From ee9260a1555f72d7470bb2169d05b9fa97c6ab91 Mon Sep 17 00:00:00 2001 From: limingyang Date: Wed, 24 Sep 2025 10:23:08 +0800 Subject: [PATCH] Update chaste/2019.1. --- package/amara/1.2.0.2/install.sh | 12 ++++- package/vtk/6.2.0/install.sh | 2 +- .../chaste/2019.1/data.chaste.arm.cpu.config | 45 +++++++++---------- 3 files changed, 32 insertions(+), 27 deletions(-) diff --git a/package/amara/1.2.0.2/install.sh b/package/amara/1.2.0.2/install.sh index 4a67c8ae..9af672cd 100755 --- a/package/amara/1.2.0.2/install.sh +++ b/package/amara/1.2.0.2/install.sh @@ -2,9 +2,17 @@ set -x set -e . ${DOWNLOAD_TOOL} -u https://repo.huaweicloud.com/repository/pypi/packages/af/0e/e81dfe4b4fb24023207d86e4d4ff418b0e83927f2155ed3552b0e3196846/Amara-1.2.0.2.tar.gz#sha256=0814dae65bfeb3b309d65d7efb01e2e7a8c30611e7232f839c390816edac27cb -f Amara-1.2.0.2.tar.gz +. ${DOWNLOAD_TOOL} -u https://mirrors.aliyun.com/pypi/packages/9a/5c/4ad2ee5f12028e0b40f3f6487cbdfe977ca8c112ecd88c175bc20de189fd/4Suite-XML-1.0.2.tar.bz2 + +cd ${JARVIS_TMP} +rm -rf 4Suite-XML-1.0.2 +tar -xvf ${JARVIS_DOWNLOAD}/4Suite-XML-1.0.2.tar.bz2 +cd 4Suite-XML-1.0.2 +sed -i "653,656 s/^/#/" ./Ft/Lib/DistExt/Dist.py +python setup.py install + cd ${JARVIS_TMP} rm -rf Amara-1.2.0.2 tar -xvzf ${JARVIS_DOWNLOAD}/Amara-1.2.0.2.tar.gz - cd Amara-1.2.0.2 -python setup.py install +pip install . -i https://mirrors.aliyun.com/pypi/simple --timeout=3600 diff --git a/package/vtk/6.2.0/install.sh b/package/vtk/6.2.0/install.sh index d61267c5..30661ab0 100755 --- a/package/vtk/6.2.0/install.sh +++ b/package/vtk/6.2.0/install.sh @@ -4,7 +4,7 @@ set -e . ${DOWNLOAD_TOOL} -u https://vtk.org/files/release/6.2/VTK-6.2.0.tar.gz cd ${JARVIS_TMP} rm -rf VTK-6.2.0 -tar -xvf ${JARVIS_DOWNLOAD}/VTK-6.2.0.tar.gz +tar -xvzf ${JARVIS_DOWNLOAD}/VTK-6.2.0.tar.gz cd VTK-6.2.0 mkdir build && cd build cmake -DCMAKE_INSTALL_PREFIX=$1 .. \ diff --git a/templates/chaste/2019.1/data.chaste.arm.cpu.config b/templates/chaste/2019.1/data.chaste.arm.cpu.config index 1ab014b7..4aa74d5a 100644 --- a/templates/chaste/2019.1/data.chaste.arm.cpu.config +++ b/templates/chaste/2019.1/data.chaste.arm.cpu.config @@ -6,32 +6,29 @@ chaste/2019.1 $JARVIS_PROXY/Chaste/Chaste/archive/refs/tags/release_2019.1.tar.g [DEPENDENCY] . ${DOWNLOAD_TOOL} -u https://chaste.github.io/old_releases/release_3.3/UserTutorials/CardiacExecutable/Propagation3d/Propagation3d.tgz -yum install libxml2-devel libxslt-devel libXt-devel libX11-devel libXext-devel -y +yum install libxml2-devel libxslt-devel libXt-devel libX11-devel libXext-devel openblas-devel -y set -x set -e module purge +./jarvis -install hpckit/25.1.0 any module use ./software/modulefiles -./jarvis -install bisheng/4.1.0 com -./jarvis -install python2/2.7.16 com - -module load bisheng/4.1.0 -export CC=clang CXX=clang++ FC=flang +module use ./software/modulefiles/hpckit25.1.0 +module use ./software/moduledeps/bisheng4.2.0.2 +module load bisheng/compiler4.2.0.2/bishengmodule +module load bisheng/hmpi25.1.0/release -./jarvis -install kml/2.4.0/bisheng clang -./jarvis -install hmpi/2.4.2 clang +./jarvis -install python2/2.7.16 com ./jarvis -install boost/1.70.0/clang clang ./jarvis -install sundials/5.8.0 clang ./jarvis -install xerces/3.3.0 clang ./jarvis -install vtk/6.2.0 clang - module load xerces/3.3.0 ./jarvis -install xsd/4.0.0 clang - -module load hmpi/2.4.2 module load python2/2.7.16 -./jarvis -install amara/1.2.0.2/ clang -pip install rdflib lxml +pip install --upgrade pip -i https://mirrors.aliyun.com/pypi/simple +./jarvis -install amara/1.2.0.2 clang +pip install rdflib lxml -i https://mirrors.aliyun.com/pypi/simple export CC=mpicc CXX=mpicxx FC=mpifort ./jarvis -install petsc/3.6.2 clang+mpi @@ -39,16 +36,18 @@ export CC=mpicc CXX=mpicxx FC=mpifort [ENV] module purge module use ./software/modulefiles -module load bisheng/4.1.0 -module load kml-bisheng/2.4.0 -module load hmpi/2.4.2 +module use ./software/modulefiles/hpckit25.1.0 +module use ./software/moduledeps/bisheng4.2.0.2 +module load bisheng/compiler4.2.0.2/bishengmodule +module load bisheng/hmpi25.1.0/release +module load python2/2.7.16 module load boost-clang/1.70.0 -module load petsc/3.6.2 module load sundials/5.8.0 module load xerces/3.3.0 -module load xsd/4.0.0 module load vtk/6.2.0 -module load python2/2.7.16 +module load xsd/4.0.0 +module use ./software/moduledeps/bisheng4.2.0.2-hmpi25.1.0 +module load petsc/3.6.2 [APP] app_name = chaste @@ -57,12 +56,10 @@ binary_dir = ${JARVIS_ROOT}/Chaste-release_2019.1/chaste_build/apps case_dir = ${JARVIS_ROOT}/Chaste-release_2019.1/examples/Propagation3d [BUILD] -cd /pacific_ext/l00855193/work/chaste rm -rf Chaste-release_2019.1 tar -zxvf $JARVIS_DOWNLOAD/Chaste-release_2019.1.tar.gz cd Chaste-release_2019.1 sed -i '452s|^|#|' CMakeLists.txt - sed -i '6s|\-Werror||g' ./cmake/Modules/ChasteCompilerFlags.cmake sed -i '1830s|#||1' python/pycml/translators.py sed -i '1831s|^\([[:space:]]*\)\([a-zA-Z]\)|\1#\2|' python/pycml/translators.py @@ -86,8 +83,8 @@ cmake .. -DCMAKE_INSTALL_PREFIX=$(realpath ../chaste_install) \ -DSUNDIALS_sundials_nvecserial_LIBRARY=${SUNDIALS_PATH}/lib64/libsundials_nvecserial.so \ -DChaste_SUNDIALS_VERSION=50800 -DSUNDIALS_VERSION_MAJOR=5 -DSUNDIALS_VERSION_MINOR=8 \ -DXERCESC_LIBRARY=${XERCES_PATH}/lib/libxerces-c.so \ - -DCMAKE_C_FLAGS="-O3 -Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${VTK_PATH}/include/vtk-6.2 -L${BOOST_CLANG_PATH}/lib -lboost_serialization -lboost_system -lboost_filesystem" \ - -DCMAKE_CXX_FLAGS="-O3 -std=c++14 -stdlib=libc++ -Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${VTK_PATH}/include/vtk-6.2 -L${BOOST_CLANG_PATH}/lib -lboost_serialization -lboost_system -lboost_filesystem" \ + -DCMAKE_C_FLAGS="-Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${VTK_PATH}/include/vtk-6.2 -L${BOOST_CLANG_PATH}/lib -lboost_serialization -lboost_system -lboost_filesystem" \ + -DCMAKE_CXX_FLAGS="-std=c++14 -stdlib=libc++ -Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-command-line-argument -lopenblas -I${VTK_PATH}/include/vtk-6.2 -L${BOOST_CLANG_PATH}/lib -lboost_serialization -lboost_system -lboost_filesystem" \ -DX11_X11_INCLUDE_PATH=/usr/include/X11/ -DX11_X11_LIB=/usr/lib64 make VERBOSE=1 -j Continuous @@ -100,6 +97,6 @@ tar -xvzf ${JARVIS_DOWNLOAD}/Propagation3d.tgz make clean [RUN] -run = time -p mpirun -np 32 --allow-run-as-root --map-by ppr:8:numa:pe=1 -x UCX_TLS=self,sm -mca pml ucx -mca btl ^vader,tcp,openib,uct -x OMP_NUM_THREADS=1 +run = time -p mpirun -np 32 --allow-run-as-root -x OMP_NUM_THREADS=1 binary = Chaste ChasteParameters.xml nodes = 1 -- Gitee