DynamO<\/a> is a free and open-source event-driven particle simulator, used a molecular dynamics package to study model fluids or as a granular dynamics package to investigate solid particle processes.<\/p>\n Version 1.5.0 (stable branch) is installed on the CSF. It was compiled with the GCC 4.8.2 compiler and Boost 1.5.1 libraries.<\/p>\n Please note that the DynamO visualizer (Coil) is not available on the CSF. All work should be run in batch.<\/p>\n There are no restrictions on accessing this software on the CSF. If you publish results calculated by using this software, please use the citation as detailed at the dynamo publications page<\/a>.<\/p>\n To access the software you must first load one<\/strong> of the following modulefiles:<\/p>\n File formats changed between these versions so please use the version appropriate to any existing files.<\/p>\n This modulefile will load the required GCC and BOOST modulefiles automatically.<\/p>\n Please do not run DynamO on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n Several DynamO executables are available, the main ones being Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Some DynamO operations can use multiple threads. You must add the Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview DynamO is a free and open-source event-driven particle simulator, used a molecular dynamics package to study model fluids or as a granular dynamics package to investigate solid particle processes. Version 1.5.0 (stable branch) is installed on the CSF. It was compiled with the GCC 4.8.2 compiler and Boost 1.5.1 libraries. Please note that the DynamO visualizer (Coil) is not available on the CSF. All work should be run in batch. Restrictions on use There.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1845","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1845","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=1845"}],"version-history":[{"count":5,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1845\/revisions"}],"predecessor-version":[{"id":1854,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1845\/revisions\/1854"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=1845"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
\n
module load apps\/gcc\/dynamo\/140918-master<\/pre>\n<\/li>\n
module load apps\/gcc\/dynamo\/1.5.0<\/pre>\n<\/li>\n<\/ul>\n
Running the application<\/h2>\n
dynamod<\/code> and dynarun<\/code>. The dynarun<\/code> application can be run with multiple threads (see below for an example jobscript).<\/p>\nSerial batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n\r\ndynarun --out-data-file out.xml.bz2 -o config.out.xml.bz2 --engine 1 config-files\r\n #\r\n # The 'engine' can be 1, 2 or 3\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Parallel batch job submission<\/h3>\n
-N numthreads<\/em><\/code> option if supported and specifty the Parallel Environment in the jobscript. For example:<\/p>\n\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n#$ -pe smp.pe 8 # Use 8 cores (in this example)\r\n\r\n# $NSLOTS is automatically replaced by the number of cores from above\r\ndynarun -N $NSLOTS --out-data-file out.xml.bz2 -o config.out.xml.bz2 --engine 1 config-files\r\n #\r\n # The 'engine' can be 1, 2 or 3\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Further info<\/h2>\n
\n
Updates<\/h2>\n