From d5f6147cd43a2642e2fa04b89c795a34181b249e Mon Sep 17 00:00:00 2001 From: xiaolinjunhao <981755938@qq.com> Date: Fri, 4 Apr 2025 02:06:43 +0800 Subject: [PATCH 01/58] =?UTF-8?q?=E6=96=B0=E5=A2=9E=E5=BA=94=E7=94=A8krake?= =?UTF-8?q?n2=20v2.1.2?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../kraken2/2.1.2/data.kraken2.arm.cpu.config | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 templates/kraken2/2.1.2/data.kraken2.arm.cpu.config diff --git a/templates/kraken2/2.1.2/data.kraken2.arm.cpu.config b/templates/kraken2/2.1.2/data.kraken2.arm.cpu.config new file mode 100644 index 0000000..c0f6bc0 --- /dev/null +++ b/templates/kraken2/2.1.2/data.kraken2.arm.cpu.config @@ -0,0 +1,47 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +kraken2/2.1.2 https://github.com/DerrickWood/kraken2/archive/refs/tags/v2.1.2.tar.gz kraken2-2.1.2.tar.gz + +[DEPENDENCY] +set -e +set -x +./jarvis -install bisheng/4.1.0 com +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 + +rm -rf kraken2-2.1.2 +tar -xvf ${JARVIS_DOWNLOAD}/kraken2-2.1.2.tar.gz + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 + +[APP] +app_name = kraken2 +build_dir = ${JARVIS_ROOT}/kraken2-2.1.2 +binary_dir = ${JARVIS_ROOT}/kraken2-2.1.2/bin/ +case_dir = ${JARVIS_ROOT}/kraken2-2.1.2 + +[BUILD] +cp src/Makefile src/Makefile.bak +sed -i '1s/^CXX *= *g++/CXX = clang++/' src/Makefile +sed -i '2{/[^ ]-fsigned-char/!s/$/ -fsigned-char/}' src/Makefile +mkdir -p bin +sh install_kraken2.sh bin + +[CLEAN] +rm -rf bin + +[RUN] +run = +binary = kraken2 -h +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all -- Gitee From 0a7a7e613042c01a25d6c75a3477f39d0b088a6c Mon Sep 17 00:00:00 2001 From: jsfhd <2162443403@qq.com> Date: Tue, 15 Apr 2025 17:38:45 +0800 Subject: [PATCH 02/58] add qe-7.3 templates --- .../qe/7.3/data.qe-common.arm.cpu.config | 90 +++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 templates/qe/7.3/data.qe-common.arm.cpu.config diff --git a/templates/qe/7.3/data.qe-common.arm.cpu.config b/templates/qe/7.3/data.qe-common.arm.cpu.config new file mode 100644 index 0000000..72e6715 --- /dev/null +++ b/templates/qe/7.3/data.qe-common.arm.cpu.config @@ -0,0 +1,90 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +qe/7.3 $JARVIS_PROXY/QEF/q-e/archive/refs/tags/qe-7.3.tar.gz +bench/master $JARVIS_PROXY/QEF/benchmarks/archive/refs/heads/master.zip + +[DEPENDENCY] +module purge +./jarvis -install package/hpckit/2024.12.30/ any +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi + + +[ENV] +module purge +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi + +export KML_LIB=$JARVIS_UTILS/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/lib +export BLAS_PATH=$KML_LIB/sve/kblas/omp +export LAPACK_PATH=$KML_LIB/sve +export KM_LIB=$KML_LIB/noarch + +export BLAS_LIBS="-L$BLAS_PATH -lkblas" +export LAPACK_LIBS="-L$LAPACK_PATH $KM_LIB -lkm -lkscalapack_full -lklapack_full" + +export PATH=${JARVIS_LIBS}/bisheng4.1.0/qe/7.3/bin:$PATH +export LD_LIBRARY_PATH=$LAPACK_PATH:$KM_LIB:$BLAS_PATH:$LD_LIBRARY_PATH + + +[APP] +app_name = QE +build_dir = ${JARVIS_TMP} +binary_dir = ${JARVIS_LIBS}/bisheng4.1.0/qe/7.3/bin +case_dir = ${JARVIS_ROOT}/workloads/benchmarks-master + +[BUILD] +rm q-e-qe-7.3 -rf +tar -xvf ${JARVIS_DOWNLOAD}/qe-7.3.tar.gz +cd q-e-qe-7.3 + +./configure F90=flang F77=flang FC=flang MPIF90=mpifort MPIF77=mpifort CC=mpicc FCFLAGS="-O3 -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true" CFLAGS="-O3 -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true" --with-scalapack=yes --enable-openmp --prefix=$JARVIS_LIBS/bisheng4.1.0/qe/7.3 +sed -i 's/gfortran/flang/g' make.inc +make -j pwall +make install + +cd ${JARVIS_ROOT}/workloads +rm benchmarks-master -rf +unzip ${JARVIS_DOWNLOAD}/master.zip + +[CLEAN] +make clean + +[RUN] +run = +binary = +nodes = 1 + + +[BATCH] + +LOG_FILE="qe-proformance.log" +>"$LOG_FILE" +cd ${JARVIS_ROOT}/workloads/benchmarks-master/other-inputs/water/ + +#$RUN_TOOL "qe pw.x" "time -p mpirun --allow-run-as-root -mca pml ucx -mca btl tcp -x UCX_TLS=sm,tcp -np 128 -x OMP_NUM_THREADS=1 -np pw.x -input pw.in " + +( time -p mpirun --allow-run-as-root -mca pml ucx -mca btl tcp -x UCX_TLS=sm,tcp -np 128 pw.x -input pw.in ) 2>&1 |tee $LOG_FILE + +[JOB] +#!/bin/sh +#DSUB -n qe_test +#DSUB --mpi hmpi +#DSUB -q default +#DSUB -N 1 +#DSUB -R cpu=128 +#DSUB -oo qe.%J.out +#DSUB -oe qe.%J.err + +LOG_FILE="qe-proformance.log" + +>"$LOG_FILE" +cd ${JARVIS_ROOT}/workloads/benchmarks-master/other-inputs/water/ + +#$RUN_TOOL "qe pw.x" "time -p mpirun --allow-run-as-root -mca pml ucx -mca btl tcp -x UCX_TLS=sm,tcp -np 128 -x OMP_NUM_THREADS=1 -np pw.x -input pw.in " + +( time -p mpirun --allow-run-as-root -mca pml ucx -mca btl tcp -x UCX_TLS=sm,tcp -np 128 -input pw.in ) 2>&1 |tee $LOG_FILE -- Gitee From 3697c4c81f4d2573a117acf5ac444b570a79becc Mon Sep 17 00:00:00 2001 From: jsfhd <2162443403@qq.com> Date: Wed, 16 Apr 2025 10:02:41 +0800 Subject: [PATCH 03/58] add wrf-4.6.0 templates --- templates/wrf/4.6.0/data.wrf.cpu.sve.config | 145 ++++++++++++++++++++ 1 file changed, 145 insertions(+) create mode 100644 templates/wrf/4.6.0/data.wrf.cpu.sve.config diff --git a/templates/wrf/4.6.0/data.wrf.cpu.sve.config b/templates/wrf/4.6.0/data.wrf.cpu.sve.config new file mode 100644 index 0000000..37dfa65 --- /dev/null +++ b/templates/wrf/4.6.0/data.wrf.cpu.sve.config @@ -0,0 +1,145 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +wrf/4.6.0 https://github.com/wrf-model/WRF/releases/download/v4.6.0/v4.6.0.tar.gz WRFV4.6.0.tar.gz + +[DEPENDENCY] +set -e +set -x +sudo yum -y install rpcbind libtirpc* +./jarvis -install package/hpckit/2024.12.30/ any +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module load bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi + +export CC=clang CXX=clang++ FC=flang +export CFLAGS="-Wno-implicit-function-declaration -Wno-incompatible-function-pointer-types" +./jarvis -install jasper/1.900.2 bisheng + +export CC=mpicc FC=mpifort CXX=mpicxx + +./jarvis -install package/hdf5/1.12.0/clang bisheng+mpi +module use ${JARVIS_ROOT}/software/moduledeps/bisheng4.1.0-hmpi2.4.3/ +module load hdf5-clang/1.12.0 +./jarvis -install package/pnetcdf/1.11.2 bisheng+mpi +module load pnetcdf/1.11.2 +./jarvis -install package/netcdf/4.7.4/clang bisheng+mpi +module load netcdf-clang/4.7.4 +module load bisheng/kml2.5.0/kml bisheng/kml2.5.0/kblas/pthread + +./jarvis -install jasper/1.900.2 bisheng +# basic system components +yum install -y time zlib zlib-devel libtirpc libtirpc-devel patch + +[ENV] +#!/bin/bash +module purge +module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module load bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi +module use ./software/moduledeps/bisheng4.1.0-hmpi2.4.3/ +module load hdf5-clang/1.12.0 +module load pnetcdf/1.11.2 +module load netcdf-clang/4.7.4 +module load bisheng/kml2.5.0/kml bisheng/kml2.5.0/kblas/pthread +module use ./software/moduledeps/bisheng4.1.0/ +module load jasper/1.900.2 + +export WRFIO_NCD_LARGE_FILE_SUPPORT=1 +export NETCDF=${NETCDF_CLANG_PATH} +export HDF5=${HDF5_CLANG_PATH} +export PHDF5=${HDF5} +export PNETCDF=${PNETCDF_PATH} +export JASPER=${JASPER_PATH} +export JASPERLIB=${JASPER_PATH}/lib +export JASPREINC=${JASPER_PATH}/include +export MPI_DIR=`dirname $(dirname $(which mpirun))` +export BISHENG_DIR=`dirname $(dirname $(which clang))` +export CPPFLAGS="-I${HDF5}/include -I${PNETCDF}/include -I${NETCDF}/include -I${MPI_DIR}/include" +export LDFLAGS="-L${HDF5}/lib -L${PNETCDF}/lib -L${NETCDF}/lib -lnetcdf -lnetcdff -lpnetcdf -lhdf5_hl -lhdf5 -lz" +export CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif90 F90=mpif90 +export MPI_LIB="-L${MPI_DIR}/lib -lmpi -lomp" +export C_INCLUDE=-I${HDF5}/include:$C_INCLUDE +export CPLUS_INCLUDE=-I${HDF5}/include:$C_INCLUDE + + +export PATH=$JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/WRFV4.6.0/main:$PATH + +[APP] +app_name = WRF +build_dir = $JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/WRFV4.6.0 +binary_dir = ${WRF_DIR}/run +case_dir = $JARVIS_ROOT/case/wrf/conus12km + +[BUILD] +set -x +mkdir -p $JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/WRFV4.6.0 +tar -xvf ${JARVIS_DOWNLOAD}/WRFV4.6.0.tar.gz --strip-components 1 -C $JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/WRFV4.6.0 +cd ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/WRFV4.6.0 +sed -i "2181c\SFC = flang" arch/configure.defaults +sed -i "2182c\SCC = clang" arch/configure.defaults +sed -i "2183c\CCOMP = clang" arch/configure.defaults +sed -i "2192c\CFLAGS_LOCAL = -w -O3 -c -Wno-implicit-function-declaration -Wno-int-conversion -Wno-implicit-int -mtune=native -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true -L${BISHENG_DIR}/lib -I${BISHENG_DIR}/include " arch/configure.defaults +sed -i "2194c\FCOPTIM = -O3 -mcpu=native -funroll-loops -mtune=native -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true -lmathlib -fopenmp -L${BISHENG_DIR}/lib -Wl,-rpath,${BISHENG_DIR}/lib -L/home/drh/hpcrunner-bak/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/lib/noarch -lkm_l9" arch/configure.defaults + + +echo -e "12\n1" | ./configure + +./compile -j 16 em_real 2>&1 | tee -a compile.log + +[CLEAN] +./clean -a + +[RUN] +run = mpirun --allow-run-as-root -n 32 -x OMP_NUM_THREADS=1 -bind-to core ${WRF_DIR}/run/wrf.exe +binary = +nodes = 1 + + +[BATCH] +#定义日志文件 +LOG_FILE="ww3-proformance.log" + +#清空日志文件 +>"$LOG_FILE" + +#复制run目录到运行目录 +mv namelist.input namelist.input-bak +cp -rf $JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/WRFV4.6.0/run/* ./ +ln -sf CAMtr_volume_mixing_ratio CAMtr_volume_mixing_ratio.SSP245 +ln -sf MPTABLE.TBL $JARVIS_ROOT/software/apps/bisheng4.1.0-hmpi2.4.3/WRFV4.6.0/phys/noahmp/parameters/MPTABLE.TBL +mv namelist.input-bak namelist.input +trdnum=4 +mynp=32 + +#执行每个命令并统计性能 +#$ROOT_TOOL "mpirun" "time -p mpirun --allow-run-as-root -x PATH -x LD_LIBRARY_PATH --map-by ppr:${mynp}:node:pe=${trdnum} -x OMP_NUM_THREADS=${trdnum} --rank-by core --bind-to core --mca pml ucx -mca btl ^vader,tcp,openib wrf.exe" $LOG_FILE + +mpirun --allow-run-as-root -x PATH -x LD_LIBRARY_PATH --map-by ppr:${mynp}:node:pe=${trdnum} -x OMP_NUM_THREADS=${trdnum} --rank-by core --bind-to core --mca pml ucx -mca btl ^vader,tcp,openib wrf.exe + +echo "ALL commands executed. Performance log saved to $LOG_FILE" + + +[JOB] +#!/bin/sh +#DSUB -n wrf_test +#DSUB --mpi hmpi +#DSUB -q default +#DSUB -N 1 +#DSUB -R cpu=128 +#DSUB -oo wrf.%J.out +#DSUB -oe wrf.%J.err + + +#定义日志文件 +LOG_FILE="wrf-proformance.log" + +#清空日志文件 +>"$LOG_FILE" + +#执行每个命令并统计性能 +$ROOT_TOOL "mpirun" "mpirun -x PATH -x LD_LIBRARY_PATH --map-by ppr:${mynp}:node:pe=${trdnum} -x OMP_NUM_THREADS=${trdnum} --rank-by core --bind-to core --mca pml ucx -mca btl ^vader,tcp,openib wrf.exe" $LOG_FILE +echo "ALL commands executed. Performance log saved to $LOG_FILE" + + -- Gitee From c179097d34d7c5a9c1357ed9e656f184e3cd5aef Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 15:41:56 +0800 Subject: [PATCH 04/58] Add templates app modeller-10.6 --- .../10.6/modeller.arm.bisheng.hmpi.config | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 templates/modeller/10.6/modeller.arm.bisheng.hmpi.config diff --git a/templates/modeller/10.6/modeller.arm.bisheng.hmpi.config b/templates/modeller/10.6/modeller.arm.bisheng.hmpi.config new file mode 100644 index 0000000..b52cdb8 --- /dev/null +++ b/templates/modeller/10.6/modeller.arm.bisheng.hmpi.config @@ -0,0 +1,53 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +modeller/10.6 https://salilab.org/modeller/10.6/modeller-10.6.tar.gz +soap_protein_od.hdf5/modeller>9.13 https://salilab.org/SOAP/soap_protein_od.hdf5 + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install hmpi/2.4.2 bisheng +module load hmpi/2.4.2 +./jarvis -install hdf5/1.10.7/clang bisheng+mpi +module load hdf5-clang/1.10.7 +tar -zxvf ${JARVIS_DOWNLOAD}/modeller-10.6.tar.gz -C ${JARVIS_TMP_DOWNLOAD} +mkdir -p ${JARVIS_ROOT}/software/app/modeller + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load hmpi/2.4.2 +module load hdf5-clang/1.10.7 +export PATH=${JARVIS_ROOT}/software/app/modeller/bin:$PATH + +[APP] +app_name = modeller +build_dir = ${JARVIS_TMP_DOWNLOAD}/modeller-10.6/ +binary_dir = +case_dir = ${JARVIS_ROOT}/software/app/modeller/examples/ + +[BUILD] +./Install < Date: Tue, 22 Apr 2025 16:29:14 +0800 Subject: [PATCH 05/58] Add templates app hefei-namd-master --- .../master/hefei-namd.arm.bisheng.config | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 templates/hefei-namd/master/hefei-namd.arm.bisheng.config diff --git a/templates/hefei-namd/master/hefei-namd.arm.bisheng.config b/templates/hefei-namd/master/hefei-namd.arm.bisheng.config new file mode 100644 index 0000000..b1cca30 --- /dev/null +++ b/templates/hefei-namd/master/hefei-namd.arm.bisheng.config @@ -0,0 +1,49 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +hefei-namd/master ${JARVIS_PROXY}/QijingZheng/Hefei-NAMD/archive/refs/heads/master.zip Hefei-NAMD-master.zip + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 + +unzip ${JARVIS_DOWNLOAD}/Hefei-NAMD-master.zip -d ${JARVIS_TMP_DOWNLOAD} +mkdir -p ${JARVIS_ROOT}/software/apps/hefei-namd/bin + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 + +[APP] +app_name = hefei-namd +build_dir = ${JARVIS_TMP_DOWNLOAD}/Hefei-NAMD-master/src/dish +binary_dir = ${JARVIS_ROOT}/software/apps/hefei-namd/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/Hefei-NAMD-master/doc/training_2020/example/results/namd/ + +[BUILD] +sed -i '4c FC= flang' Makefile +make +cp -ar dish ${JARVIS_ROOT}/software/apps/hefei-namd/bin +cd ../namd/ +sed -i '4c FC= flang -assume byterecl' Makefile +sed -i '5c FC= flang' Makefile +make +cp -ar namd ${JARVIS_ROOT}/software/apps/hefei-namd/bin +cd ../namdK/ +sed -i '4c FC= flang' Makefile +sed -i '6c FFLAGS= -g -O2 -fIntel-compatibility' Makefile +make +cp -ar namdk ${JARVIS_ROOT}/software/apps/hefei-namd/bin + +sed -i 's/! LCPEXT/ LCPEXT/' ../../doc/training_2020/example/results/namd/inp + +[CLEAN] + +[RUN] +run = time +binary = namd +nodes = 1 -- Gitee From 241a9bb32d7c1e6c27a6333db7a7546dbee1439a Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 16:38:50 +0800 Subject: [PATCH 06/58] Add templates app interproscan-5.73-104.0 --- .../5.73-104.0/interproscan.arm.py39.config | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 templates/interproscan/5.73-104.0/interproscan.arm.py39.config diff --git a/templates/interproscan/5.73-104.0/interproscan.arm.py39.config b/templates/interproscan/5.73-104.0/interproscan.arm.py39.config new file mode 100644 index 0000000..f01fd31 --- /dev/null +++ b/templates/interproscan/5.73-104.0/interproscan.arm.py39.config @@ -0,0 +1,65 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +interproscan/5.53-87.0 http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.73-104.0/interproscan-5.73-104.0-64-bit.tar.gz +bisheng-jdk/11.0.25 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_jdk/bisheng-jdk-11.0.25-linux-aarch64.tar.gz bisheng-jdk-11-aarch64.tar.gz +bisheng-jre/11.0.25 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_jdk/bisheng-jre-11.0.25-linux-aarch64.tar.gz bisheng-jre-11-aarch64.tar.gz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install python3/3.9.9 bisheng +module load python3/3.9.9 +tar -zxvf ${JARVIS_DOWNLOAD}/bisheng-jdk-11-aarch64.tar.gz -C ${JARVIS_COMPILER} +tar -zxvf ${JARVIS_DOWNLOAD}/bisheng-jre-11-aarch64.tar.gz -C ${JARVIS_COMPILER}/bisheng-jdk-11.0.25/ --transform='s/bisheng-jre-11.0.25/jre/' +echo -e "\033[0;32mCheck the execution dependency \"hmmer\" ...\033[0m" +file1="${JARVIS_ROOT}/hmmer/bin/hmmscan" +file2="${JARVIS_ROOT}/hmmer/bin/hmmsearch" +if [[ $( file -b --mime-encoding ${file1} ) = "binary" ]];then + if [[ $( file -b --mime-encoding ${file2} ) = "binary" ]];then + echo -e "\033[0;32mAlready installed the execution dependency \"hmmer\"\033[0m" + fi +else + echo -e "\033[0;31mPlease install the execution dependency \"hmmer\" in ${JARVIS_ROOT} or configuer the hmmer executabla file environment variables after installation.\033[0m" + exit 1 +fi + +mkdir -p ${JARVIS_ROOT}/software/apps +tar -zxvf ${JARVIS_DOWNLOAD}/interproscan-5.73-104.0-64-bit.tar.gz -C ${JARVIS_ROOT}/software/apps/ --transform='s/interproscan-5.73-104.0/interproscan/' + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load python3/3.9.9 +export PATH=${JARVIS_COMPILER}/bisheng-jdk-11.0.25/bin:${JARVIS_COMPILER}/bisheng-jdk-11.0.25/jre/bin:$PATH + +[APP] +app_name = interproscan +build_dir = ${JARVIS_ROOT}/software/apps/interproscan +binary_dir = ${JARVIS_ROOT}/software/apps/interproscan +case_dir = ${JARVIS_ROOT}/software/apps/interproscan + +[BUILD] +yes | cp -ar ${JARVIS_ROOT}/hmmer/bin/* bin/hmmer/hmmer3/3.3/ +python3 setup.py -f interproscan.properties + +echo -e "\033[0;32mExample: Testing the \"sfld\" module\033[0m" +file -b bin/sfld/sfld_postprocess | grep -qi 'ARM\|aarch64' +if [ $? -eq 0 ];then + echo -e "\033[0;32mAlready \"sfld\" module aarch64 platform binary\033[0m" + echo -e "\033[0;32mNext command ./jarvis -r\033[0m" +else + echo -e "\033[0;31mTo be compiled and replaced with \"bin/sfld/sfld_postprocess\" binaries for aarch64 platforms!\033[0m" + exit 1 +fi + +[CLEAN] + +[RUN] +run = bash interproscan.sh -i +binary = test_all_appl.fasta -f tsv -dp -appl sfld +nodes = 1 -- Gitee From 06d619eb7f1b5871a83b1892d7907bee36a71181 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 16:44:41 +0800 Subject: [PATCH 07/58] Add templates app jax-0.4.30 --- templates/jax/0.4.30/jax.arm.py39.cpu.config | 38 ++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 templates/jax/0.4.30/jax.arm.py39.cpu.config diff --git a/templates/jax/0.4.30/jax.arm.py39.cpu.config b/templates/jax/0.4.30/jax.arm.py39.cpu.config new file mode 100644 index 0000000..04e4a2d --- /dev/null +++ b/templates/jax/0.4.30/jax.arm.py39.cpu.config @@ -0,0 +1,38 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +jax/0.4.30 https://github.com/jax-ml/jax/archive/refs/tags/jax-v0.4.30.tar.gz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install python3/3.9.9 bisheng +module load python3/3.9.9 +tar -zxvf ${JARVIS_DOWNLOAD}/jax-v0.4.30.tar.gz -C ${JARVIS_TMP_DOWNLOAD} + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load python3/3.9.9 + +[APP] +app_name = jax +build_dir = ${JARVIS_TMP_DOWNLOAD}/jax-jax-v0.4.30 +binary_dir = +case_dir = ${JARVIS_TMP_DOWNLOAD}/jax-jax-v0.4.30/tests + +[BUILD] +pip3 install . +pip3 install absl-py + +[CLEAN] +pip3 uninstall jax -y + +[RUN] +run = python3 +binary = jax_jit_test.py +nodes = 1 -- Gitee From 97bd36c37b5c86b5614e775c341f770f0e5cca9f Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 16:53:57 +0800 Subject: [PATCH 08/58] Add templates app wtdbg2-2.5 --- .../wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 templates/wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config diff --git a/templates/wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config b/templates/wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config new file mode 100644 index 0000000..a96679f --- /dev/null +++ b/templates/wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config @@ -0,0 +1,59 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +wtdbg2/2.5 ${JARVIS_PROXY}/ruanjue/wtdbg2/archive/refs/tags/v2.5.tar.gz wtdbg2-2.5.tar.gz +sse2neon/ ${JARVIS_PROXY}/jratcliff63367/sse2neon/archive/master.zip sse2neon-master.zip +case/E.coli http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install kgcc/10.3.1 com +module load kgcc/10.3.1 +./jarvis -install hmpi/2.4.2 gcc +module load hmpi/2.4.2 + +mkdir -p ${JARVIS_ROOT}/software/apps/wtdbg2/bin +tar -zxvf ${JARVIS_DOWNLOAD}/wtdbg2-2.5.tar.gz -C ${JARVIS_TMP_DOWNLOAD} +unzip -j ${JARVIS_DOWNLOAD}/sse2neon-master.zip 'sse2neon-master/SSE2NEON.h' -d ${JARVIS_TMP_DOWNLOAD}/wtdbg2-2.5/ + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +module load hmpi/2.4.2 + +[APP] +app_name = wtdbg2 +build_dir = ${JARVIS_TMP_DOWNLOAD}/wtdbg2-2.5 +binary_dir = ${JARVIS_ROOT}/software/apps/wtdbg2/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/wtdbg2-2.5/wtdbg2_test + +[BUILD] +mv SSE2NEON.h sse2neon.h +sed -i 's/^CC :=.*/CC := mpicc/' Makefile +sed -i 's/^BIN :=.*/BIN := \${JARVIS_ROOT}\/software\/apps\/wtdbg2\/bin/' Makefile +sed -i 's/\-mpopcnt \-msse4.2/\-march=armv8-a/' Makefile +sed -i '/^GENERIC_SRC=.*/s/$/\ sse2neon.h/' Makefile +sed -i '/^#include /a #include \"sse2neon.h\"' ksw.c +sed -i '/^#include /s/^/\/\//' ksw.c +sed -i '/^#include /a #include \"sse2neon.h\"' poacns.h +sed -i '/^#include /s/^/\/\//' poacns.h +sed -i '/^#include /s/^/\/\//' poacns.h +sed -i '/SMASK =.*/s/^/\/\//' poacns.h +make +make install +cp -ar wtdbg2.pl ${JARVIS_ROOT}/software/apps/wtdbg2/bin + +mkdir -p wtdbg2_test +cd wtdbg2_test/ +cp -ar ${JARVIS_DOWNLOAD}/selfSampleData.tar.gz . + +[CLEAN] +make clean + +[RUN] +run = ${JARVIS_ROOT}/software/apps/wtdbg2/bin/wtdbg2 -x rs -g 4.6m -t $(nproc) -i selfSampleData.tar.gz -fo ecoli && +binary = wtpoa-cns -t $(nproc) -i ecoli.ctg.lay.gz -fo ecoli.ctg.fa +nodes = 1 -- Gitee From cdd9e0e80c02530550ea172b3cde5e6da81892af Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 17:00:17 +0800 Subject: [PATCH 09/58] Add templates app wannier_tools-2.7.1 --- ...nnier_tools.arm.hpckit.bisheng.hmpi.config | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 templates/wannier_tools/2.7.1/wannier_tools.arm.hpckit.bisheng.hmpi.config diff --git a/templates/wannier_tools/2.7.1/wannier_tools.arm.hpckit.bisheng.hmpi.config b/templates/wannier_tools/2.7.1/wannier_tools.arm.hpckit.bisheng.hmpi.config new file mode 100644 index 0000000..dc5a284 --- /dev/null +++ b/templates/wannier_tools/2.7.1/wannier_tools.arm.hpckit.bisheng.hmpi.config @@ -0,0 +1,55 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +wannier_tools/2.7.1 ${JARVIS_PROXY}/quanshengwu/wannier_tools/archive/refs/tags/v2.7.1.tar.gz wannier_tools-2.7.1.tar.gz + +[DEPENDENCY] +module purge +./jarvis -install hpckit/2024.12.30 any +module use ./software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles +module load bisheng/compiler4.1.0/bishengmodule +module load bisheng/hmpi2.4.3/hmpi +module load bisheng/kml2.5.0/kml +module unload bisheng/kml2.5.0/kspblas/omp +module unload bisheng/kml2.5.0/kvml/serial + +mkdir -p ${JARVIS_ROOT}/software/app/wannier_tools/bin +tar -zxvf ${JARVIS_DOWNLOAD}/wannier_tools-2.7.1.tar.gz -C ${JARVIS_TMP_DOWNLOAD} + +[ENV] +module purge +module use ./software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles +module load bisheng/compiler4.1.0/bishengmodule +module load bisheng/hmpi2.4.3/hmpi +module load bisheng/kml2.5.0/kml +module unload bisheng/kml2.5.0/kspblas/omp +module unload bisheng/kml2.5.0/kvml/serial +export CC=mpicc +export CXX=mpicxx +export FC=mpifort +export F77=mpifort +export F90=mpifort + +[APP] +app_name = wannier_tools +build_dir = ${JARVIS_TMP_DOWNLOAD}/wannier_tools-2.7.1/src +binary_dir = ${JARVIS_ROOT}/software/app/wannier_tools/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/wannier_tools-2.7.1/examples/Bi2Se3 + +[BUILD] +echo yes | cp Makefile.gfortran-mpi Makefile +sed -i 's/^F90 =.*/F90 = mpif90 -cpp -DMPI/' Makefile +sed -i 's/^LIBS =.*/LIBS = -L\${JARVIS_UTILS}\/hpckit\/2024.12.30\/HPCKit\/24.12.30\/kml\/bisheng\/lib -lkml_rt/' Makefile +sed -i '1285,1289d' module.f90 +sed -i "1285c character(10) , dimension(magnetic_number_max, angular_number) :: orb_sign = reshape([character(10) :: '','','','s','','','','','','py','pz','px','','','','dxy','dyz','dz2','dxz','dx2-y2','','fy(3x2-y2)','fxyz','fyz2','fz3','fxz2','fz(x2-y2)','fx(x2-3y2)'], [magnetic_number_max, angular_number])" module.f90 +make +cp -ar ../bin/wt.x ${JARVIS_ROOT}/software/app/wannier_tools/bin/ + +[CLEAN] +make clean + +[RUN] +run = tar -zxvf Bi2Se3_hr.tar.gz && mpirun --allow-run-as-root -np $(nproc) +binary = wt.x && cat WT.out | tail -n 40 +nodes = 1 -- Gitee From 0faf86fa40d019f8cccf8b58b080fe2450ab0cdc Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 17:04:56 +0800 Subject: [PATCH 10/58] Add templates app velvet-1.2.10 --- .../velvet/1.2.10/velvet.arm.kgcc.hmpi.config | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 templates/velvet/1.2.10/velvet.arm.kgcc.hmpi.config diff --git a/templates/velvet/1.2.10/velvet.arm.kgcc.hmpi.config b/templates/velvet/1.2.10/velvet.arm.kgcc.hmpi.config new file mode 100644 index 0000000..c7405b7 --- /dev/null +++ b/templates/velvet/1.2.10/velvet.arm.kgcc.hmpi.config @@ -0,0 +1,45 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +velvet/1.2.10 ${JARVIS_PROXY}/dzerbino/velvet/archive/refs/tags/v1.2.10.tar.gz velvet-1.2.10.tgz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install kgcc/10.3.1 com +module load kgcc/10.3.1 +./jarvis -install hmpi/2.4.2 gcc +module load hmpi/2.4.2 + +tar -zxvf ${JARVIS_DOWNLOAD}/velvet-1.2.10.tgz -C ${JARVIS_TMP_DOWNLOAD} +mkdir -p ${JARVIS_ROOT}/software/apps/velvet/bin + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +module load hmpi/2.4.2 +export OMP_NUM_THREADS=96 +export OMP_THREAD_LIMIT=95 + +[APP] +app_name = velvet +build_dir = ${JARVIS_TMP_DOWNLOAD}/velvet-1.2.10 +binary_dir = ${JARVIS_ROOT}/software/apps/velvet/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/velvet-1.2.10 + +[BUILD] +sed -ri 's/\-m64/\-mabi=lp64/g' Makefile +sed -ri 's/CC = gcc/CC = mpicc/g' Makefile +sed -ri 's/CC = gcc/CC = mpicc/g' contrib/MetaVelvet-v0.3.1/Makefile +make 'GATEGORIES=10' 'MAXKMERLENGTH=57' 'LONGSEQUENCES=1' 'OPENMP=1' 'BUNDLEDZLIB=1' +cp -ar velveth velvetg ${JARVIS_ROOT}/software/apps/velvet/bin +mkdir -p ${JARVIS_TMP_DOWNLOAD}/velvet-1.2.10/output + +[CLEAN] + +[RUN] +run = ${JARVIS_ROOT}/software/apps/velvet/bin/velveth output 31 -shortPaired -fastq.gz tests/read1.fq.gz -shortPaired -fastq.gz tests/read2.fq.gz && +binary = velvetg output -min_contig_lgth 100 -cov_cutoff 9 +nodes = 1 -- Gitee From 1731aa88c78e6f5289e699edbffd73220cddf7f9 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 17:09:10 +0800 Subject: [PATCH 11/58] Add templates app tophat-2.1.1 --- .../2.1.1/tophat.arm.kgcc.hmpi.py27.config | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 templates/tophat/2.1.1/tophat.arm.kgcc.hmpi.py27.config diff --git a/templates/tophat/2.1.1/tophat.arm.kgcc.hmpi.py27.config b/templates/tophat/2.1.1/tophat.arm.kgcc.hmpi.py27.config new file mode 100644 index 0000000..9107a37 --- /dev/null +++ b/templates/tophat/2.1.1/tophat.arm.kgcc.hmpi.py27.config @@ -0,0 +1,60 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +TopHat/2.1.1 https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz +test_data/ https://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install kgcc/10.3.1 com +module load kgcc/10.3.1 +./jarvis -install hmpi/2.4.2 gcc +module load hmpi/2.4.2 +sed -i '/cd Python-2.7.16/a sed -i "s/-fp-model strict/-ffloat-store/" configure' ${JARVIS_ROOT}/package/python2/2.7.16/install.sh +./jarvis -install python2/2.7.16 gcc+mpi +module load python2/2.7.16 +sed -i '/cd bowtie2-2.4.5/a sed -i "s/zlib.net/zlib.net\\/fossils/g" Makefile' ${JARVIS_ROOT}/package/bowtie2/2.4.5/install.sh +sed -i 's/-stdlib=libc++/-stdlib=libstdc++/g' ${JARVIS_ROOT}/package/bowtie2/2.4.5/install.sh +./jarvis -install bowtie2/2.4.5 gcc+mpi +export PATH=/opt/hpcrunner/software/libs/bisheng2.1.0/bowtie2/2.4.5/bin:$PATH +sed -i 's/python3/python2/g' ${JARVIS_ROOT}/package/boost-python/1.72.0/install.sh +sed -i 's/\.\/bootstrap.sh/\.\/bootstrap.sh --with-libraries=system,thread/' ${JARVIS_ROOT}/package/boost-python/1.72.0/install.sh +./jarvis -install boost-python/1.72.0 gcc+mpi +module load boost-python/1.72.0 + +mkdir -p ${JARVIS_ROOT}/software/apps/tophat +tar -zxvf ${JARVIS_DOWNLOAD}/tophat-2.1.1.tar.gz -C ${JARVIS_TMP_DOWNLOAD} +tar -zxvf ${JARVIS_DOWNLOAD}/test_data.tar.gz -C ${JARVIS_TMP_DOWNLOAD}/tophat-2.1.1/ + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +module load hmpi/2.4.2 +module load python2/2.7.16 +export PATH=/opt/hpcrunner/software/libs/bisheng2.1.0/bowtie2/2.4.5/bin:$PATH +module load boost-python/1.72.0 + +[APP] +app_name = tophat +build_dir = ${JARVIS_TMP_DOWNLOAD}/tophat-2.1.1 +binary_dir = ${JARVIS_ROOT}/software/apps/tophat/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/tophat-2.1.1/test_data + +[BUILD] +sed -i 's/^CC=.*/CC= mpicc/' src/samtools-0.1.18/Makefile +sed -i 's/^CC=.*/CC= mpicc/' src/samtools-0.1.18/bcftools/Makefile +sed -i 's///g' src/tophat_reports.cpp +PYTHON=`which python3` CC=`which mpicc` CXX=`which mpicxx` ./configure --prefix=${JARVIS_ROOT}/software/apps/tophat --with-boost=${JARVIS_LIBS}/kgcc10.3.1/hmpi2.4.2/boost-python/1.72.0 +make +make install + +[CLEAN] +make clean + +[RUN] +run = +binary = tophat -r 20 test_ref reads_1.fq reads_2.fq +nodes = 1 -- Gitee From f6c0d00da049a9e465c7d5f2f9359a98d404656e Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 17:12:43 +0800 Subject: [PATCH 12/58] Add templates app sundials-7.3.0 --- .../sundials.arm.hpckit.bisheng.hmpi.config | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 templates/sundials/7.3.0/sundials.arm.hpckit.bisheng.hmpi.config diff --git a/templates/sundials/7.3.0/sundials.arm.hpckit.bisheng.hmpi.config b/templates/sundials/7.3.0/sundials.arm.hpckit.bisheng.hmpi.config new file mode 100644 index 0000000..e794db3 --- /dev/null +++ b/templates/sundials/7.3.0/sundials.arm.hpckit.bisheng.hmpi.config @@ -0,0 +1,50 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +sundials/7.3.0 ${JARVIS_PROXY}/LLNL/sundials/releases/download/v7.3.0/sundials-7.3.0.tar.gz + +[DEPENDENCY] +module purge +./jarvis -install hpckit/2024.12.30 any +module use software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles +module load bisheng/compiler4.1.0/bishengmodule +module load bisheng/hmpi2.4.3/hmpi +module load bisheng/kml2.5.0/kml +module unload bisheng/kml2.5.0/kspblas/omp +module unload bisheng/kml2.5.0/kvml/serial + +mkdir -p ${JARVIS_ROOT}/software/apps/sundials +tar -zxvf ${JARVIS_DOWNLOAD}/sundials-7.3.0.tar.gz -C ${JARVIS_TMP_DOWNLOAD} + +[ENV] +module purge +module use software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles +module load bisheng/compiler4.1.0/bishengmodule +module load bisheng/hmpi2.4.3/hmpi +module load bisheng/kml2.5.0/kml +module unload bisheng/kml2.5.0/kspblas/omp +module unload bisheng/kml2.5.0/kvml/serial + +[APP] +app_name = sundials +build_dir = ${JARVIS_TMP_DOWNLOAD}/sundials-7.3.0 +binary_dir = +case_dir = ${JARVIS_ROOT}/software/apps/sundials/examples/arkode/C_manyvector + +[BUILD] +rm -rf build +mkdir build +cd build/ +cmake .. -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/sundials -DEXAMPLES_INSTALL_PATH=${JARVIS_ROOT}/software/apps/sundials/examples -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_Fortran_COMPILER=mpifort -DENABLE_MPI=ON -DBUILD_FORTRAN_MODULE_INTERFACE=ON -DENABLE_LAPACK=ON -DBLAS_LIBRARIES=${JARVIS_UTILS}/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/lib/neon/kblas/pthread/libkblas.so -DLAPACK_LIBRARIES=${JARVIS_UTILS}/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/lib/neon/libklapack_full.so +make +make install +make test + +[CLEAN] +rm -rf build + +[RUN] +run = make && ./ark_brusselator1D_manyvec +binary = +nodes = 1 -- Gitee From e65ff0227314426f98e4fe27310665d80fddc454 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 17:16:19 +0800 Subject: [PATCH 13/58] Add templates app Seurat-5.1.0 --- .../5.1.0/seurat.arm.bisheng.hmpi.R.config | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 templates/Seurat/5.1.0/seurat.arm.bisheng.hmpi.R.config diff --git a/templates/Seurat/5.1.0/seurat.arm.bisheng.hmpi.R.config b/templates/Seurat/5.1.0/seurat.arm.bisheng.hmpi.R.config new file mode 100644 index 0000000..8feaa91 --- /dev/null +++ b/templates/Seurat/5.1.0/seurat.arm.bisheng.hmpi.R.config @@ -0,0 +1,46 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +Seurat/5.1.0 https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_5.1.0.tar.gz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install hmpi/2.4.2 bisheng +module load hmpi/2.4.2 +./jarvis -install libpng/1.6.37 bisheng+mpi +module load libpng/1.6.37 +./jarvis -install R/4.4.3 bisheng+mpi +module load R/4.4.3 + +tar -zxvf ${JARVIS_DOWNLOAD}/Seurat_5.1.0.tar.gz -C ${JARVIS_TMP_DOWNLOAD} + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load hmpi/2.4.2 +module load libpng/1.6.37 +module load R/4.4.3 + +[APP] +app_name = Seurat +build_dir = ${JARVIS_TMP_DOWNLOAD}/Seurat +binary_dir = +case_dir = ${JARVIS_TMP_DOWNLOAD}/Seurat/tests + +[BUILD] +R --vanilla -e 'install.packages(c("SeuratObject", "cowplot", "fastDummies", "fitdistrplus", "future", "future.apply", "generics", "ggplot2", "ggrepel", "ggridges", "httr", "ica", "igraph", "irlba", "jsonlite", "leiden", "lifecycle", "lmtest", "matrixStats", "miniUI", "patchwork", "pbapply", "plotly", "png", "progressr", "purrr", "RANN", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppHNSW", "reticulate", "rlang", "ROCR", "RSpectra", "Rtsne", "scales", "scattermore", "sctransform", "shiny", "spatstat.explore", "spatstat.geom", "tibble", "uwot", "RcppEigen", "RcppProgress", "testthat"), repos="https://cloud.r-project.org/"); q()' +R CMD INSTALL . + +[CLEAN] +detach("package:Seurat", unload = T) +remove.packages("Seurat") + +[RUN] +run = R --vanilla -e "testthat::test_file(\"testthat.R\"); q()" +binary = +nodes = 1 -- Gitee From 5482be06c204ff9c9a2d9759b2753fd8fb74fc0a Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 17:20:51 +0800 Subject: [PATCH 14/58] Add templates app scanpy-1.10.3 --- .../scanpy/1.10.3/scanpy.arm.py39.config | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 templates/scanpy/1.10.3/scanpy.arm.py39.config diff --git a/templates/scanpy/1.10.3/scanpy.arm.py39.config b/templates/scanpy/1.10.3/scanpy.arm.py39.config new file mode 100644 index 0000000..a00150d --- /dev/null +++ b/templates/scanpy/1.10.3/scanpy.arm.py39.config @@ -0,0 +1,40 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +scanpy/1.10.3 https://files.pythonhosted.org/packages/09/b0/fa244677155c5535ea1458214e9ab6e2d571ba0f64f2cca00ad0ef0d03fe/scanpy-1.10.3.tar.gz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install python3/3.9.9 bisheng +module load python3/3.9.9 + +tar -zxvf ${JARVIS_DOWNLOAD}/scanpy-1.10.3.tar.gz -C ${JARVIS_TMP_DOWNLOAD} + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load python3/3.9.9 + +[APP] +app_name = scanpy +build_dir = ${JARVIS_TMP_DOWNLOAD}/scanpy-1.10.3 +binary_dir = +case_dir = ${JARVIS_TMP_DOWNLOAD}/scanpy-1.10.3 + +[BUILD] +# pip>=21.3 +python3.9 -m pip install --upgrade pip==22.2.2 setuptools==68.2.2 setuptools-scm==8.0.4 +pip3 install '.[dev,test]' --trusted-host mirrors.huaweicloud.com -i https://mirrors.huaweicloud.com/repository/pypi/simple + +[CLEAN] +pip3 uninstall scanpy -y + +[RUN] +run = pytest +binary = tests/test_datasets.py +nodes = 1 -- Gitee From f99ff4c81ee6eaafff9ad696ea2744f5a453f635 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 17:27:07 +0800 Subject: [PATCH 15/58] Add templates app PyRosetta4 --- .../4/pyrosetta4.aarch64.py39.config | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 templates/PyRosetta/4/pyrosetta4.aarch64.py39.config diff --git a/templates/PyRosetta/4/pyrosetta4.aarch64.py39.config b/templates/PyRosetta/4/pyrosetta4.aarch64.py39.config new file mode 100644 index 0000000..5cb275a --- /dev/null +++ b/templates/PyRosetta/4/pyrosetta4.aarch64.py39.config @@ -0,0 +1,39 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +PyRosetta4/py39 https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python39.aarch64/PyRosetta4.Release.python39.aarch64.release-342.tar.bz2 + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install python3/3.9.9 bisheng +module load python3/3.9.9 + +tar -jxvf ${JARVIS_DOWNLOAD}/PyRosetta4.Release.python39.aarch64.release-342.tar.bz2 -C ${JARVIS_TMP_DOWNLOAD} +mv ${JARVIS_TMP_DOWNLOAD}/PyRosetta4.Release.python39.aarch64.release-342 ${JARVIS_TMP_DOWNLOAD}/PyRosetta4.py39 + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load python3/3.9.9 + +[APP] +app_name = pyrosetta +build_dir = ${JARVIS_TMP_DOWNLOAD}/PyRosetta4.py39/setup +binary_dir = +case_dir = ${JARVIS_TMP_DOWNLOAD}/PyRosetta4.py39/test + +[BUILD] +python3 setup.py install + +[CLEAN] +pip3 uninstall pyrosetta -y + +[RUN] +run = python3 +binary = T000_Imports.py +nodes = 1 -- Gitee From 0090c845627b9f3db264cd5a10d041eed5cc8fb9 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 17:31:01 +0800 Subject: [PATCH 16/58] Add templates app PWDFT-master --- .../master/pwdft.arm.bisheng.hmpi.config | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 templates/PWDFT/master/pwdft.arm.bisheng.hmpi.config diff --git a/templates/PWDFT/master/pwdft.arm.bisheng.hmpi.config b/templates/PWDFT/master/pwdft.arm.bisheng.hmpi.config new file mode 100644 index 0000000..db8fe22 --- /dev/null +++ b/templates/PWDFT/master/pwdft.arm.bisheng.hmpi.config @@ -0,0 +1,44 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +PWDFT/master ${JARVIS_PROXY}/ebylaska/PWDFT/archive/refs/heads/master.zip PWDFT-master.zip + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install hmpi/2.4.2 bisheng +module load hmpi/2.4.2 + +mkdir -p ${JARVIS_ROOT}/software/apps/pwdft/bin +unzip ${JARVIS_DOWNLOAD}/PWDFT-master.zip -d ${JARVIS_TMP_DOWNLOAD} + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load hmpi/2.4.2 + +[APP] +app_name = pwdft +build_dir = ${JARVIS_TMP_DOWNLOAD}/PWDFT-master +binary_dir = ${JARVIS_ROOT}/software/apps/pwdft/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/PWDFT-master/test + +[BUILD] +sed -ri 's/\-m64/\-mabi=lp64/g' Nwpw/CMakeLists.txt +sed -ri 's/\-mfpmath=sse//g' Nwpw/CMakeLists.txt +cmake -H. -Bbuild -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_Fortran_COMPILER=mpifort ./Nwpw +cd build/ +make +cp -ar pwdft ${JARVIS_ROOT}/software/apps/pwdft/bin/ + +[CLEAN] +rm -rf build + +[RUN] +run = mpirun --allow-run-as-root -np $(nproc) --mca btl ^openib +binary = pwdft eric0.nw +nodes = 1 -- Gitee From d92ab4ffc18ac6feb8cd3b131122079f7170a411 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 22 Apr 2025 17:35:12 +0800 Subject: [PATCH 17/58] Add templates app proteinmpnn-0.1.3 --- .../0.1.3/proteinmpnn.arm.py39.config | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 templates/proteinmpnn/0.1.3/proteinmpnn.arm.py39.config diff --git a/templates/proteinmpnn/0.1.3/proteinmpnn.arm.py39.config b/templates/proteinmpnn/0.1.3/proteinmpnn.arm.py39.config new file mode 100644 index 0000000..8293e6e --- /dev/null +++ b/templates/proteinmpnn/0.1.3/proteinmpnn.arm.py39.config @@ -0,0 +1,40 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +proteinmpnn/0.1.3 https://files.pythonhosted.org/packages/8c/5a/7451c7db78ae19ef856b47c286fadb17a84269ea727e120b91d05e44d840/proteinmpnn-0.1.3.tar.gz +ProteinMPNN/main ${JARVIS_PROXY}/dauparas/ProteinMPNN/archive/refs/tags/v1.0.1.tar.gz ProteinMPNN-1.0.1.tar.gz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install python3/3.9.9 bisheng +module load python3/3.9.9 + +tar -zxvf ${JARVIS_DOWNLOAD}/proteinmpnn-0.1.3.tar.gz -C ${JARVIS_TMP_DOWNLOAD} +tar -zxvf ${JARVIS_DOWNLOAD}/ProteinMPNN-1.0.1.tar.gz -C ${JARVIS_TMP_DOWNLOAD}/proteinmpnn-0.1.3/ --transform='s/ProteinMPNN-1.0.1/test_files/' + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load python3/3.9.9 + +[APP] +app_name = proteinmpnn +build_dir = ${JARVIS_TMP_DOWNLOAD}/proteinmpnn-0.1.3 +binary_dir = +case_dir = ${JARVIS_TMP_DOWNLOAD}/proteinmpnn-0.1.3/test_files + +[BUILD] +python3 setup.py install + +[CLEAN] +pip3 uninstall proteinmpnn -y + +[RUN] +run = proteinmpnn +binary = --jsonl-path outputs/example_1_outputs/parsed_pdbs.jsonl --out-folder outputs/example_1_outputs/ --num-seq-per-target 2 --sampling-temp "0.1" --seed 3 --batch-size 1 +nodes = 1 -- Gitee From 8cfdf8a269b1deb7900c98e84b2ab3c34f6b53a6 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Wed, 23 Apr 2025 14:23:42 +0800 Subject: [PATCH 18/58] Update package udunits-2.2.28 --- package/udunits/2.2.28/install.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package/udunits/2.2.28/install.sh b/package/udunits/2.2.28/install.sh index da426de..15ec822 100644 --- a/package/udunits/2.2.28/install.sh +++ b/package/udunits/2.2.28/install.sh @@ -1,11 +1,12 @@ #!/bin/bash set -x set -e -. ${DOWNLOAD_TOOL} -u https://artifacts.unidata.ucar.edu/repository/downloads-udunits/2.2.28/udunits-2.2.28.tar.gz +. ${DOWNLOAD_TOOL} -u https://downloads.unidata.ucar.edu/udunits/2.2.28/udunits-2.2.28.tar.gz cd ${JARVIS_TMP} rm -rf udunits-2.2.28 tar xvf ${JARVIS_DOWNLOAD}/udunits-2.2.28.tar.gz cd udunits-2.2.28 +yum install -y expat-devel ./configure --prefix=$1 make -j make install -- Gitee From e3d65098bc5f6d5fea2bdc21e34f9cd238aa6a27 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Wed, 23 Apr 2025 14:56:35 +0800 Subject: [PATCH 19/58] Add templates app NOVOPlasty-4.3.1 --- .../NOVOPlasty/4.3.1/novoplasty.arm.config | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 templates/NOVOPlasty/4.3.1/novoplasty.arm.config diff --git a/templates/NOVOPlasty/4.3.1/novoplasty.arm.config b/templates/NOVOPlasty/4.3.1/novoplasty.arm.config new file mode 100644 index 0000000..062f05b --- /dev/null +++ b/templates/NOVOPlasty/4.3.1/novoplasty.arm.config @@ -0,0 +1,29 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +NOVOPlasty/4.3.1 ${JARVIS_PROXY}/ndierckx/NOVOPlasty/archive/refs/tags/NOVOPlasty4.3.1.tar.gz + +[DEPENDENCY] +module purge +mkdir -p ${JARVIS_ROOT}/software/app +tar -zxvf ${JARVIS_DOWNLOAD}/NOVOPlasty4.3.1.tar.gz -C ${JARVIS_ROOT}/software/app --transform='s/NOVOPlasty-NOVOPlasty4.3.1/NOVOPlasty/' + +[ENV] +module purge + +[APP] +app_name = NOVOPlasty +build_dir = ${JARVIS_ROOT}/software/app/NOVOPlasty/ +binary_dir = ${JARVIS_ROOT}/software/app/NOVOPlasty/ +case_dir = ${JARVIS_ROOT}/software/app/NOVOPlasty/Test\ datasets/Chloroplast\ assembly/ + +[BUILD] +chmod +x NOVOPlasty4.3.1.pl + +[CLEAN] + +[RUN] +run = perl +binary = NOVOPlasty4.3.1.pl -c config_test_chloro.txt +nodes = 1 -- Gitee From 2922b2f9af3c1301eafb3817380b44a036bd279e Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Wed, 23 Apr 2025 15:01:53 +0800 Subject: [PATCH 20/58] Add package app R-4.4.3 --- package/R/4.4.3/install.sh | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 package/R/4.4.3/install.sh diff --git a/package/R/4.4.3/install.sh b/package/R/4.4.3/install.sh new file mode 100644 index 0000000..4aa0d65 --- /dev/null +++ b/package/R/4.4.3/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +. $CHECK_ROOT && yum install -y libXt-devel readline-devel texinfo texlive texlive-inconsolata +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://cloud.r-project.org/src/base/R-4/R-4.4.3.tar.gz +cd ${JARVIS_TMP} +tar -xvf ${JARVIS_DOWNLOAD}/R-4.4.3.tar.gz +cd R-4.4.3 +./configure --prefix=$1 -enable-R-shlib --with-libpng --with-jpeglib +make all -j +make install -- Gitee From cf81e99dcb76c555a7a71b228c7406df877d7b68 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Thu, 24 Apr 2025 15:34:53 +0800 Subject: [PATCH 21/58] Add templates app monocle3-1.3.7 --- .../1.3.7/monocle3.arm.bisheng.hmpi.R.config | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 templates/monocle3/1.3.7/monocle3.arm.bisheng.hmpi.R.config diff --git a/templates/monocle3/1.3.7/monocle3.arm.bisheng.hmpi.R.config b/templates/monocle3/1.3.7/monocle3.arm.bisheng.hmpi.R.config new file mode 100644 index 0000000..6508de5 --- /dev/null +++ b/templates/monocle3/1.3.7/monocle3.arm.bisheng.hmpi.R.config @@ -0,0 +1,75 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +monocle3/master ${JARVIS_PROXY}/cole-trapnell-lab/monocle3/archive/refs/heads/master.zip monocle3-master.zip + +[DEPENDENCY] +yum install -y libgit2-devel freetype-devel fontconfig-devel libtiff-devel geos-devel libXext-devel harfbuzz-devel fribidi-devel libjpeg-turbo-devel +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install hmpi/2.4.2 bisheng +module load hmpi/2.4.2 +./jarvis -install libjpeg/v9b bisheng+mpi +module load libjpeg/v9b +./jarvis -install libpng/1.6.37 bisheng+mpi +module load libpng/1.6.37 +./jarvis -install proj/5.2.0 bisheng+mpi +module load proj/5.2.0 +./jarvis -install gdal/2.2.4 bisheng+mpi +module load gdal/2.2.4 +./jarvis -install udunits/2.2.28 bisheng+mpi +module load udunits/2.2.28 +./jarvis -install pixman/0.38.0 bisheng+mpi +module load pixman/0.38.0 +export PKG_CONFIG_PATH=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/pixman/0.38.0/lib/pkgconfig:$PKG_CONFIG_PATH +./jarvis -install cairo/1.16.0 bisheng+mpi +module load cairo/1.16.0 +export PKG_CONFIG_PATH=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/cairo/1.16.0/lib/pkgconfig:$PKG_CONFIG_PATH +./jarvis -install R/4.4.3 bisheng+mpi +module load R/4.4.3 + +unzip ${JARVIS_DOWNLOAD}/monocle3-master.zip -d ${JARVIS_TMP_DOWNLOAD} + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load hmpi/2.4.2 +module load libjpeg/v9b +module load libpng/1.6.37 +module load proj/5.2.0 +module load gdal/2.2.4 +module load udunits/2.2.28 +module load pixman/0.38.0 +export PKG_CONFIG_PATH=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/pixman/0.38.0/lib/pkgconfig:$PKG_CONFIG_PATH +module load cairo/1.16.0 +export PKG_CONFIG_PATH=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/cairo/1.16.0/lib/pkgconfig:$PKG_CONFIG_PATH +module load R/4.4.3 + +[APP] +app_name = monocle3 +build_dir = ${JARVIS_TMP_DOWNLOAD}/monocle3-master +binary_dir = +case_dir = ${JARVIS_TMP_DOWNLOAD}/monocle3-master/tests + +[BUILD] +R --vanilla -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager", repos="https://cloud.r-project.org/"); q()' +R --vanilla -e 'BiocManager::install(version = "3.20", ask=FALSE, update=TRUE); q()' +R --vanilla -e 'BiocManager::install("terra", configure.args="--with-proj-include=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/proj/5.2.0/include --with-proj-lib=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/proj/5.2.0/lib"); q()' +R --vanilla -e 'BiocManager::install("units", configure.args="--with-udunits2-lib=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/udunits/2.2.28/lib --with-udunits2-include=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/udunits/2.2.28/include"); q()' +R --vanilla -e 'BiocManager::install("sf", configure.args="--with-proj-include=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/proj/5.2.0/include --with-proj-lib=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/proj/5.2.0/lib"); q()' +R --vanilla -e 'BiocManager::install(c("BiocGenerics", "DelayedArray", "DelayedMatrixStats", "limma", "lme4", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "batchelor", "HDF5Array", "ggrastr")); q()' +R --vanilla -e 'install.packages(c("devtools", "testthat"), repos="https://cloud.r-project.org/"); q()' +R CMD INSTALL . + +[CLEAN] +detach("package:monocle3", unload = T) +remove.packages("monocle3") + +[RUN] +run = R --vanilla -e "testthat::test_file(\"testthat.R\"); q()" +binary = +nodes = 1 -- Gitee From 23cc8abcc05838f2d6a8ae8a310428829c308c34 Mon Sep 17 00:00:00 2001 From: Zerry <996002763@qq.com> Date: Mon, 14 Apr 2025 15:44:05 +0800 Subject: [PATCH 22/58] =?UTF-8?q?=E6=96=B0=E5=A2=9E=E8=BD=AF=E4=BB=B6vaspk?= =?UTF-8?q?it-0.52?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../0.52/data.vaspkit.arm-920.cpu.config | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 templates/vaspkit/0.52/data.vaspkit.arm-920.cpu.config diff --git a/templates/vaspkit/0.52/data.vaspkit.arm-920.cpu.config b/templates/vaspkit/0.52/data.vaspkit.arm-920.cpu.config new file mode 100644 index 0000000..c650cb9 --- /dev/null +++ b/templates/vaspkit/0.52/data.vaspkit.arm-920.cpu.config @@ -0,0 +1,49 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +vaspkit/0.52 https://sourceforge.net/projects/vaspkit/files/Src/vaspkit.0.52.tar.gz + +[DEPENDENCY] +yum install make cmake gcc g++ -y + +module purge +./jarvis -install bisheng/4.1.0 com +module use ./software/modulefiles +module load bisheng/4.1.0 +export CC=clang CXX=clang++ FC=flang + +cd ${JARVIS_TMP_DOWNLOAD} +rm -rf vaspkit-0.52 +tar -xzvf ${JARVIS_DOWNLOAD}/vaspkit.0.52.tar.gz + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 + +[APP] +app_name = vaspkit +build_dir = ${JARVIS_TMP_DOWNLOAD}/vaspkit.0.52/ +binary_dir = ${JARVIS_TMP_DOWNLOAD}vaspkit.0.52/src/ +case_dir = + +[BUILD] +sed -i "6c FC=flang" make.inc +sed -i "12c CC=clang" make.inc +cd src +make + +[CLEAN] +cd src +make clean + +[RUN] +run = +binary = vaspkit +nodes = 1 + +[PERF] +perf= +nsys= +ncu= -- Gitee From 073119341097ac57d4359788864eaa6425421e68 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Tue, 6 May 2025 11:38:43 +0800 Subject: [PATCH 23/58] 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 30983483fb3c4a79fc329b00da232b13186d3e62 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Tue, 6 May 2025 11:44:26 +0800 Subject: [PATCH 24/58] 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 ' 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 -- Gitee From f61130539bcf71db2ebc57e451d20f7c569410e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Tue, 6 May 2025 14:43:35 +0800 Subject: [PATCH 25/58] tensorflow --- .../2.4.1/data.tensorflow.arm.cpu.kgcc.config | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config 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 0000000..921f09a --- /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 + -- Gitee From b69b38c96f85d96eacad802f119cf55251003071 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Tue, 6 May 2025 20:05:49 +0800 Subject: [PATCH 26/58] code_aster --- .../code_aster/14.6.0/code_aster.arm.cpu.kgcc.hmpi.config | 5 ----- 1 file changed, 5 deletions(-) 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 index 059e320..6641f78 100644 --- 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 @@ -26,16 +26,12 @@ tar -xvf ${JARVIS_DOWNLOAD}/aster-full-src-14.6.0-1.noarch.tar.gz mkdir -p CODE-ASTER [ENV] -yum install -y vim tar git wget automake autoconf libtool make cmake module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module purge module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi export CC=`which gcc` export CXX=`which g++` export FC=`which gfortran` -yum -y install zlib* lapack* blas* python3.aarch64 python3-devel.aarch64 cmake3 boost-python* boost boost-devel numpy* python-numpy flex bison tcl tk -yum install -y lapack lapack-devel -yum install -y openblas openblas-devel [APP] app_name = code_aster @@ -74,7 +70,6 @@ cd .. echo y | python3 setup.py --prefix=${JARVIS_ROOT}/CODE-ASTER [CLEAN] -make clean [RUN] run = -- Gitee From ca8d7f05fa6e9ad69480b6eafaf761c0e83618f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Tue, 6 May 2025 20:11:22 +0800 Subject: [PATCH 27/58] abyss --- templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config | 2 -- 1 file changed, 2 deletions(-) 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 index 52d94b9..0363a04 100644 --- 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 @@ -27,13 +27,11 @@ 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` -- Gitee From 4acbb7005f5e1d6a0c1989cd0c5d8a7020bcf6f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Wed, 7 May 2025 11:08:31 +0800 Subject: [PATCH 28/58] tensorflow --- .../2.4.1/data.tensorflow.arm.cpu.kgcc.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) 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 index 921f09a..dd53461 100644 --- a/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config +++ b/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config @@ -24,7 +24,6 @@ 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 @@ -32,8 +31,6 @@ 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 @@ -43,7 +40,10 @@ case_dir = ${JARVIS_ROOT}/tensorflow-2.4.1/tensorflow/examples/speech_commands/ [BUILD] -#conda env remove -n tensorflow-2.4.1 +if conda env list | grep -wq "\btensorflow-2.4.1\b"; then + echo "环境 tensorflow-2.4.1 存在" + conda env remove -n tensorflow-2.4.1 +fi 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 @@ -66,7 +66,7 @@ pip install flatbuffers==23.5.9 [CLEAN] -make clean +./jarvis -CLS [RUN] run = conda activate tensorflow-2.4.1 && time python train.py -- Gitee From d60ba311b75518c6bafb0a55ec806a47c6d8d5e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Wed, 7 May 2025 11:26:12 +0800 Subject: [PATCH 29/58] copasi --- .../4.27.217/data.copasi.arm.kgcc.config | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 templates/copasi/4.27.217/data.copasi.arm.kgcc.config diff --git a/templates/copasi/4.27.217/data.copasi.arm.kgcc.config b/templates/copasi/4.27.217/data.copasi.arm.kgcc.config new file mode 100644 index 0000000..4993eae --- /dev/null +++ b/templates/copasi/4.27.217/data.copasi.arm.kgcc.config @@ -0,0 +1,61 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +copasi/4.27.217 https://codeload.github.com/copasi/COPASI/tar.gz/Build-217 COPASI-Build-217.tar.gz +copasi-dependencies/v4.26.213 https://codeload.github.com/copasi/copasi-dependencies/tar.gz/v4.26.213 v4.26.213 + +[DEPENDENCY] +set -e +set -x + +module purge +module use ./software/modulefiles +./jarvis -install kgcc/10.3.1 com +module load kgcc/10.3.1 +yum install qt.aarch64 qt-devel.aarch64 -y +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` +tar -vzxf ${JARVIS_DOWNLOAD}/COPASI-Build-217.tar.gz + +#wget https://codeload.github.com/copasi/copasi-dependencies/tar.gz/v4.26.213 +tar -xvf v4.26.213 +cd copasi-dependencies-4.26.213 +./createLinux.sh +cp -r ./bin/lib64/* ./bin/lib +cd .. + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` + +[APP] +app_name = copasi +build_dir = ${JARVIS_ROOT}/COPASI-Build-217/ +binary_dir = ${JARVIS_ROOT}/COPASI-Build-217/build/bin/ +case_dir = ${JARVIS_ROOT}/COPASI-Build-217/TestSuite/events + +[BUILD] +mkdir build +cd build +cmake -DBUILD_GUI=OFF -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/COPASI-Build-217/build -DCOPASI_DEPENDENCY_DIR=${JARVIS_ROOT}/copasi-dependencies-4.26.213/bin ../ +make install + + +[CLEAN] +make clean + +[RUN] +run = +binary = CopasiSE --nologo EventTest10.cps && cat EventTest10.1.txt +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all -- Gitee From 41d8c6328bb299559007c804691e190d48aeb95d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Wed, 7 May 2025 11:44:27 +0800 Subject: [PATCH 30/58] tensorflow --- .../tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) 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 index dd53461..e0885a0 100644 --- a/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config +++ b/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config @@ -11,9 +11,10 @@ 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 anaconda3/2023.3 +source ${ANACONDA3_PATH}/etc/profile.d/conda.sh +./jarvis -install kgcc/10.3.1 com module load kgcc/10.3.1 export CC=`which gcc` export CXX=`which g++` @@ -25,8 +26,9 @@ mkdir -p tensorflow [ENV] module purge -source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh module use software/modulefiles +module load anaconda3/2023.3 +source ${ANACONDA3_PATH}/etc/profile.d/conda.sh module load kgcc/10.3.1 export CC=`which gcc` export CXX=`which g++` -- Gitee From 6435cbad42f9dcade52ada5f9fdb1a38726b940d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Wed, 7 May 2025 14:38:06 +0800 Subject: [PATCH 31/58] tensorflow --- .../tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) 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 index e0885a0..dd53461 100644 --- a/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config +++ b/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config @@ -11,10 +11,9 @@ set -x yum install -y vim tar git wget module purge ./jarvis -install package/anaconda3/2023.3 any -module use software/modulefiles -module load anaconda3/2023.3 -source ${ANACONDA3_PATH}/etc/profile.d/conda.sh +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++` @@ -26,9 +25,8 @@ mkdir -p tensorflow [ENV] module purge +source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh module use software/modulefiles -module load anaconda3/2023.3 -source ${ANACONDA3_PATH}/etc/profile.d/conda.sh module load kgcc/10.3.1 export CC=`which gcc` export CXX=`which g++` -- Gitee From 4396dcbf2c56ad3e88d18eeb8231f7b9a2c0dd5e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Wed, 7 May 2025 14:44:28 +0800 Subject: [PATCH 32/58] copasi --- templates/copasi/4.27.217/data.copasi.arm.kgcc.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/copasi/4.27.217/data.copasi.arm.kgcc.config b/templates/copasi/4.27.217/data.copasi.arm.kgcc.config index 4993eae..7de696c 100644 --- a/templates/copasi/4.27.217/data.copasi.arm.kgcc.config +++ b/templates/copasi/4.27.217/data.copasi.arm.kgcc.config @@ -20,7 +20,7 @@ export FC=`which gfortran` tar -vzxf ${JARVIS_DOWNLOAD}/COPASI-Build-217.tar.gz #wget https://codeload.github.com/copasi/copasi-dependencies/tar.gz/v4.26.213 -tar -xvf v4.26.213 +tar -xvf ${JARVIS_DOWNLOAD}/v4.26.213 cd copasi-dependencies-4.26.213 ./createLinux.sh cp -r ./bin/lib64/* ./bin/lib -- Gitee From 4cfbd4e12b240036521d2255fe80d4b7f49f3fd4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Wed, 7 May 2025 15:15:36 +0800 Subject: [PATCH 33/58] copasi --- templates/copasi/4.27.217/data.copasi.arm.kgcc.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/copasi/4.27.217/data.copasi.arm.kgcc.config b/templates/copasi/4.27.217/data.copasi.arm.kgcc.config index 7de696c..970ebcf 100644 --- a/templates/copasi/4.27.217/data.copasi.arm.kgcc.config +++ b/templates/copasi/4.27.217/data.copasi.arm.kgcc.config @@ -13,7 +13,7 @@ module purge module use ./software/modulefiles ./jarvis -install kgcc/10.3.1 com module load kgcc/10.3.1 -yum install qt.aarch64 qt-devel.aarch64 -y +yum install qt.aarch64 qt-devel.aarch64 cmake make -y export CC=`which gcc` export CXX=`which g++` export FC=`which gfortran` -- Gitee From 21b45157c6061e2383f8ef133faa735edb4eff2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Thu, 8 May 2025 10:44:15 +0800 Subject: [PATCH 34/58] deepmd-kit --- .../2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config new file mode 100644 index 0000000..4fb22bb --- /dev/null +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -0,0 +1,60 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] + +[DEPENDENCY] +set -e +set -x + +./jarvis -install package/anaconda3/2023.3 any +source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh +./jarvis -install hpckit/2024.12.30 any +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 install -y cmake +mkdir -p deepmdkit_install +git clone -b v2.2.10 https://github.com/deepmodeling/deepmd-kit +cd deepmd-kit +pip install . +cd source +mkdir build + +[ENV] +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` + +[APP] +app_name = QE +build_dir = ${JARVIS_ROOT}/deepmd-kit/source/build/ +binary_dir = ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/envs/deepmd-kit-tensorflow/bin/ +case_dir = ${JARVIS_ROOT}/deepmd-kit/examples/water/se_e2_a/ + +[BUILD] +conda create -n deepmd-kit-tensorflow python=3.9 -y +conda activate deepmd-kit-tensorflow +conda install tensorflow -y +cmake -DTENSORFLOW_ROOT=${JARVIS_ROOT}/software/utils/anaconda3/2023.3/envs/deepmd-kit-tensorflow/lib/python3.9/site-packages/tensorflow -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/deepmdkit_install .. +make -j +make install + +[CLEAN] +make clean + +[RUN] +run = time +binary = dp train input.json +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all -- Gitee From f23568bd210b355c412e6be57096cbf04f78a6c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Thu, 8 May 2025 11:27:35 +0800 Subject: [PATCH 35/58] deepmd-kit --- .../deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index 4fb22bb..6fafd5e 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -7,11 +7,13 @@ set -e set -x +module purge ./jarvis -install package/anaconda3/2023.3 any +module use ./software/modulefiles +module load anaconda3/2023.3 source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh ./jarvis -install hpckit/2024.12.30 any -module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles -module purge +module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi export CC=`which gcc` export CXX=`which g++` -- Gitee From 10c2731301966c81fb1c562ee3f1f46c5ef8d29b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Thu, 8 May 2025 11:32:56 +0800 Subject: [PATCH 36/58] deepmd-kit --- .../deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index 6fafd5e..7a4d1c7 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -11,7 +11,7 @@ module purge ./jarvis -install package/anaconda3/2023.3 any module use ./software/modulefiles module load anaconda3/2023.3 -source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh +source ${ANACONDA3_PATH}/etc/profile.d/conda.sh ./jarvis -install hpckit/2024.12.30 any module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi @@ -37,14 +37,14 @@ export FC=`which gfortran` [APP] app_name = QE build_dir = ${JARVIS_ROOT}/deepmd-kit/source/build/ -binary_dir = ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/envs/deepmd-kit-tensorflow/bin/ +binary_dir = ${ANACONDA3_PATH}/envs/deepmd-kit-tensorflow/bin/ case_dir = ${JARVIS_ROOT}/deepmd-kit/examples/water/se_e2_a/ [BUILD] conda create -n deepmd-kit-tensorflow python=3.9 -y conda activate deepmd-kit-tensorflow conda install tensorflow -y -cmake -DTENSORFLOW_ROOT=${JARVIS_ROOT}/software/utils/anaconda3/2023.3/envs/deepmd-kit-tensorflow/lib/python3.9/site-packages/tensorflow -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/deepmdkit_install .. +cmake -DTENSORFLOW_ROOT=${ANACONDA3_PATH}/envs/deepmd-kit-tensorflow/lib/python3.9/site-packages/tensorflow -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/deepmdkit_install .. make -j make install -- Gitee From 956aa5e87044df4f7e908a2e97884743a62dd5b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Thu, 8 May 2025 14:37:06 +0800 Subject: [PATCH 37/58] deepmd-kit --- templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index 7a4d1c7..e543d55 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -35,7 +35,7 @@ export CXX=`which g++` export FC=`which gfortran` [APP] -app_name = QE +app_name = deepmd-kit build_dir = ${JARVIS_ROOT}/deepmd-kit/source/build/ binary_dir = ${ANACONDA3_PATH}/envs/deepmd-kit-tensorflow/bin/ case_dir = ${JARVIS_ROOT}/deepmd-kit/examples/water/se_e2_a/ -- Gitee From 28d0b2714e3294becfde37b523eed3239f52fea4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Thu, 8 May 2025 16:26:22 +0800 Subject: [PATCH 38/58] deepmd-kit --- .../deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index e543d55..23e72de 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -27,8 +27,11 @@ cd source mkdir build [ENV] -module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module purge +module use ./software/modulefiles +module load anaconda3/2023.3 +source ${ANACONDA3_PATH}/etc/profile.d/conda.sh +module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi export CC=`which gcc` export CXX=`which g++` -- Gitee From d2e6ce35007cc89dc97888e6188e00f7e68a086e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Thu, 8 May 2025 20:21:13 +0800 Subject: [PATCH 39/58] deepmd-kit --- .../2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index 23e72de..eebe9cd 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -7,10 +7,11 @@ set -e set -x +yum install -y cmake module purge -./jarvis -install package/anaconda3/2023.3 any +./jarvis -install package/anaconda3/2024.10 any module use ./software/modulefiles -module load anaconda3/2023.3 +module load anaconda3/2024.10 source ${ANACONDA3_PATH}/etc/profile.d/conda.sh ./jarvis -install hpckit/2024.12.30 any module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles @@ -18,18 +19,13 @@ 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 install -y cmake mkdir -p deepmdkit_install git clone -b v2.2.10 https://github.com/deepmodeling/deepmd-kit -cd deepmd-kit -pip install . -cd source -mkdir build [ENV] module purge module use ./software/modulefiles -module load anaconda3/2023.3 +module load anaconda3/2024.10 source ${ANACONDA3_PATH}/etc/profile.d/conda.sh module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi @@ -39,7 +35,7 @@ export FC=`which gfortran` [APP] app_name = deepmd-kit -build_dir = ${JARVIS_ROOT}/deepmd-kit/source/build/ +build_dir = ${JARVIS_ROOT}/deepmd-kit binary_dir = ${ANACONDA3_PATH}/envs/deepmd-kit-tensorflow/bin/ case_dir = ${JARVIS_ROOT}/deepmd-kit/examples/water/se_e2_a/ @@ -47,6 +43,10 @@ case_dir = ${JARVIS_ROOT}/deepmd-kit/examples/water/se_e2_a/ conda create -n deepmd-kit-tensorflow python=3.9 -y conda activate deepmd-kit-tensorflow conda install tensorflow -y +pip install . +cd source +mkdir build +cd build cmake -DTENSORFLOW_ROOT=${ANACONDA3_PATH}/envs/deepmd-kit-tensorflow/lib/python3.9/site-packages/tensorflow -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/deepmdkit_install .. make -j make install -- Gitee From 6007e234cbc9175199f99f526a3cc102559c06b1 Mon Sep 17 00:00:00 2001 From: xiaolinjunhao <981755938@qq.com> Date: Fri, 9 May 2025 00:35:46 +0800 Subject: [PATCH 40/58] =?UTF-8?q?=E4=BF=AE=E6=94=B9=E5=AD=98=E9=87=8F?= =?UTF-8?q?=E8=84=9A=E6=9C=AC=E9=94=99=E8=AF=AF=E5=91=BD=E5=90=8D?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../2.7.1a/{data.blat.arm.cpu.config => data.star.arm.cpu.config} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename templates/star/2.7.1a/{data.blat.arm.cpu.config => data.star.arm.cpu.config} (100%) diff --git a/templates/star/2.7.1a/data.blat.arm.cpu.config b/templates/star/2.7.1a/data.star.arm.cpu.config similarity index 100% rename from templates/star/2.7.1a/data.blat.arm.cpu.config rename to templates/star/2.7.1a/data.star.arm.cpu.config -- Gitee From 7df6344daf574ab2857d8a2a3e01c43ced53c057 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Fri, 9 May 2025 09:42:44 +0800 Subject: [PATCH 41/58] deepmd-kit --- templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 1 + 1 file changed, 1 insertion(+) diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index eebe9cd..546cc3d 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -40,6 +40,7 @@ binary_dir = ${ANACONDA3_PATH}/envs/deepmd-kit-tensorflow/bin/ case_dir = ${JARVIS_ROOT}/deepmd-kit/examples/water/se_e2_a/ [BUILD] +#conda clean --all --yes conda create -n deepmd-kit-tensorflow python=3.9 -y conda activate deepmd-kit-tensorflow conda install tensorflow -y -- Gitee From cd6a551d35a33bce3b3a3fcd7b0f87c75982bf3d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Fri, 9 May 2025 11:13:15 +0800 Subject: [PATCH 42/58] deepmd-kit --- .../2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index 546cc3d..357d0a2 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -11,8 +11,8 @@ yum install -y cmake module purge ./jarvis -install package/anaconda3/2024.10 any module use ./software/modulefiles -module load anaconda3/2024.10 -source ${ANACONDA3_PATH}/etc/profile.d/conda.sh +#module load anaconda3/2024.10 +source ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/etc/profile.d/conda.sh ./jarvis -install hpckit/2024.12.30 any module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi @@ -25,8 +25,8 @@ git clone -b v2.2.10 https://github.com/deepmodeling/deepmd-kit [ENV] module purge module use ./software/modulefiles -module load anaconda3/2024.10 -source ${ANACONDA3_PATH}/etc/profile.d/conda.sh +#module load anaconda3/2024.10 +source ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/etc/profile.d/conda.sh module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi export CC=`which gcc` @@ -36,7 +36,7 @@ export FC=`which gfortran` [APP] app_name = deepmd-kit build_dir = ${JARVIS_ROOT}/deepmd-kit -binary_dir = ${ANACONDA3_PATH}/envs/deepmd-kit-tensorflow/bin/ +binary_dir = ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/envs/deepmd-kit-tensorflow/bin/ case_dir = ${JARVIS_ROOT}/deepmd-kit/examples/water/se_e2_a/ [BUILD] @@ -48,7 +48,7 @@ pip install . cd source mkdir build cd build -cmake -DTENSORFLOW_ROOT=${ANACONDA3_PATH}/envs/deepmd-kit-tensorflow/lib/python3.9/site-packages/tensorflow -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/deepmdkit_install .. +cmake -DTENSORFLOW_ROOT=${JARVIS_ROOT}/software/utils/anaconda3/2024.10/envs/deepmd-kit-tensorflow/lib/python3.9/site-packages/tensorflow -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/deepmdkit_install .. make -j make install -- Gitee From 12be1482729f80f2717b92f848a91ee468900033 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Fri, 9 May 2025 16:34:08 +0800 Subject: [PATCH 43/58] deepmd-kit --- .../deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index 357d0a2..0e495d9 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -11,7 +11,6 @@ yum install -y cmake module purge ./jarvis -install package/anaconda3/2024.10 any module use ./software/modulefiles -#module load anaconda3/2024.10 source ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/etc/profile.d/conda.sh ./jarvis -install hpckit/2024.12.30 any module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles @@ -25,7 +24,6 @@ git clone -b v2.2.10 https://github.com/deepmodeling/deepmd-kit [ENV] module purge module use ./software/modulefiles -#module load anaconda3/2024.10 source ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/etc/profile.d/conda.sh module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi @@ -40,7 +38,6 @@ binary_dir = ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/envs/deepmd-kit-ten case_dir = ${JARVIS_ROOT}/deepmd-kit/examples/water/se_e2_a/ [BUILD] -#conda clean --all --yes conda create -n deepmd-kit-tensorflow python=3.9 -y conda activate deepmd-kit-tensorflow conda install tensorflow -y @@ -54,6 +51,7 @@ make install [CLEAN] make clean +conda clean --all --yes [RUN] run = time -- Gitee From b8b17dffd0f5458ea1369913d4a976620efbd04f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Fri, 9 May 2025 16:38:31 +0800 Subject: [PATCH 44/58] tensorflow --- templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 index dd53461..6278fb0 100644 --- a/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config +++ b/templates/tensorflow/2.4.1/data.tensorflow.arm.cpu.kgcc.config @@ -66,7 +66,7 @@ pip install flatbuffers==23.5.9 [CLEAN] -./jarvis -CLS +conda clean --all --yes [RUN] run = conda activate tensorflow-2.4.1 && time python train.py -- Gitee From 08f6804d26e39e3b25144dc63972e9003280b640 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Fri, 9 May 2025 18:00:24 +0800 Subject: [PATCH 45/58] diamond --- .../2.0.4/diamond.arm.cpu.bisheng.hmpi.config | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config diff --git a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config new file mode 100644 index 0000000..b82edfe --- /dev/null +++ b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config @@ -0,0 +1,69 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +diamond/2.0.4 https://github.com/bbuchfink/diamond/archive/v2.0.4.tar.gz diamond-2.0.4.tar.gz +swissprot http://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/swissprot.gz swissprot.gz +human_g1k_v37 http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz human_g1k_v37.fasta.gz + +[DEPENDENCY] +set -e +set -x + +yum install -y vim tar git wget make cmake +module purge +./jarvis -install bisheng/4.1.0 com +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 +tar -vzxf ${JARVIS_DOWNLOAD}/diamond-2.0.4.tar.gz +mkdir -p DIAMOND +mkdir -p TESTCASE +cp -r ${JARVIS_DOWNLOAD}/swissprot.gz ./TESTCASE +cp -r ${JARVIS_DOWNLOAD}/human_g1k_v37.fasta.gz ./TESTCASE +cd ./TESTCASE +gzip -dk swissprot.gz +gzip -dk human_g1k_v37.fasta.gz +split -l 1000000 human_g1k_v37.fasta human_g1k_part_ +cd .. + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` +module use ./software/moduledeps/bisheng4.1.0 +module load hmpi/2.4.2 + +[APP] +app_name = diamond +build_dir = ${JARVIS_ROOT}/diamond-2.0.4/ +binary_dir = ${JARVIS_ROOT}/DIAMOND/bin/ +case_dir = ${JARVIS_ROOT}/TESTCASE/ + +[BUILD] +mkdir build +cd build +cmake -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/DIAMOND ../ +make -j 16 +make install + +[CLEAN] +make clean + +[RUN] +run = +binary = diamond blastp -p 16 -q human_g1k_part_aa -d swissprot -o out_part_aa.tsv --very-sensitive +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all -- Gitee From 1c9acc06c697ed47a6d3d07a0681d1888b72c7bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Fri, 9 May 2025 18:10:50 +0800 Subject: [PATCH 46/58] diamond --- templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config index b82edfe..d2da120 100644 --- a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config +++ b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config @@ -28,7 +28,7 @@ cp -r ${JARVIS_DOWNLOAD}/swissprot.gz ./TESTCASE cp -r ${JARVIS_DOWNLOAD}/human_g1k_v37.fasta.gz ./TESTCASE cd ./TESTCASE gzip -dk swissprot.gz -gzip -dk human_g1k_v37.fasta.gz +gzip -dk human_g1k_v37.fasta.gz || true split -l 1000000 human_g1k_v37.fasta human_g1k_part_ cd .. -- Gitee From b0554618a2e3be083e26f9fbf7ede851910f31df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Mon, 12 May 2025 11:43:36 +0800 Subject: [PATCH 47/58] deepmd-kit --- templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config index 0e495d9..de43a14 100644 --- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config +++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config @@ -19,7 +19,7 @@ export CC=`which gcc` export CXX=`which g++` export FC=`which gfortran` mkdir -p deepmdkit_install -git clone -b v2.2.10 https://github.com/deepmodeling/deepmd-kit +git clone -b v2.2.10 https://github.com/deepmodeling/deepmd-kit #使用wget获取的v2.2.10.tar.gz文件缺少.git文件，安装的时候报错，只能使用git clone获取软件文件 [ENV] module purge -- Gitee From 7cc0ba68ec557add0651b682cfd41b8e8c777281 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Mon, 12 May 2025 14:30:47 +0800 Subject: [PATCH 48/58] diamond --- templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config | 1 + 1 file changed, 1 insertion(+) diff --git a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config index d2da120..33619c3 100644 --- a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config +++ b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config @@ -56,6 +56,7 @@ make -j 16 make install [CLEAN] +cd build make clean [RUN] -- Gitee From 6b59c2526ea00e07e52da2cd5ef83be40200c061 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Mon, 12 May 2025 15:06:02 +0800 Subject: [PATCH 49/58] Update templates app ARPS-5.3.4 --- package/hdf4/4.2.15/bisheng/install.sh | 28 ++++ templates/ARPS/5.3.4/data.arps.arm.cpu.config | 121 +++++++++--------- .../ARPS/5.3.4/data.arps.arm.cpu.sve.config | 72 ++++++----- 3 files changed, 127 insertions(+), 94 deletions(-) create mode 100755 package/hdf4/4.2.15/bisheng/install.sh mode change 100755 => 100644 templates/ARPS/5.3.4/data.arps.arm.cpu.config mode change 100755 => 100644 templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config diff --git a/package/hdf4/4.2.15/bisheng/install.sh b/package/hdf4/4.2.15/bisheng/install.sh new file mode 100755 index 0000000..4e6751f --- /dev/null +++ b/package/hdf4/4.2.15/bisheng/install.sh @@ -0,0 +1,28 @@ +#!/bin/bash +set -e +. ${DOWNLOAD_TOOL} -u https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.15/src/hdf-4.2.15.tar.gz +cd ${JARVIS_TMP} +rm -rf hdf-4.2.15 +tar -xvf ${JARVIS_DOWNLOAD}/hdf-4.2.15.tar.gz +cd hdf-4.2.15/ +yum install -y libtirpc-devel +sed -i '974c #if defined(__linux__) && defined __x86_64__ && !( defined SUN) || defined(__aarch64__)' hdf/src/hdfi.h +sed -i '23660a LIBS="$LIBS -ltirpc"' configure +sed -i '23662c CPPFLAGS="$SYSCPPFLAGS -I/usr/include/tirpc"' configure +sed -i 'N; s/\n\(static int32_t \*.*\)/ || defined __aarch64__\n\1/; P; D' mfhdf/libsrc/xdrposix.c +sed -i '/^\.c.lo:/{:a; $!N; /-MT/!ba; s/-MT/-std=c89 &/}' mfhdf/libsrc/Makefile.in +for file in \ + hdf/test/Makefile.in \ + hdf/util/Makefile.in \ + mfhdf/test/Makefile.in \ + mfhdf/ncdump/Makefile.in \ + mfhdf/ncgen/Makefile.in \ + mfhdf/hdfimport/Makefile.in \ + mfhdf/hdiff/Makefile.in +do + sed -i '/^\.c\.o:/{:a; $!N; /-MT/!ba; s/-MT/-std=c89 &/}' "$file" +done +export CC=mpicc CXX=mpicxx FC=mpifort +./configure --prefix=$1 --enable-production --with-zlib=/usr --enable-fortran --enable-hdf4-xdr --disable-shared --build=arm-linux --with-jpeg=${LIBJPEG_PATH} --disable-netcdf CFLAGS="-fPIC -Wno-error=int-conversion" CXXFLAGS="-fPIC" FFLAGS="-fPIC" LDFLAGS="-L/usr/lib64 -ltirpc" CPPFLAGS="-I/usr/include/tirpc" --build=aarch64-unknown-linux-gnu +make -j +make install diff --git a/templates/ARPS/5.3.4/data.arps.arm.cpu.config b/templates/ARPS/5.3.4/data.arps.arm.cpu.config old mode 100755 new mode 100644 index 48fcaf8..973a815 --- a/templates/ARPS/5.3.4/data.arps.arm.cpu.config +++ b/templates/ARPS/5.3.4/data.arps.arm.cpu.config @@ -1,59 +1,62 @@ -[SERVER] -11.11.11.11 - -[DOWNLOAD] -ARPS/5.3.4 https://arps.caps.ou.edu/ARPS/download/code/arps5.3.4.tar.gz - -[DEPENDENCY] -set -x -set -e -module purge -source ./HPCKit.env -export CC=`which mpicc` -export CXX=`which mpicxx` -export FC=`which mpifort` - -yum install hdf-devel.aarch64 -y -mkdir -p $JARVIS_ROOT/HDF4/bin -mkdir -p $JARVIS_ROOT/HDF4/lib -mkdir -p $JARVIS_ROOT/HDF4/include - -cp /usr/bin/hdf* $JARVIS_ROOT/HDF4/bin -cp /usr/lib64/hdf/* $JARVIS_ROOT/HDF4/lib -cp /usr/include/hdf/* $JARVIS_ROOT/HDF4/include - -export HDFPATH=$JARVIS_ROOT/HDF4 - -yum install -y libtirpc - -tar xzf $JARVIS_DOWNLOAD/arps5.3.4.tar.gz -#cd arps5.3.4 - -[ENV] -export HDFPATH=$JARVIS_ROOT/HDF4 - -[APP] -app_name = ARPS -build_dir = $JARVIS_ROOT/arps5.3.4 -binary_dir = -case_dir = - -[BUILD] -cd $JARVIS_ROOT/arps5.3.4 -sed -i '259s/ifort/mpifort/g' makearps -sed -i '3254s/-ffree-form/-ffree-form -Wno-argument-mismatch/g' makearps -sed -i 's/-fp-model source//g' makearps -sed -i 's/-C -P -traditional/-P -traditional/g' makearps -sed -i 's/-ljpeg/-ljpeg -ltirpc/g' makearps -sed -i 's/DIRECTORY/FILE/g' src/arps/lnxlib3d.F -which mpifort -./makearps -io hdf arps -./makearps -io hdf arps_mpi - -[CLEAN] -make clean - -[RUN] -run = -binary = -nodes = 1 +[SERVER] +11.11.11.11 + +[DOWNLOAD] +ARPS/5.3.4 https://arps.caps.ou.edu/ARPS/download/code/arps5.3.4.tar.gz + +[DEPENDENCY] +set -e +yum install -y tcsh libtirpc-devel libjpeg-turbo-devel +export LIBJPEG_PATH=/usr +module purge +module use ./software/modulefiles +./jarvis -install kgcc/10.3.1 com +module load kgcc/10.3.1 +./jarvis -install hmpi/2.4.2 gcc +module load hmpi/2.4.2 +./jarvis -install hdf4/4.2.15 gcc+mpi + +tar -zxvf ${JARVIS_DOWNLOAD}/arps5.3.4.tar.gz -C ${JARVIS_TMP_DOWNLOAD} +mkdir -p ${JARVIS_ROOT}/software/app/arps + +[ENV] +export LIBJPEG_PATH=/usr +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +module load hmpi/2.4.2 +export HDFPATH=${JARVIS_LIBS}/kgcc10.3.1/hmpi2.4.2/hdf4/4.2.15 + +[APP] +app_name = ARPS +build_dir = ${JARVIS_TMP_DOWNLOAD}/arps5.3.4 +binary_dir = ${JARVIS_ROOT}/software/app/arps/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/arps5.3.4/sounding + +[BUILD] +sed -i '259s/ifort/mpifort/g' makearps +sed -i 's/-fp-model source/-fallow-argument-mismatch/g' makearps +sed -i 's/-convert big_endian/-fconvert=big-endian/g' makearps +sed -i 's/-module /-J/g' makearps +sed -i 's/-ljpeg/-ljpeg -ltirpc/g' makearps +sed -i 's/-DINQUIREDIR//g' makearps +sed -i 's/-c module_precision.f90/-cpp -c module_precision.f90/g' src/arps/Makefile +sed -i 's/-c module_mp_wsm6.f90/-cpp -c module_mp_wsm6.f90/g' src/arps/Makefile +sed -i 's/-c lnxlib3d.f90/-cpp -c lnxlib3d.f90/g' src/arps/Makefile + +./makearps -io hdf arps +./makearps -io hdf arps_mpi + +cp -ar ./bin ./lib ./modules ${JARVIS_ROOT}/software/app/arps + +# nproc_x、nproc_y 乘积应与-np数相等 +sed -i '211s/nproc_x = 1/nproc_x = 2/g' ./input/arps.input +sed -i '212s/nproc_y = 1/nproc_y = 4/g' ./input/arps.input + +[CLEAN] +./makearps clean + +[RUN] +run = mpirun --allow-run-as-root -mca pml ucx -mca btl ^vader,tcp,openib,uct -x UCX_TLS=self,sm --bind-to core --map-by socket --rank-by core -x UCX_BUILTIN_ALLREDUCE_ALGORITHM=8 -np $(nproc) +binary = arps_mpi ../input/arps.input arps.output +nodes = 1 diff --git a/templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config b/templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config old mode 100755 new mode 100644 index 88640ba..822c79d --- a/templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config +++ b/templates/ARPS/5.3.4/data.arps.arm.cpu.sve.config @@ -5,57 +5,59 @@ ARPS/5.3.4 https://arps.caps.ou.edu/ARPS/download/code/arps5.3.4.tar.gz [DEPENDENCY] -set -x set -e +yum install -y tcsh libtirpc-devel libjpeg-turbo-devel +export LIBJPEG_PATH=/usr module purge -source ./HPCKit.env -export CC=`which mpicc` -export CXX=`which mpicxx` -export FC=`which mpifort` +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install hmpi/2.4.2 bisheng +module load hmpi/2.4.2 +./jarvis -install hdf4/4.2.15/bisheng bisheng+mpi -yum install hdf-devel.aarch64 -y -mkdir -p $JARVIS_ROOT/HDF4/bin -mkdir -p $JARVIS_ROOT/HDF4/lib -mkdir -p $JARVIS_ROOT/HDF4/include - -cp /usr/bin/hdf* $JARVIS_ROOT/HDF4/bin -cp /usr/lib64/hdf/* $JARVIS_ROOT/HDF4/lib -cp /usr/include/hdf/* $JARVIS_ROOT/HDF4/include - -export HDFPATH=$JARVIS_ROOT/HDF4 - -yum install -y libtirpc - -tar xzf $JARVIS_DOWNLOAD/arps5.3.4.tar.gz -#cd arps5.3.4 +tar -zxvf ${JARVIS_DOWNLOAD}/arps5.3.4.tar.gz -C ${JARVIS_TMP_DOWNLOAD} +mkdir -p ${JARVIS_ROOT}/software/app/arps [ENV] -export HDFPATH=$JARVIS_ROOT/HDF4 +export LIBJPEG_PATH=/usr +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load hmpi/2.4.2 +export HDFPATH=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/hdf4-bisheng/4.2.15 [APP] app_name = ARPS -build_dir = $JARVIS_ROOT/arps5.3.4 -binary_dir = -case_dir = +build_dir = ${JARVIS_TMP_DOWNLOAD}/arps5.3.4 +binary_dir = ${JARVIS_ROOT}/software/app/arps/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/arps5.3.4/sounding [BUILD] -cd $JARVIS_ROOT/arps5.3.4 sed -i '259s/ifort/mpifort/g' makearps -sed -i '3254s%-ffree-form%-ffree-form%g' makearps -sed -i 's%-w -convert big_endian%-w -convert big_endian -mtune=native -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true %g' makearps -sed -i 's%FFLAGS=%FFLAGS= -mtune=native -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true %g' makearps -sed -i 's/-fp-model source//g' makearps -sed -i 's/-C -P -traditional/-P -traditional/g' makearps +sed -i 's/-DINQUIREDIR//g' makearps sed -i 's/-ljpeg/-ljpeg -ltirpc/g' makearps -sed -i 's/DIRECTORY/FILE/g' src/arps/lnxlib3d.F -which mpifort +sed -i 's/-fp-model source/-mtune=native -mcpu=hip09 -mllvm -force-customized-pipeline=true/g' makearps +sed -i 's/-c module_precision.f90/-cpp -c module_precision.f90/g' src/arps/Makefile +sed -i 's/-c module_mp_wsm6.f90/-cpp -c module_mp_wsm6.f90/g' src/arps/Makefile +sed -i 's/-c lnxlib3d.f90/-cpp -c lnxlib3d.f90/g' src/arps/Makefile + ./makearps -io hdf arps ./makearps -io hdf arps_mpi +#查看是否使能SVE特性 +#objdump -d bin/arps_mpi | grep 'z0' + +cp -ar ./bin ./lib ./modules ${JARVIS_ROOT}/software/app/arps + +# nproc_x、nproc_y 乘积应与-np数相等 +sed -i '211s/nproc_x = 1/nproc_x = 2/g' ./input/arps.input +sed -i '212s/nproc_y = 1/nproc_y = 4/g' ./input/arps.input [CLEAN] -make clean +./makearps clean [RUN] -run = -binary = +# need CPU 7270Z and higher +run = mpirun --allow-run-as-root -mca pml ucx -mca btl ^vader,tcp,openib,uct -x UCX_TLS=self,sm --bind-to core --map-by socket --rank-by core -x UCX_BUILTIN_ALLREDUCE_ALGORITHM=8 -np $(nproc) +binary = arps_mpi ../input/arps.input arps.output nodes = 1 -- Gitee From 093d8d62e2705864fcf39fdd1a31c9ad5cfc38c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Mon, 12 May 2025 16:31:49 +0800 Subject: [PATCH 50/58] espressomd --- ...ata.espressomd.arm.cpu.bisheng.hmpi.config | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config diff --git a/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config b/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config new file mode 100644 index 0000000..6ff19fc --- /dev/null +++ b/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config @@ -0,0 +1,76 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +ESPResSo/4.1.4 https://github.com/espressomd/espresso/releases/download/4.1.4/espresso-4.1.4.tar.gz +boost/1.72.0 https://nchc.dl.sourceforge.net/project/boost/boost/1.72.0/boost_1_72_0.tar.bz2 + +[DEPENDENCY] +set -e +set -x + +yum install zlib-devel git cmake make git vim tar time glibc-headers gcc-c++ -y +yum install fftw-devel fftw3-devel -y +yum install libxml2-devel libxslt-devel cmake -y +pip install numpy --upgrade --force-reinstall +pip3 install cython +sudo dnf install python3-devel -y +./jarvis -install hpckit/2024.12.30 any +module use ./software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi +export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` +./jarvis -install fftw/3.3.8 clang+mpi +module use ./software/moduledeps/bisheng4.1.0-hmpi2.4.3 +module load fftw/3.3.8 +tar -vzxf ${JARVIS_DOWNLOAD}/espresso-4.1.4.tar.gz +tar -xf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.bz2 +mkdir -p boost/1_72_0 +cd boost_1_72_0/ +sed -i "60c #ifdef PTHREAD_STACK_MIN" boost/thread/pthread/thread_data.hpp +sed -i "61c \\\tif (size(PTHREAD_STACK_MIN)) size=PTHREAD_STACK_MIN;" boost/thread/pthread/thread_data.hpp +sed -i "59c #if 1" boost/mpl/aux_/integral_wrapper.hpp +./bootstrap.sh --with-toolset=clang --prefix=${JARVIS_ROOT}/boost/1_72_0 +sed -i '$ a\using mpi : mpicxx ;' project-config.jam +./b2 install --prefix=${JARVIS_ROOT}/boost/1_72_0 toolset=clang +export Boost_INCLUDE_PATH=${JARVIS_ROOT}/boost/1_72_0/include + + +[ENV] +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi +export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` +module use ./software/moduledeps/bisheng4.1.0-hmpi2.4.3 +module load fftw/3.3.8 + +[APP] +app_name = espresso +build_dir = ${JARVIS_ROOT}/espresso/ +binary_dir = +case_dir = ${JARVIS_ROOT}/espresso/build/ + +[BUILD] +sed -i "25i\SET(CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH} \"${JARVIS_ROOT}/software/libs/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/include\")" cmake/FindFFTW3.cmake +sed -i "26i\SET(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} \"${JARVIS_ROOT}/software/libs/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/lib\")" cmake/FindFFTW3.cmake +mkdir build +cd build +cmake .. -DBOOST_ROOT=${JARVIS_ROOT}/boost/1_72_0 -DBoost_INCLUDE_DIR=${JARVIS_ROOT}/boost/1_72_0/include +make + +[CLEAN] +make clean + +[RUN] +run = { time -p mpirun --allow-run-as-root -np 8 -mca pml ucx -mca btl ^vader,tcp,openib,uct -x UCX_TLS=self,sm --bind-to core --map-by socket --rank-by core -x UCX_BUILTIN_ALLREDUCE_ALGORITHM=8 ./pypresso ../samples/constraints.py > run.log ;} 2>>run.log && cat run.log +binary = +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all -- Gitee From 5e9c4e66b417c6e0d1ddd62ae60e9bc2b38f8544 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Tue, 13 May 2025 16:34:57 +0800 Subject: [PATCH 51/58] espressomd --- .../4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config b/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config index 6ff19fc..9b3a939 100644 --- a/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config +++ b/templates/espressomd/4.1.4/data.espressomd.arm.cpu.bisheng.hmpi.config @@ -12,7 +12,7 @@ set -x yum install zlib-devel git cmake make git vim tar time glibc-headers gcc-c++ -y yum install fftw-devel fftw3-devel -y yum install libxml2-devel libxslt-devel cmake -y -pip install numpy --upgrade --force-reinstall +pip3 install numpy --upgrade --force-reinstall pip3 install cython sudo dnf install python3-devel -y ./jarvis -install hpckit/2024.12.30 any -- Gitee From d5c968d0f99623acb8757fae54dea88316ed0f1d Mon Sep 17 00:00:00 2001 From: chenshaoheng Date: Tue, 20 May 2025 08:08:56 +0000 Subject: [PATCH 52/58] update templates/qe/7.3/data.qe-common.arm.cpu.config. Signed-off-by: chenshaoheng --- templates/qe/7.3/data.qe-common.arm.cpu.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/qe/7.3/data.qe-common.arm.cpu.config b/templates/qe/7.3/data.qe-common.arm.cpu.config index 72e6715..25a3f37 100644 --- a/templates/qe/7.3/data.qe-common.arm.cpu.config +++ b/templates/qe/7.3/data.qe-common.arm.cpu.config @@ -25,7 +25,7 @@ export LAPACK_PATH=$KML_LIB/sve export KM_LIB=$KML_LIB/noarch export BLAS_LIBS="-L$BLAS_PATH -lkblas" -export LAPACK_LIBS="-L$LAPACK_PATH $KM_LIB -lkm -lkscalapack_full -lklapack_full" +export LAPACK_LIBS="-L$LAPACK_PATH -L$KM_LIB -lkm -lkscalapack_full -lklapack_full" export PATH=${JARVIS_LIBS}/bisheng4.1.0/qe/7.3/bin:$PATH export LD_LIBRARY_PATH=$LAPACK_PATH:$KM_LIB:$BLAS_PATH:$LD_LIBRARY_PATH -- Gitee From baa51282fbceb9ace688c6d1704343d6b5161d67 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 20 May 2025 08:26:59 +0000 Subject: [PATCH 53/58] add package/hpckit. Signed-off-by: cfmin <1163105507@qq.com> --- package/hpckit/2025.03.30 | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 package/hpckit/2025.03.30 diff --git a/package/hpckit/2025.03.30 b/package/hpckit/2025.03.30 new file mode 100644 index 0000000..e69de29 -- Gitee From 67e1573acc4588067c46f10d7b3ec842bcb8d4a1 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 20 May 2025 08:27:33 +0000 Subject: [PATCH 54/58] =?UTF-8?q?=E5=88=A0=E9=99=A4=E6=96=87=E4=BB=B6=20pa?= =?UTF-8?q?ckage/hpckit/2025.03.30?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- package/hpckit/2025.03.30 | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 package/hpckit/2025.03.30 diff --git a/package/hpckit/2025.03.30 b/package/hpckit/2025.03.30 deleted file mode 100644 index e69de29..0000000 -- Gitee From 2e82b8c4048b84ae018d7758d69ccaf9901c68ec Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 20 May 2025 08:27:46 +0000 Subject: [PATCH 55/58] =?UTF-8?q?=E6=96=B0=E5=BB=BA=202025.3.30?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- package/hpckit/2025.3.30/.keep | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 package/hpckit/2025.3.30/.keep diff --git a/package/hpckit/2025.3.30/.keep b/package/hpckit/2025.3.30/.keep new file mode 100644 index 0000000..e69de29 -- Gitee From d6a89edfc2bcaaea8166e5adfdd169378c920c2c Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 20 May 2025 08:28:18 +0000 Subject: [PATCH 56/58] =?UTF-8?q?=E9=87=8D=E5=91=BD=E5=90=8D=20package/hpc?= =?UTF-8?q?kit/2025.3.30/.keep=20=E4=B8=BA=20package/hpckit/2025.3.30/inst?= =?UTF-8?q?all.sh?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- package/hpckit/2025.3.30/{.keep => install.sh} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename package/hpckit/2025.3.30/{.keep => install.sh} (100%) diff --git a/package/hpckit/2025.3.30/.keep b/package/hpckit/2025.3.30/install.sh similarity index 100% rename from package/hpckit/2025.3.30/.keep rename to package/hpckit/2025.3.30/install.sh -- Gitee From 8ea615df0f4729ae4da2656c056ee88fab75f8a6 Mon Sep 17 00:00:00 2001 From: cfmin <1163105507@qq.com> Date: Tue, 20 May 2025 08:28:59 +0000 Subject: [PATCH 57/58] update package/hpckit/2025.3.30/install.sh Signed-off-by: cfmin <1163105507@qq.com> --- package/hpckit/2025.3.30/install.sh | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/package/hpckit/2025.3.30/install.sh b/package/hpckit/2025.3.30/install.sh index e69de29..776f800 100644 --- a/package/hpckit/2025.3.30/install.sh +++ b/package/hpckit/2025.3.30/install.sh @@ -0,0 +1,4 @@ +#!/bin/bash +set -e +export hpckit_ver="25.0.0" +../meta.sh $1 \ No newline at end of file -- Gitee From caf6f6ba7d6e1dbb5f64be12ccb34e77f984a0b2 Mon Sep 17 00:00:00 2001 From: xgitee666 Date: Fri, 23 May 2025 14:58:52 +0800 Subject: [PATCH 58/58] =?UTF-8?q?=E6=B5=8B=E8=AF=95?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3a2fa7c..f800e16 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ ## ***愿景：自动容器化助力极简部署，一站式调优HPC应用*** ![贾维斯](./images/jarvis-logo.png) ### 项目背景 - +# ​ HPC被喻为是IT行业“金字塔上的明珠”，其部署、编译、运行、性能采集分析的门槛非常高，不同的机器上部署HPC应用耗费大量精力，而且很多情况下需要同时部署ARM/X86两套环境进行验证，增加了很多的重复性工作，无法聚焦核心算法优化。 ![贾维斯功能概览](./images/jarvis.png) -- Gitee