From 44b28da3bc741cc29c8fd891f8b1930271be7489 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Wed, 30 Apr 2025 09:42:27 +0800
Subject: [PATCH 1/2] abyss

---
 .../data.abyss.arm.cpu.bisheng.hmpi.config    | 71 +++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config

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 0000000..52d94b9
--- /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
-- 
Gitee


From 96f25294da8080a3914c5e1ea2d950a38cafd09c Mon Sep 17 00:00:00 2001
From: root <root@localhost.localdomain>
Date: Wed, 30 Apr 2025 15:00:13 +0800
Subject: [PATCH 2/2] code_aster

---
 .../code_aster.arm.cpu.kgcc.hmpi.config       | 87 +++++++++++++++++++
 1 file changed, 87 insertions(+)
 create mode 100644 templates/code_aster/14.6.0/code_aster.arm.cpu.kgcc.hmpi.config

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 0000000..059e320
--- /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 <ostream>' tfel-3.2.1/mfront/src/NewtonRaphsonSolvers.cxx
+sed -i '19i #include <ostream>' tfel-3.2.1/mfront/src/NewtonRaphsonSolvers.cxx
+sed -i '18i #include <ostream>' tfel-3.2.1/mfront/src/BroydenSolvers.cxx
+sed -i '18i #include <ostream>' tfel-3.2.1/mfront/src/SecondBroydenSolver.cxx
+sed -i '18i #include <ostream>' tfel-3.2.1/mfront/src/LevenbergMarquardtSolvers.cxx
+sed -i '21i #include <ostream>' 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
-- 
Gitee