EasyBuild<\/a> is a software build and installation framework written in Python, which allows to deploy and manage (scientific) applications on High Performance Computing systems. EasyBuild v3.6.2 is currently installed on ABACUS2.0 and can be loaded as a module:<\/p>\n The shell command\u00a0 The output shows the list of well-tested easyconfig\u00a0files which include the instructions to configure, build and install the application with a particular compiler toolchain. The full list of toolchains implemented in the EasyBuild environment is printed with the command:\u00a0 It is possible to check all the dependencies defined in a particular software easyconfig file by executing the\u00a0 All the dependencies marked with\u00a0 The additional option\u00a0 By default, EasyBuild will install the software in\u00a0 An overview of the EasyBuild configuration settings is given by The user can define new easyconfig files to install applications which are not currently reported on the online repository. EasyBuild provides templates to implement procedures for building and installing software, called easyblocks<\/a>. For example, the following easyconfig file can be used to install a particular release of the RStudio software:<\/p>\n In this case EasyBuild leverages the\u00a0 Sometimes it can be useful to build a new software where some of the dependencies are already installed on ABACUS2.0. In this case, any of these dependencies must be indicated as Metadata for the external module\u00a0 The location of the file with the external module metadata can be specified with the configuration option\u00a0 Similarly, the Intel Fortran compiler in What is EasyBuild ? EasyBuild is a software build and installation framework written in Python, which allows to deploy and manage (scientific) applications on High Performance Computing systems. EasyBuild v3.6.2 is currently installed on ABACUS2.0 Read more…<\/a><\/p>\n","protected":false},"author":5,"featured_media":3986,"parent":0,"menu_order":8,"comment_status":"closed","ping_status":"closed","template":"page-templates\/template-fullwidth.php","meta":[],"_links":{"self":[{"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/pages\/4072"}],"collection":[{"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/comments?post=4072"}],"version-history":[{"count":89,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/pages\/4072\/revisions"}],"predecessor-version":[{"id":6379,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/pages\/4072\/revisions\/6379"}],"wp:featuredmedia":[{"embeddable":true,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/media\/3986"}],"wp:attachment":[{"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/media?parent=4072"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}testuser@fe1:~$ module load\u00a0easybuild<\/code><\/pre>\nHow to search for a particular software<\/h4>\n
eb -S<\/code>\u00a0is used to search for\u00a0easyconfig files <\/em>included in the EasyBuild online\u00a0repository<\/a>. Easyconfig files are used to specify the version, dependencies and build parameters of the software. For example:<\/p>\ntestuser@fe1:~$ eb\u00a0-S\u00a0'^Python-3.6.4-*'\n...\n * $CFGS1\/Python-3.6.4-foss-2017a.eb\n * $CFGS1\/Python-3.6.4-foss-2018a.eb\n * $CFGS1\/Python-3.6.4-golf-2018a.eb\n * $CFGS1\/Python-3.6.4-intel-2018a.eb\n * $CFGS1\/Python-3.6.4-iomkl-2018.02.eb\n * $CFGS1\/Python-3.6.4-iomkl-2018a.eb<\/code><\/pre>\neb --list-toolchains<\/code>. Currently, the following toolchains are installed on ABACUS2.0 and can be loaded together with the\u00a0easybuild<\/code>\u00a0module.<\/p>\nfoss date binutils GCC Open MPI OpenBLAS LAPACK ScaLAPACK FFTW\n2017b Jul 2017 2.28 6.4.0 2.1.1\t 0.2.20 (incl. with OpenBLAS) 2.0.20 \t3.3.6\n2018a Jan 2018 2.28 6.4.0 2.1.2\t 0.2.20 (incl. with OpenBLAS) 2.0.20 \t3.3.7\n2018b Jul 2018 2.30 7.3.0 3.1.1\t 0.3.1 (incl. with OpenBLAS) 2.0.20 \t3.3.8\n\ngoolfc\tdate\t binutils GCC Open MPI\t OpenBLAS LAPACK \t ScaLAPACK\tFFTW\tCUDA\n2018a Jan 2018 2.28 6.4.0 2.1.2\t 0.2.20 (incl. with OpenBLAS) 2.0.20 \t3.3.7\t9.1.85\n\nintel\tdate binutils GCC Intel compilers\t Intel MPI\t Intel MKL\n2018a\tJan 2018 2.28\t 6.4.0 2018.1.163\t 2018.1.163\t 2018.1.163\n2018b\tJul 2018 2.30\t 7.3.0 2018.3.222\t 2018.3.222\t 2018.3.222\n\niomkl\tdate binutils GCC Intel Compilers\t Open MPI\t Intel MKL\n2018a\tJan 2018 2.28\t 6.4.0 2018.1.163 \t 2.1.2 \t 2018.1.163\n2018b\tJul 2018 2.30\t 7.3.0 2018.3.222 3.1.1 \t 2018.3.222<\/code> \n<\/code><\/pre>\nHow to install a software using the online repository<\/h4>\n
eb<\/code>\u00a0command with the option\u00a0--dry-run<\/code>\u00a0(or\u00a0-D<\/code>). For example:<\/p>\ntestuser@fe1:~$ eb GROMACS-2018-foss-2018a.eb -D\nDry run: printing build status of easyconfigs and dependencies\n...\n * [x] $CFGS\/m\/M4\/M4-1.4.18.eb (module: M4\/1.4.18)\n * [x] $CFGS\/z\/zlib\/zlib-1.2.11.eb (module: zlib\/1.2.11)\n * [x] $CFGS\/h\/help2man\/help2man-1.47.4.eb (module: help2man\/1.47.4)\n * [x] $CFGS\/m\/M4\/M4-1.4.17.eb (module: M4\/1.4.17)\n * [x] $CFGS\/b\/Bison\/Bison-3.0.4.eb (module: Bison\/3.0.4)\n * [x] $CFGS\/f\/flex\/flex-2.6.3.eb (module: flex\/2.6.3)\n * [x] $CFGS\/b\/binutils\/binutils-2.28.eb (module: binutils\/2.28)\n * [x] $CFGS\/g\/GCCcore\/GCCcore-6.4.0.eb (module: GCCcore\/6.4.0)\n * [x] $CFGS\/m\/M4\/M4-1.4.18-GCCcore-6.4.0.eb (module: M4\/1.4.18-GCCcore-6.4.0)\n * [x] $CFGS\/z\/zlib\/zlib-1.2.11-GCCcore-6.4.0.eb (module: zlib\/1.2.11-GCCcore-6.4.0)\n * [x] $CFGS\/h\/help2man\/help2man-1.47.4-GCCcore-6.4.0.eb (module: help2man\/1.47.4-GCCcore-6.4.0)\n * [x] $CFGS\/b\/Bison\/Bison-3.0.4-GCCcore-6.4.0.eb (module: Bison\/3.0.4-GCCcore-6.4.0)\n * [x] $CFGS\/f\/flex\/flex-2.6.4-GCCcore-6.4.0.eb (module: flex\/2.6.4-GCCcore-6.4.0)\n * [x] $CFGS\/b\/binutils\/binutils-2.28-GCCcore-6.4.0.eb (module: binutils\/2.28-GCCcore-6.4.0)\n * [x] $CFGS\/g\/GCC\/GCC-6.4.0-2.28.eb (module: GCC\/6.4.0-2.28)\n * [x] $CFGS\/o\/OpenBLAS\/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb (module: OpenBLAS\/0.2.20-GCC-6.4.0-2.28)\n * [x] $CFGS\/a\/Autoconf\/Autoconf-2.69-GCCcore-6.4.0.eb (module: Autoconf\/2.69-GCCcore-6.4.0)\n * [x] $CFGS\/a\/Automake\/Automake-1.15.1-GCCcore-6.4.0.eb (module: Automake\/1.15.1-GCCcore-6.4.0)\n * [x] $CFGS\/n\/ncurses\/ncurses-6.0-GCCcore-6.4.0.eb (module: ncurses\/6.0-GCCcore-6.4.0)\n * [ ] $CFGS\/c\/CMake\/CMake-3.10.2-GCCcore-6.4.0.eb (module: CMake\/3.10.2-GCCcore-6.4.0)\n * [x] $CFGS\/l\/libtool\/libtool-2.4.6-GCCcore-6.4.0.eb (module: libtool\/2.4.6-GCCcore-6.4.0)\n * [x] $CFGS\/a\/Autotools\/Autotools-20170619-GCCcore-6.4.0.eb (module: Autotools\/20170619-GCCcore-6.4.0)\n * [x] $CFGS\/n\/numactl\/numactl-2.0.11-GCCcore-6.4.0.eb (module: numactl\/2.0.11-GCCcore-6.4.0)\n * [x] $CFGS\/h\/hwloc\/hwloc-1.11.8-GCCcore-6.4.0.eb (module: hwloc\/1.11.8-GCCcore-6.4.0)\n * [x] $CFGS\/o\/OpenMPI\/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb (module: OpenMPI\/2.1.2-GCC-6.4.0-2.28)\n * [x] $CFGS\/g\/gompi\/gompi-2018a.eb (module: gompi\/2018a)\n * [x] $CFGS\/f\/FFTW\/FFTW-3.3.7-gompi-2018a.eb (module: FFTW\/3.3.7-gompi-2018a)\n * [x] $CFGS\/s\/ScaLAPACK\/ScaLAPACK-2.0.2-gompi-2018a-OpenBLAS-0.2.20.eb (module: ScaLAPACK\/2.0.2-gompi-2018a-OpenBLAS-0.2.20)\n * [x] $CFGS\/f\/foss\/foss-2018a.eb (module: foss\/2018a)\n * [ ] $CFGS\/g\/GROMACS\/GROMACS-2018-foss-2018a.eb (module: GROMACS\/2018-foss-2018a)\n== Temporary log file(s) \/tmp\/eb-tXC0pK\/easybuild-smjQ9R.log* have been removed.\n== Temporary directory \/tmp\/eb-tXC0pK has been removed.<\/code><\/pre>\n[x]<\/code> are already installed on ABACUS2.0 and can be loaded together with the EasyBuild module. The user can enforce the installation of the missing dependencies using\u00a0--robot\/-r<\/code>, e.g.<\/p>\n\u00a0
testuser@fe1:~$ eb GROMACS-2018-foss-2018a.eb -d --robot<\/code><\/pre>\n--debug\/-d<\/code>\u00a0enables debug logging, which includes all the details of the software build and installation in the log file.<\/p>\n$HOME\/easybuild\/software<\/code>\u00a0and the corresponding Lua module file in\u00a0$HOME\/easybuild\/modules\/all<\/code>. The path of the module file is automatically added to\u00a0$MODULEPATH<\/code>, once the EasyBuild module is loaded. The user can also specify a different installation path for a particular software and the corresponding module using the option\u00a0--installpath<\/code>\u00a0(or, more specifically,\u00a0\u00a0--installpath-software<\/code>\u00a0and\u00a0--installpath-modules<\/code>). In this case the new module path must be added with the command:\u00a0module use <new_module_path><\/code>.<\/p>\neb --show-config<\/code>.<\/p>\nHow to create new easyconfig files<\/h4>\n
easyblock = 'PackedBinary'\nname = 'RStudio'\nversion = '1.1.456'\nhomepage = 'https:\/\/www.rstudio.com\ndescription = \"RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.\"\n\ntoolchain = {'name': 'dummy', 'version': ''}\nsources = ['rstudio-%(version)s-amd64-debian.tar.gz']\nsource_urls = ['http:\/\/download1.rstudio.org']\n\nskipsteps = ['build']\n\nsanity_check_paths = {\n\u00a0 'files': ['bin\/rstudio'],\n\u00a0 'dirs': ['R']\n}\n\nmoduleclass = 'tools'<\/code><\/pre>\nPackedBinary<\/code>\u00a0easyblock<\/a>, which provides the support for installing packed binary software. Since the software is not compiled, it is used in the dummy<\/code>\u00a0toolchain.<\/p>\nHow to include external dependencies<\/h4>\n
EXTERNAL_MODULE<\/code>\u00a0and added as separate metadata. For example, in the following the repository\u00a0 easyconfig file for the Intel C\/C++ compilers in the\u00a0intel-2018b<\/code>\u00a0toolchain is tweaked in order to use the preinstalled Intel compiler module:<\/p>\n# new easyconfig file icc-2018.3.222-GCC-7.3.0-2.30.eb\nname = 'icc'\nversion = '2018.3.222'\n\nhomepage = 'http:\/\/software.intel.com\/en-us\/intel-compilers\/'\ndescription = \"Intel C and C++ compilers\"\n\ntoolchain = {'name': 'dummy', 'version': 'dummy'}\ngccver = '7.3.0'\nbinutilsver = '2.30'\nversionsuffix = '-GCC-%s-%s' % (gccver, binutilsver)\n\ndependencies = [\n ('GCCcore', gccver),\n ('binutils', binutilsver, '', ('GCCcore', gccver)),\n ('intel\/2018.05', EXTERNAL_MODULE)\n]\n\nskipsteps = ['configure', 'build', 'install']\n\ndontcreateinstalldir = 'True'\n\npath_compiler = '\/opt\/sys\/apps\/intel\/2018.05\/bin'\nsanity_check_paths = {\n 'files': [path_compiler+\"\/icc\", path_compiler+\"\/icpc\"],\n 'dirs': [],\n}\n\nlicense_file = '\/opt\/sys\/apps\/intel\/licenses\/USE_SERVER.lic'\n\nmoduleclass = 'compiler'\n<\/code><\/pre>\nintel\/2018.05<\/code>\u00a0must be declared in a separate file, in this case called ext_module_metadata.cfg<\/code>, as follows:<\/p>\n[intel\/2018.05]\nname = icc, icpc, ifort\nversion = 18.0.3, 18.0.3, 18.0.3\nprefix = \/opt\/sys\/apps\/intel\/2018.05\/bin\/<\/code><\/pre>\n--external_module_metadata<\/code>. For example, if both\u00a0icc-2018.3.222-GCC-7.3.0-2.30.eb<\/code>\u00a0 and\u00a0 ext_module_metadata.cfg<\/code>\u00a0are located in the same directory, then the following command is used to install the icc<\/code> compiler and define the environmental variables to load the external module\u00a0intel\/2018.05<\/code>:<\/p>\ntestuser@fe1:~$ eb icc-2018.1.163-GCC-6.4.0-2.28.eb --external-modules-metadata=ext_module_metadata.cfg --robot <\/code><\/pre>\nintel\/2018.05<\/code>\u00a0can be linked to a modified\u00a0ifort-2018.3.222-GCC-7.3.0-2.30.eb<\/code>\u00a0easyconfig file of the\u00a0intel-2018b<\/code> toolchain. In this case, it is not necessary to run the eb<\/code>\u00a0 command with the option for the metadata file, because the external module is already configured.<\/p>\nFurther information:<\/h4>\n
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