz +#!/bin/bash +set -x +set -e + +cd ${JARVIS_TMP} +tar -xvf ${JARVIS_DOWNLOAD}/hdf5-1.10.1.tar.gz +cd hdf5-1.10.1 +#CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort -Wno-incompatible-pointer-types-discards-qualifiers +./configure --prefix=$1 --build=aarch64-unknown-linux-gnu --build=aarch64-unknown-linux-gnu --enable-fortran --enable-static=yes --enable-parallel --enable-shared CFLAGS="-O3 -fPIC -Wno-incompatible-pointer-types-discards-qualifiers -Wno-non-literal-null-conversion" FCFLAGS="-O3 -fPIC" LDFLAGS="-Wl,--build-id" +sed -i '11835c wl="-Wl,"' libtool +make -j +make install diff --git a/package/jasper/1.900.2/install.sh b/package/jasper/1.900.2/install.sh new file mode 100644 index 0000000..b61c9f4 --- /dev/null +++ b/package/jasper/1.900.2/install.sh @@ -0,0 +1,13 @@ +#download from https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.2.tar.gz +#!/bin/bash +set -x +set -e + +cd ${JARVIS_TMP} +rm -rf jasper-1.900.2 +tar -xvf ${JARVIS_DOWNLOAD}/jasper-1.900.2.tar.gz +cd jasper-1.900.2 +#CC=clang CXX=clang++ +./configure --prefix=$1 +make -j +make install diff --git a/templates/bwa/0.7.17/data.bwa.arm.cpu.config b/templates/bwa/0.7.17/data.bwa.arm.cpu.config new file mode 100644 index 0000000..c667b95 --- /dev/null +++ b/templates/bwa/0.7.17/data.bwa.arm.cpu.config @@ -0,0 +1,33 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +bwa/0.7.17 https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 +sse2neon/master https://github.com/jratcliff63367/sse2neon/archive/refs/heads/master.zip sse2neon.zip +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com + + +[ENV] +module purge +module use ${JARVIS_ROOT}/software/modulefiles +module add bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[APP] +app_name = bwa +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = + +[BUILD] +./jarvis -install bwa/0.7.17 clang + +[RUN] +run = +binary = +node = 1 diff --git a/templates/grads/2.0.a4/data.grads.arm.cpu.config b/templates/grads/2.0.a4/data.grads.arm.cpu.config new file mode 100644 index 0000000..d0db6b6 --- /dev/null +++ b/templates/grads/2.0.a4/data.grads.arm.cpu.config @@ -0,0 +1,32 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +grads/2.0.a4 https://sourceforge.net/projects/opengrads/files/grads2/2.0.a4-1/grads-2.0.a4.oga.1-src.tar.gz +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com +module load bisheng2/2.1.0 + +[ENV] +module purge +module use ${JARVIS_ROOT}/software/modulefiles +module add bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[APP] +app_name = grads +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = + +[BUILD] +./jarvis -install grads/2.0.a4 clang + +[RUN] +run = +binary = +node = 1 diff --git a/templates/hdf5/1.10.1/data.hdf5.arm.cpu.config b/templates/hdf5/1.10.1/data.hdf5.arm.cpu.config new file mode 100644 index 0000000..b519741 --- /dev/null +++ b/templates/hdf5/1.10.1/data.hdf5.arm.cpu.config @@ -0,0 +1,38 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +zlib/1.2.11 https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +hucx/1.1.1 https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip hucx-1.1.1-huawei.zip +xucg/1.1.1 https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip xucg-1.1.1-huawei.zip +hmpi/1.1.1 https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip hmpi-1.1.1-huawei.zip + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com +module load bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang +./jarvis -install hmpi/1.1.1 clang +module load hmpi1/1.1.1 + +[ENV] +module purge +module use ${JARVIS_ROOT}/software/modulefiles +module add bisheng2/2.1.0 +export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort + +[APP] +app_name = hdf5 +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = + +[BUILD] +./jarvis -install hdf5/1.10.1 clang + +[RUN] +run = +binary = +node = 1 diff --git a/templates/jasper/1.900.2/data.jasper.arm.cpu.config b/templates/jasper/1.900.2/data.jasper.arm.cpu.config new file mode 100644 index 0000000..a1d15ae --- /dev/null +++ b/templates/jasper/1.900.2/data.jasper.arm.cpu.config @@ -0,0 +1,31 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +jasper/1.900.2 https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.2.tar.gz +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com + +[ENV] +module purge +module use ${JARVIS_ROOT}/software/modulefiles +module add bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[APP] +app_name = jasper +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = + +[BUILD] +./jarvis -install jasper/1.900.2 clang + +[RUN] +run = +binary = +node = 1 -- Gitee