diff --git a/templates/OpenMolcas/master/openmolcas.arm.kgcc.config b/templates/OpenMolcas/master/openmolcas.arm.kgcc.config new file mode 100644 index 0000000000000000000000000000000000000000..adc2b23ed062130eefaf94829836c98aa26296d6 --- /dev/null +++ b/templates/OpenMolcas/master/openmolcas.arm.kgcc.config @@ -0,0 +1,42 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +OpenMolcas/master + +[DEPENDENCY] +module purge +./jarvis -install hpckit/2024.12.30 any +module use ./software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles +module load gcc/compiler12.3.1/gccmodule + +mkdir -p ${JARVIS_ROOT}/software/app/openmolcas +git clone https://github.com/Molcas/OpenMolcas.git ${JARVIS_TMP_DOWNLOAD}/OpenMolcas + +[ENV] +module purge +module use ./software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles +module load gcc/compiler12.3.1/gccmodule + +[APP] +app_name = openmolcas +build_dir = ${JARVIS_TMP_DOWNLOAD}/OpenMolcas +binary_dir = ${JARVIS_ROOT}/software/app/openmolcas +case_dir = ${JARVIS_TMP_DOWNLOAD}/OpenMolcas/build/ + +[BUILD] +git submodule update --init External/lapack +rm -rf build/ +mkdir build +cd build/ +cmake .. -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/app/openmolcas/ +make +make install + +[CLEAN] +make clean + +[RUN] +run = +binary = pymolcas verify +nodes = 1 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 0000000000000000000000000000000000000000..db8fe22a56989562786000e9c0ecace9872996ef --- /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 diff --git a/templates/PyRosetta/4/pyrosetta4.aarch64.py39.config b/templates/PyRosetta/4/pyrosetta4.aarch64.py39.config new file mode 100644 index 0000000000000000000000000000000000000000..5cb275ab64d83d9a87ecc4516856199afac2a6c4 --- /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 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 0000000000000000000000000000000000000000..b1cca30e713d7a0f448769d5a79dd5382cac260f --- /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 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 0000000000000000000000000000000000000000..f01fd319aa250cb3500e0d4b130d4d89f62a6656 --- /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 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 0000000000000000000000000000000000000000..04e4a2d9258dae9874ce44947f3fc20ed074047d --- /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 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 0000000000000000000000000000000000000000..8293e6e852622a1aaaefa867dd6772fc9842e79c --- /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 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 0000000000000000000000000000000000000000..a00150db13ec0d8c0359e97208db1e77351516e3 --- /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