def singleStageBuild(stage): stage += label(metadata={'MAINTAINER': 'Simeon Ehrig'}) stage += label(metadata={'EMAIL': '*****@*****.**'}) stage += label(metadata={'Version': str(container_version)}) stage += environment(variables={'GOL_VERSION': str(container_version)}) # copy example inside container stage += copy(src='notebook', dest='/') # copy and build the pnwriter library stage += copy(src='pngwriter', dest='/opt') stage += packages(ospackages=['libpng-dev']) cmake = CMakeBuild(prefix='/notebook/pngwriter') stage += shell(commands=[ cmake.configure_step(directory='/opt/pngwriter', opts=['-DBUILD_SHARED_LIBS=ON']), cmake.build_step(target='install'), 'rm -rf /opt/pngwriter' ]) # Copy notebook examples and pngwriter lib to the host's /tmp file system to obtain a writable file system. stage += runscript(commands=[ 'if [ ! -d /tmp/GOL-xeus-cling-cuda ]; then \n' ' mkdir /tmp/GOL-xeus-cling-cuda &&' ' cp -r /notebook/ /tmp/GOL-xeus-cling-cuda\n fi', 'cd /tmp/GOL-xeus-cling-cuda/notebook', 'jupyter-lab' ]) print(stage.__str__())
def recipe() -> str: """Generate the recipe :returns: singularity recipe :rtype: str """ hpccm.config.set_container_format('singularity') hpccm.config.set_singularity_version('3.3') stage = hpccm.Stage() stage += label(metadata={'CLING ALPAKA VERSION': str(version)}) stage += environment(variables={'CLING_ALPAKA_VERSION': version}) # the baseimage of xeus-cling-cuda is Ubuntu 16.04 with CUDA 8 if not ap_gn.add_alpaka_dep_layer(stage, '16.04', True, []): print('adding the alpaka dependencies layer failed', file=sys.stderr) exit(1) install_alpaka(stage) build_jupyter_kernel(stage) # baseimage support nothing else than dockerhub # so, manually add the baseimage command to the recipe recipe = stage.__str__() recipe = 'Bootstrap: library\nFrom: sehrig/default/xeus-cling-cuda-cxx:2.2\n\n' + recipe return recipe
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04', gpu=True, cuda_version='11.0', desktop=True): config.set_container_format(container_format) if gpu: image = f'nvcr.io/nvidia/cuda:{cuda_version}-devel-{os_release}{os_version}' else: image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={'maintainer': 'Luhan Cheng', 'email': '*****@*****.**'}) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) if gpu: stage0 += environment(variables=from_prefix('/usr/local/cuda')) stage0 += packages(apt=['wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev']) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) if desktop: stage0 += comment('Installing vglrun and TurboVNC') stage0 += packages(apt=['ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5', 'pyqt5-dev', 'python3-tk']) stage0 += shell(commands=[ 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb', 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb', 'apt update', 'apt -y upgrade' ]) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={'maintainer': 'Luhan Cheng', 'email': '*****@*****.**'}) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += packages(apt=['wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev']) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += packages(apt=['g++', 'clang', 'cmake', 'make', 'bison', 'flex', 'ronn', 'fuse3', 'pkg-config', 'binutils-dev', 'libarchive-dev', 'libboost-context-dev', 'libboost-filesystem-dev', 'libboost-program-options-dev', 'libboost-python-dev', 'libboost-regex-dev', 'libboost-system-dev', 'libboost-thread-dev', 'libevent-dev', 'libjemalloc-dev', 'libdouble-conversion-dev', 'libiberty-dev', 'liblz4-dev', 'liblzma-dev', 'libssl-dev', 'libunwind-dev', 'libdwarf-dev', 'libelf-dev', 'libfmt-dev', 'libfuse3-dev', 'libgoogle-glog-dev']) stage0 += generic_cmake( prefix='/usr/local/dwarfs', repository='https://github.com/mhx/dwarfs.git', branch='v0.5.5', recursive=True, cmake_opts=["-D WITH_TESTS=1"], ) stage0 += environment(variables=from_prefix('/usr/local/dwarfs')) return stage0
def build(image="Characterisation-Virtual-Laboratory/CharacterisationVL-Software:2004", _bootstrap='shub', mash_version='v2.2.2', capnp_version='0.8.0', quicktree_version='v2.5'): stage0 = hpccm.Stage() hpccm.config.set_container_format("singularity") stage0 += baseimage(image=image, _bootstrap=_bootstrap, _distro='ubuntu20') stage0 += label(metadata={'maintainer': 'Luhan Cheng', 'email': '*****@*****.**'}) stage0 += packages(ospackages=['cpanminus', 'libexpat1-dev', 'sqlite3', 'libsqlite3-dev', 'autoconf']) stage0 += generic_build( repository='https://github.com/khowe/quicktree', branch=quicktree_version, build=['make'], install=[ 'mv quicktree /usr/local/bin', 'mv include/* /usr/local/include/' ], ) stage0 += boost() stage0 += generic_autotools( url=f'https://capnproto.org/capnproto-c++-{capnp_version}.tar.gz' ) stage0 += shell(commands=['cpanm -l /usr/local/perl5 --notest BioPerl Bio::Sketch::Mash DBD::SQLite DBI']) stage0 += generic_autotools( repository=f'https://github.com/marbl/Mash', preconfigure=['./bootstrap.sh'], branch=mash_version, with_capnp='/usr/local/', with_boost='/usr/local/boost/', ) stage0 += environment(variables={'PERL5LIB': '$PERL5LIB:/usr/local', **from_prefix('/usr/local/mashtree')}) stage0 += shell(commands=['cpanm -f -l /usr/local/mashtree Mashtree']) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash' ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += conda(eula=True, channels=['defaults', 'conda-forge', 'bioconda'], packages=['python=3.6', 'nullarbor']) stage0 += environment(variables={'PATH': '/usr/local/anaconda/bin:$PATH'}) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04', gpu=True, cuda_version='11.0', desktop=True): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={'maintainer': 'Luhan Cheng', 'email': '*****@*****.**'}) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += packages(apt=['wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev', 'dirmngr', 'gpg-agent']) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += shell(commands=[ "wget -O- http://neuro.debian.net/lists/bionic.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list", "apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9 2>&1", ]) stage0 += packages(apt=["fsl-complete"]) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += comment('Installing vglrun and TurboVNC') stage0 += packages(apt=[ 'ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5', 'pyqt5-dev', 'python3-tk' ]) stage0 += shell(commands=[ 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb', 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb', 'apt update', 'apt -y upgrade' ]) # coin3d stage0 += packages(apt=[ 'mesa-common-dev', 'libglu1-mesa-dev', 'freeglut3-dev', 'autoconf', 'autogen', 'doxygen' ]) compiler = gnu(version="10") stage0 += compiler stage0 += boost() stage0 += generic_cmake( repository="https://github.com/coin3d/coin", recursive=True, cmake_opts=[ '-G "Unix Makefiles"', "-DCMAKE_BUILD_TYPE=Release", "-DCOIN_BUILD_DOCUMENTATION=OFF", "-DCMAKE_INSTALL_PREFIX=/usr/local/coin3d" ], postinstall=['cd cpack.d', 'cpack --config debian.cmake']) return stage0
def CVL_ubuntu_stage(gpu=False, stage_name='stage0'): image = "Characterisation-Virtual-Laboratory/CharacterisationVL-Software:2004" if not gpu else 'Characterisation-Virtual-Laboratory/CharacterisationVL-Software:2004-cuda11.0' stage0 = hpccm.Stage(name=stage_name) hpccm.config.set_container_format("singularity") stage0 += baseimage(image=image, _bootstrap='shub', _distro='ubuntu20') stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04', cuda_version='11.0'): config.set_container_format(container_format) image = f'nvcr.io/nvidia/cuda:{cuda_version}-devel-{os_release}{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += environment(variables=from_prefix('/usr/local/cuda')) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += comment('Installing vglrun and TurboVNC') stage0 += packages(apt=[ 'ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5', 'pyqt5-dev', 'python3-tk' ]) stage0 += shell(commands=[ 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb', 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb', 'apt update', 'apt -y upgrade' ]) stage0 += packages(apt=[ "qt5-qmake", 'qtmultimedia5-dev', 'libqt5multimediawidgets5', 'libqt5multimedia5-plugins', 'libqt5multimedia5', 'libglew-dev', 'glew-utils', 'libqglviewer-dev-qt5', 'libnetcdf-dev', 'libnetcdf-cxx-legacy-dev', 'freeglut3-dev', 'libassimp-dev' ]) stage0 += shell(commands=[ 'mkdir -p /opt/', "cd /opt", 'git clone --branch v-2.7linux https://github.com/nci/drishti.git', 'cd drishti/drishti', 'qmake -qt=5', 'export LDFLAGS="$LDFLAGS -L/usr/lib/x86_64-linux-gnu/ -lassimp"', 'ln -s /usr/lib/x86_64-linux-gnu/libQGLViewer-qt5.so /usr/lib/x86_64-linux-gnu/libQGLViewer.so', 'make' ]) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04', openmpi_version='3.1.6', gnu_version='10', ucx_version="1.12.1", cuda_version='11.0', gdrcopy_version="1.3", knem_version="1.1.3"): config.set_container_format(container_format) image = f'nvcr.io/nvidia/cuda:{cuda_version}-devel-{os_release}{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash' ]) stage0 += environment(variables=from_prefix('/usr/local/cuda')) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += gnu(version=gnu_version) stage0 += gdrcopy(version=gdrcopy_version, ldconfig=True) stage0 += knem(version=knem_version, ldconfig=True) stage0 += ucx(knem='/usr/local/knem', version=ucx_version, ldconfig=True) stage0 += openmpi(cuda=False, infiniband=True, version=openmpi_version, ucx="/usr/local/ucx", ldconfig=True) # stage0 += shell(commands=[ # f'mkdir -p {TESTCASE_DIR} && cd {TESTCASE_DIR}', # *[f'wget {i}' for i in TESTCASES], # 'for i in *;do echo $i;done' # ]) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', 'ln -s /usr/lib/x86_64-linux-gnu/libffi.so.7 /usr/lib/x86_64-linux-gnu/libffi.so.6' ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += comment('Installing vglrun and TurboVNC') stage0 += packages(apt=[ 'ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5', 'pyqt5-dev', 'python3-tk' ]) stage0 += shell(commands=[ 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb', 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb', 'apt update', 'apt -y upgrade' ]) stage0 += primitives.copy(src='./ChimeraX-1.2.5.tar.gz', dest='/opt/ChimeraX-1.2.5.tar.gz') stage0 += shell(commands=[ 'tar xfv /opt/ChimeraX-1.2.5.tar.gz -C /opt', 'rm /opt/ChimeraX-1.2.5.tar.gz' ]) stage0 += environment( variables=from_prefix('/opt/chimerax-1.2.5-rc-2021.05.24')) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={'maintainer': 'Luhan Cheng', 'email': '*****@*****.**'}) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += packages(apt=['wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev', 'bc', 'cmake', 'bison', 'flex', 'libx11-dev', 'x11proto-core-dev', 'libxi6', 'libxi-dev', 'libxmu6', 'libxmu-dev', 'libxmu-headers', 'libgl1-mesa-dev', 'libglu1-mesa-dev', 'libjpeg-dev', 'libevent-dev', 'libncurses-dev', 'pkg-config', 'libopenblas-dev']) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += comment('Installing vglrun and TurboVNC') stage0 += packages(apt=['ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5', 'pyqt5-dev', 'python3-tk']) stage0 += shell(commands=[ 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb', 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb', 'apt update', 'apt -y upgrade' ]) stage0 += generic_cmake( repository='https://github.com/BIC-MNI/minc-toolkit-v2.git', branch='release-1.9.18.1', recursive=True, prefix='/opt/minc/1.9.18', preconfigure=['sed -i -e \'s/http\:\/\/mirrors\.ibiblio\.org\/gnu\/ftp\/gnu\/gsl/http\:\/\/ftp\.\sun\.ac\.za\/ftp\/pub\/mirrors\/ftp\.gnu\.org\/gsl/g\' cmake-modules/BuildGSL.cmake', ], cmake_opts=['-DCMAKE_BUILD_TYPE:STRING=Release', '-DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.18', '-DMT_BUILD_ABC:BOOL=ON', '-DMT_BUILD_ANTS:BOOL=ON', '-DMT_BUILD_C3D:BOOL=ON', '-DMT_BUILD_ELASTIX:BOOL=ON', '-DMT_BUILD_IM:BOOL=OFF', '-DMT_BUILD_ITK_TOOLS:BOOL=ON', '-DMT_BUILD_LITE:BOOL=OFF', '-DMT_BUILD_SHARED_LIBS:BOOL=ON', '-DMT_BUILD_VISUAL_TOOLS:BOOL=ON', '-DMT_USE_OPENMP:BOOL=ON', '-DUSE_SYSTEM_FFTW3D:BOOL=OFF', '-DUSE_SYSTEM_FFTW3F:BOOL=OFF', '-DUSE_SYSTEM_GLUT:BOOL=OFF', '-DUSE_SYSTEM_GSL:BOOL=OFF', '-DUSE_SYSTEM_HDF5:BOOL=OFF', '-DUSE_SYSTEM_ITK:BOOL=OFF', '-DUSE_SYSTEM_NETCDF:BOOL=OFF', '-DUSE_SYSTEM_NIFTI:BOOL=OFF', '-DUSE_SYSTEM_PCRE:BOOL=OFF', '-DUSE_SYSTEM_ZLIB:BOOL=OFF'] ) stage0 += environment(variables=from_prefix('/opt/minc/1.9.18.1')) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += comment('Installing vglrun and TurboVNC') stage0 += packages(apt=[ 'ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5', 'pyqt5-dev', 'python3-tk', 'cmake', 'libgtk2.0-dev', 'libasound2-dev', 'libavformat-dev', 'libjack-jackd2-dev', 'uuid-dev' ]) stage0 += shell(commands=[ 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb', 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb', 'apt update', 'apt -y upgrade' ]) stage0 += shell(commands=['pip install conan']) stage0 += generic_cmake(repository='https://github.com/audacity/audacity/', branch='Audacity-3.0.5') return stage0
def build(container_format='singularity', gnu_version='9', fermi_lite_version='0.1', macs_version='3.0.0a5'): image = 'ubuntu:20.04' config.set_container_format(container_format) stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += packages(apt=[ 'wget', 'software-properties-common', 'build-essential', 'git', 'python-dev', 'zlib1g-dev' ]) compilers = gnu(version=gnu_version) stage0 += compilers stage0 += generic_build(repository='https://github.com/lh3/fermi-lite', branch=f'v{fermi_lite_version}', build=['make'], install=[ 'mkdir -p /usr/local/fermi_lite/', 'mv * /usr/local/fermi_lite/' ], toolchain=compilers.toolchain) stage0 += environment( variables={ 'PATH': '/usr/local/fermi_lite/:/usr/local/anaconda/bin:$PATH', 'LIBRARY_PATH': '/usr/local/fermi_lite/:$LIBRARY_PATH', 'C_INCLUDE_PATH': '/usr/local/fermi_lite/:$C_INCLUDE_PATH' }) stage0 += conda(packages=['python=3.8', 'numpy', 'cython', 'cykhash'], channels=['anaconda', 'conda-forge'], eula=True) stage0 += generic_build( repository='https://github.com/macs3-project/MACS.git', recursive=True, branch=f'v{macs_version}', build=['python3 setup.py install'], ) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={'maintainer': 'Luhan Cheng', 'email': '*****@*****.**'}) stage0 += shell(commands=['rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash']) stage0 += packages(apt=['wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev']) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += comment('Installing vglrun and TurboVNC') stage0 += packages(apt=['ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5', 'pyqt5-dev', 'python3-tk']) stage0 += shell(commands=[ 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb', 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb', 'apt update', 'apt -y upgrade' ]) stage0 += shell(commands=[ 'curl -sL https://deb.nodesource.com/setup_12.x | bash -', 'apt install -y nodejs npm' ]) prefix = '/var/www' stage0 += shell(commands=[ f'mkdir {prefix} && cd {prefix}', 'git clone --branch 1.16.10-release https://github.com/gmod/jbrowse .', './setup.sh', ]) stage0 += environment(variables={ 'PATH': f'{prefix}/bin:$PATH' }) stage0 += runscript(commands=[ f'cd {prefix}', 'npm run start $*' ]) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += packages(apt=[ 'perl', 'libmodule-install-perl', 'libxml-parser-perl', 'cpanminus' ]) stage0 += shell(commands=[ 'cpanm inc::latest', 'cpanm BioPerl Bio::SeqIO Getopt::Euclid List::Util Math::Random::MT version' ]) stage0 += shell(commands=[ 'wget https://sourceforge.net/projects/biogrinder/files/biogrinder/Grinder-0.5.4/Grinder-0.5.4.tar.gz && tar -xf Grinder-0.5.4.tar.gz && rm Grinder-0.5.4.tar.gz', 'cd Grinder-0.5.4', 'perl Makefile.PL', 'make', 'make install' ]) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04', conda_packages=['conda', 'numpy', 'scipy', 'pandas'], python_version='3.9.1', channels=['anaconda', 'defaults', 'conda-forge'], anaconda_version='4.9.2'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash' ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += conda(eula=True, packages=[f'python={python_version}'] + conda_packages, channels=channels, version=anaconda_version) stage0 += environment(variables=from_prefix('/usr/local/anaconda')) stage0 += runscript(commands=[ 'source /usr/local/anaconda/etc/profile.d/conda.sh', '/usr/local/anaconda/bin/python3 $*' ]) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={'maintainer': 'Luhan Cheng', 'email': '*****@*****.**'}) stage0 += shell(commands=['rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash']) stage0 += packages(apt=['wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev', 'perl', 'openssh-server', 'libssl-dev', 'gnuplot', 'globus-gridftp-server-progs', 'rsync', 'acl-dev']) stage0 += gnu(version='10') stage0 += shell(commands=[ 'yes | cpan Data::MessagePack', 'yes | cpan IO::Socket::SSL' ]) stage0 += generic_build( repository='https://github.com/eeertekin/bbcp.git', commit='64af832', prefix='/usr/local/bbcp/', build=['make -C src'], install=['mv bin/amd64_linux/bbcp /usr/local/bbcp/'] ) stage0 += environment(variables=add_binary('/usr/local/bbcp')) stage0 += generic_build( repository='https://github.com/pkolano/shift.git', commit='ffb7f5f', prefix='/usr/local/shift', directory='shift/c', build=['make nolustre'], install=['mdkir /usr/local/shift/bin && mv c/shift-bin /usr/local/shift/bin'] ) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04', cuda_version='11.0'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={'maintainer': 'Luhan Cheng', 'email': '*****@*****.**'}) stage0 += shell(commands=['rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash']) stage0 += packages(apt=['wget', 'git', 'software-properties-common', 'build-essential', 'locales']) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += comment('Installing vglrun and TurboVNC') stage0 += packages(apt=['ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5', 'pyqt5-dev', 'python3-tk']) stage0 += shell(commands=[ 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb', 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb', 'apt update', 'apt -y upgrade' ]) stage0 += conda( eula=True, packages=['python=3.8.5', 'openjdk', 'pip'], ) stage0 += environment(variables=from_prefix('/usr/local/anaconda')) stage0 += shell(commands=['pip install --upgrade minerl']) stage0 += shell(commands=[ 'wget https://launcher.mojang.com/download/Minecraft.deb && dpkg -i Minecraft.deb && rm Minecraft.deb', ]) stage0 += runscript(commands=['source /usr/local/anaconda/etc/profile.d/conda.sh', '/usr/local/anaconda/bin/python3 $*']) return stage0
def build(container_format='singularity', os='ubuntu20.04', cuda_version='11.0', openmpi_version='4.0.3', gnu_version='9.1.0'): baseimage = f'nvcr.io/nvidia/cuda:{cuda_version}-devel-{os}' config.set_container_format(container_format) stage0 = Stage(name='stage0') stage0 += primitives.baseimage(image=baseimage, _bootstrap='docker') stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) compilers = gnu( version=gnu_version, source=True, openacc=True, ) stage0 += openmpi(cuda=True, infiniband=False, version=openmpi_version, toolchain=compilers.toolchain) return stage0
def build(container_format='singularity', os='ubuntu:18.04'): image = os config.set_container_format(container_format) stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash' ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += shell(commands=[ 'cd /etc/apt/sources.list.d/', 'wget http://downloads.perfsonar.net/debian/perfsonar-release.list', 'wget -qO - http://downloads.perfsonar.net/debian/perfsonar-official.gpg.key | apt-key add -', 'add-apt-repository -y universe', 'apt-get update' ]) stage0 += packages(apt=[ 'perfsonar-tools', 'perfsonar-testpoint', 'perfsonar-core', 'perfsonar-centralmanagement', 'perfsonar-toolkit' ]) stage0 += shell( commands=['/usr/lib/perfsonar/scripts/install-optional-packages.py']) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04', cuda_version='11.0.3'): config.set_container_format(container_format) # image = f'{os_release}:{os_version}' image = f'nvcr.io/nvidia/cuda:{cuda_version}-devel-{os_release}{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += packages(apt=[ 'freeglut3-dev', 'build-essential', 'libx11-dev', 'libxmu-dev', 'libxi-dev', 'libglu1-mesa', 'libglu1-mesa-dev', 'mesa-utils', 'libgl1-mesa-glx' ]) stage0 += environment(variables=from_prefix('/usr/local/cuda')) stage0 += comment('Installing vglrun and TurboVNC') stage0 += packages(apt=[ 'ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5', 'pyqt5-dev', 'python3-tk' ]) stage0 += shell(commands=[ 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb', 'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb', 'apt update', 'apt -y upgrade' ]) stage0 += packages(apt=[ 'make', 'libopenmpi-dev', 'python3-tk', 'libfftw3-dev', 'libhdf5-dev', 'libtiff-dev', 'libjpeg-dev', 'libsqlite3-dev', 'openjdk-8-jdk' ]) stage0 += environment( variables={ 'LD_LIBRARY_PATH': "$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu/hdf5/serial", }) prefix = '/usr/local/scipion' stage0 += shell(commands=[ 'python3 -m pip install --user scipion-installer', f'python3 -m scipioninstaller {prefix} -j 4' ]) stage0 += environment(variables=from_prefix(prefix)) return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'): config.set_container_format(container_format) image = f'{os_release}:{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash' ]) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev', 'perl', 'ncbi-blast+', 'libx11-dev' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += gnu(version='10') stage0 += generic_build( url= 'http://search.cpan.org/CPAN/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz', prefix='/usr/local/parallel-forkmanager', build=['perl Makefile.PL', 'make install'], install=['mv * /usr/local/parallel-forkmanager/']) stage0 += environment( variables=add_binary('/usr/local/parallel-forkmanager')) stage0 += generic_build( url= 'ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/clustalw-2.1-linux-x86_64-libcppstatic.tar.gz', prefix='/usr/local/clustalw', install=['mv clustalw2 /usr/local/clustalw/clustalw']) stage0 += environment(variables=add_binary('/usr/local/clustalw')) stage0 += generic_autotools( url='ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz', prefix='/usr/local/emboss', ) stage0 += environment(variables=from_prefix('/usr/local/emboss')) stage0 += generic_autotools( url= 'https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.17.tar.gz', prefix='/usr/local/viennarna') stage0 += environment(variables=from_prefix('/usr/local/viennarna')) stage0 += generic_build( url='https://github.com/weizhongli/cdhit/archive/V4.8.1.tar.gz', prefix='/usr/local/cdhit', directory='cdhit-4.8.1', build=['make'], install=['mv * /usr/local/cdhit/']) stage0 += environment(variables=add_binary('/usr/local/cdhit')) stage0 += generic_build( repository='https://github.com/ambarishbiswas/CRISPRDetect_2.2.git', commit='0f8249f', prefix='/usr/local/crisprdetect', install=['mv * /usr/local/crisprdetect/']) stage0 += environment(variables=add_binary('/usr/local/crisprdetect')) return stage0
def build(container_format='singularity', image='ubuntu:20.04', version='3.8.7', gnu_version='10', mkl_version='2020.0-088', numpy_version='1.20.0rc2'): config.set_container_format(container_format) stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell( commands=['rm /bin/sh && ln -s /bin/bash /bin/sh', '/bin/bash']) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) filename = f'Python-{version}.tar.xz' url = f'https://www.python.org/ftp/python/{version}/{filename}' stage0 += packages(apt=[ 'wget', 'xz-utils', 'build-essential', 'software-properties-common', 'libsqlite3-dev', 'libssl-dev', 'libbz2-dev', 'libgdbm-compat-dev', 'libssl-dev', 'liblzma-dev', 'tk-dev', 'uuid-dev', 'libreadline-dev', 'zlib1g-dev', 'python-dev', 'libncurses*-dev', 'libgdbm-dev', 'libsqlite3-dev', 'libffi-dev', 'git' ]) compiler = gnu(version=gnu_version) stage0 += compiler # stage0 += shell(commands=[ # 'export LDFLAGS="-rpath /usr/local/python/bin $LDFLAGS"' # ]) stage0 += generic_autotools( url=url, directory=f'Python-{version}', prefix='/usr/local/python', with_computed_goto=True, with_threads=True, enable_shared=True, enable_profiling=True, enable_optimizations=True, with_pydebug=True, enable_ipv6=True, toolchain=compiler.toolchain, # build_environment={ # 'CPPFLAGS': '"-Wl,-rpath=/usr/local/python/lib $CPPFLAGS"' # } ) stage0 += packages(apt=['patchelf']) stage0 += shell(commands=[ # 'snap install patchelf --edge --classic', 'patchelf --set-rpath /usr/local/python/lib /usr/local/python/bin/python3', ]) stage0 += environment(variables=from_prefix('/usr/local/python')) stage0 += mkl(version=mkl_version, eula=True) stage0 += shell(commands=['source /opt/intel/mkl/bin/mklvars.sh intel64']) stage0 += pip( packages=['Cython>0.29.21', 'pytest>1.15', 'Hypothesis>5.3.0'], pip='pip3') stage0 += shell(commands=[ f'git clone --branch v{numpy_version} https://github.com/numpy/numpy.git', 'apt remove -y python-numpy python-scipy', 'rm -rf /numpy' ]) stage0 += runscript(commands=['/usr/local/python/bin/python3 $*']) return stage0
def build(container_format='singularity', flavour="devel", os_release='ubuntu', os_version='20.04', cuda_version='11.3.0', python_version='3.8', anaconda_version='4.9.2', alphafold_path="/opt/alphafold", version='2.1.2'): config.set_container_format(container_format) image = f'nvcr.io/nvidia/cuda:{cuda_version}-{flavour}-{os_release}{os_version}' stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += environment(variables={ 'LC_ALL': 'en_AU.UTF-8', 'LANGUAGE': 'en_AU.UTF-8', }) stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm -f /bin/sh && ln -s /bin/bash /bin/sh', 'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh', '/bin/bash', ]) stage0 += environment(variables=from_prefix('/usr/local/cuda')) stage0 += packages(apt=[ 'wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev', 'vim' ]) stage0 += shell(commands=['locale-gen en_AU.UTF-8']) stage0 += conda(eula=True, packages=[ f'python={python_version}', "openmm==7.5.1", "cudnn==8.2.1.32", "cudatoolkit==11.0.3", "pdbfixer==1.7", "hmmer==3.3.2", "hhsuite==3.3.0", "kalign2==2.04" ], channels=['conda-forge', 'bioconda'], version=anaconda_version) stage0 += environment(variables=from_prefix('/usr/local/anaconda')) stage0 += shell(commands=['conda activate base']) stage0 += shell(commands=[ f"mkdir -p {alphafold_path}", f'git clone -b v{version} https://github.com/deepmind/alphafold.git {alphafold_path}' ]) stage0 += environment(variables={"ALPHAFOLD_PATH": f"{alphafold_path}"}) stage0 += shell(commands=[ f'wget -q -P {alphafold_path}/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt' ]) stage0 += pip(packages=[ "absl-py==0.13.0", "biopython==1.79", "chex==0.0.7", "dm-haiku==0.0.4", "dm-tree==0.1.6", "immutabledict==2.0.0", "ml-collections==0.1.0", "numpy==1.19.5", "scipy==1.7.0", "tensorflow==2.5.0", "pandas==1.3.4", "tensorflow-cpu==2.5.0" ], pip='pip3') stage0 += pip(packages=[ "jax", "jaxlib==0.1.69+cuda111 -f https://storage.googleapis.com/jax-releases/jax_releases.html" ], upgrade=True, pip='pip3') stage0 += pip(packages=[f'-r {alphafold_path}/requirements.txt'], pip='pip3') stage0 += shell(commands=[ f'cd /usr/local/anaconda/lib/python{python_version}/site-packages/ && patch -p0 < {alphafold_path}/docker/openmm.patch' ]) stage0 += shell(commands=[ f'cd {alphafold_path}', 'wget https://raw.githubusercontent.com/0luhancheng0/hpccm-containers/main/src/hpccm_containers/alphafold/run_alphafold.sh && chmod a+x run_alphafold.sh' ]) stage0 += runscript(commands=[ 'source /usr/local/anaconda/etc/profile.d/conda.sh', f"cd {alphafold_path}", f'{alphafold_path}/run_alphafold.sh $@' ]) return stage0
Stage0 += shell(commands=[ "mkdir -p /opt/resmap", "cd /opt/resmap", "wget https://downloads.sourceforge.net/project/resmap/ResMap-1.1.4-linux64", "chmod +x ResMap-1.1.4-linux64" ]) ############################################################################### # Release stage ############################################################################### Stage1.name = 'final' Stage1 += baseimage(image="ubuntu:18.04", _as=Stage1.name) Stage1 += Stage0.runtime(_from=Stage0.name) Stage0 += label(metadata={ "MAINTAINER": "*****@*****.**", "HARDWARE": "gpu" }) # Setting up post environment vars. _export=False indicates these are only setup for container runtime Stage1 += environment( variables={ "CUDABINPATH": "/usr/local/cuda-10.1/bin", "CUDALIBPATH": "/usr/local/cuda-10.1/lib64/stubs:/usr/local/cuda-10.1/lib64/:/usr/local/cuda-10.1/lib", "MOTIONCOR2BINPATH": "/opt/MotionCor2_1.2.6", "GCTFBINPATH": "/opt/Gctf_v1.06/bin", "CTFFINDBINPATH": "/opt/ctffind-4.1.13/bin",
def main(): parser = argparse.ArgumentParser( description= 'Simple script for generating a singularity recipe for the GOL example.' ) parser.add_argument( '--build_prefix', type=str, default='/tmp/GOL_example', help= 'Define the path in which all projects will be built (default: /tmp/GOL_example).' ) parser.add_argument('-v ', '--version', action='store_true', help='print version of the container') args = parser.parse_args() if args.version: print(container_version) sys.exit(0) hpccm.config.set_container_format('singularity') hpccm.config.set_singularity_version('3.3') stage = hpccm.Stage() stage += label(metadata={'GOL_MAINTAINER': 'Simeon Ehrig'}) stage += label(metadata={'GOL_EMAIL': '*****@*****.**'}) stage += label(metadata={'GOL_Version': str(container_version)}) # copy example inside container stage += copy(src='notebook', dest='/') stage += copy(src='jupyter_notebook_config.py', dest='/') # copy and build the pnwriter library stage += packages(ospackages=['libpng-dev']) png = [] png_git = git() png.append( png_git.clone_step( repository='https://github.com/pngwriter/pngwriter.git', branch='dev', path='/opt/')) png_cmake = CMakeBuild(prefix='/notebook/pngwriter') png.append( png_cmake.configure_step(directory='/opt/pngwriter', opts=['-DBUILD_SHARED_LIBS=ON'])) png.append(png_cmake.build_step(target='install')) png.append('rm -rf /opt/pngwriter') stage += shell(commands=png) # Copy notebook examples and pngwriter lib to the host's /tmp file system to obtain a writable file system. stage += runscript(commands=[ 'if [ ! -d /tmp/GOL-xeus-cling-cuda ]; then \n' ' mkdir /tmp/GOL-xeus-cling-cuda &&' ' cp -r /notebook/ /tmp/GOL-xeus-cling-cuda &&' ' ln -s /tmp/GOL-xeus-cling-cuda/notebook/pngwriter' ' /tmp/GOL-xeus-cling-cuda/notebook/GTC_presentations/simulation/ \n fi', 'cd /tmp/GOL-xeus-cling-cuda/notebook', 'jupyter-notebook --config=/jupyter_notebook_config.py' ]) # Add the bootstrap manually because hpccm does not support .sregistry, recipe = stage.__str__() recipe = 'Bootstrap: library\nFrom: sehrig/default/xeus-cling-cuda:2.3\n\n' + recipe print(recipe)
def build(container_format='singularity', openmpi_version='2.0.4', gnu_version='10', cfdem_prefix='/usr/local/cfdem', cfdem_version='3.8.0', liggghts_prefix='/usr/local/ligghts', lpp_prefix='/usr/local/lpp', image='ubuntu:20.04', mlton_version='on-20210117-release', gmp_version='6.2.1'): config.set_container_format(container_format) stage0 = Stage(name='stage0') stage0 += baseimage(image=image, _bootstrap='docker') stage0 += label(metadata={ 'maintainer': 'Luhan Cheng', 'email': '*****@*****.**' }) stage0 += shell(commands=[ 'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash' ]) stage0 += packages(apt=[ 'locales', 'wget', 'software-properties-common', 'git', 'build-essential', 'flex', 'bison', 'cmake', 'zlib1g-dev', 'gnuplot', 'libreadline-dev', 'libncurses-dev', 'libxt-dev', 'libscotch-dev', 'libptscotch-dev', 'libvtk6-dev', 'python-numpy', 'python-dev', 'qt5-default', 'git-core', 'libboost-system-dev', 'libboost-thread-dev', 'libqt5x11extras5-dev', 'qttools5-dev', 'curl', 'libgl1-mesa-dev', 'libosmesa6-dev', 'libssh2-1', 'libtool' ]) compilers = gnu(version=gnu_version) stage0 += compilers openmpi_building_block = openmpi(version=openmpi_version, toolchain=compilers.toolchain, cuda=False) stage0 += openmpi_building_block stage0 += generic_autotools( url=f'https://gmplib.org/download/gmp/gmp-{gmp_version}.tar.xz', prefix='/usr/local/gmp', directory=f'gmp-{gmp_version}/', ) stage0 += environment(variables=from_library('/usr/local/gmp')) stage0 += generic_build(repository='https://github.com/MLton/mlton.git', branch=mlton_version, build=['make -j'], install=['make PREFIX=/usr/local/mlton']) if cfdem_version == '3.8.0': OF_release = '5.x' OF_commitHashtag = '538044ac05c4672b37c7df607dca1116fa88df88' else: raise Exception( 'Check https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC/blob/master/src/lagrangian/cfdemParticle/cfdTools/versionInfo.H' ) stage0 += comment('Obtain CFDEM source') stage0 += shell(commands=[ f'mkdir -p {cfdem_prefix} {liggghts_prefix} {lpp_prefix}', f'git clone --branch {cfdem_version} https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC.git {cfdem_prefix}', f'git clone --branch {cfdem_version} https://github.com/CFDEMproject/LIGGGHTS-PUBLIC.git {liggghts_prefix}', f'git clone https://github.com/CFDEMproject/LPP.git {lpp_prefix}' ]) stage0 += comment('Install OpenFoam') openfoam_prefix = f'/usr/local/OpenFOAM-{OF_release}' thirdparty_prefix = f'/usr/local/ThirdParty-{OF_release}' stage0 += shell(commands=[ f'mkdir -p {openfoam_prefix} {thirdparty_prefix}', f'git clone https://github.com/OpenFOAM/OpenFOAM-{OF_release}.git {openfoam_prefix} && cd {openfoam_prefix} && git checkout {OF_commitHashtag}', f'git clone https://github.com/OpenFOAM/ThirdParty-{OF_release}.git {thirdparty_prefix}', ]) stage0 += shell(commands=[ f'echo "source {openfoam_prefix}/etc/bashrc" >> ~/.bashrc', ]) # DLIB_PATH = '/usr/lib/x86_64-linux-gnu' # INCLUDE_PATH = '/usr/include' stage0 += shell_with_log(commands=[ f'{thirdparty_prefix}/Allwmake -j', # this breaks with openmpi >= 3, error: static assertion failed: "MPI_Type_extent was removed in MPI-3.0. Use MPI_Type_get_extent instead." # f'{thirdparty_prefix}/makeParaView -mpi -mesa -mesa-lib {DLIB_PATH}/libOSMesa.so -mesa-include {INCLUDE_PATH}/GL -verbose', f'{thirdparty_prefix}/makeParaView -mpi' 'wmRefresh' ]) stage0 += shell(commands=[ f'{openfoam_prefix}/Allwmake -j', ]) # /usr/bin/g++ -fPIC -O3 -DNDEBUG -Wl,--no-undefined -lc -shared -Wl,-soname,libvtkCommonSystem-pv5.4.so.1 -o ../../../lib/libvtkCommonSystem-pv5.4.so.1 CMakeFiles/vtkCommonSystem.dir/vtkClientSocket.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkDirectory.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkServerSocket.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkSocket.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkSocketCollection.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkThreadMessager.cxx.o CMakeFiles/vtkCommonSystem.dir/vtkTimerLog.cxx.o -Wl,-rpath,/usr/local/ThirdParty-5.x/build/linux64Gcc/ParaView-5.4.0/lib: ../../../lib/libvtkCommonCore-pv5.4.so.1 ../../../lib/libvtksys-pv5.4.so.1 -lpthread -ldl return stage0