{"id":4419,"date":"2020-01-10T14:59:30","date_gmt":"2020-01-10T14:59:30","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4419"},"modified":"2025-08-04T14:30:50","modified_gmt":"2025-08-04T13:30:50","slug":"ovito","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/ovito\/","title":{"rendered":"ovito"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/ovito.org\">Ovito<\/a> is a Scientific visualization and analysis software for atomistic simulation data. <\/p>\n<p>The latest Version installed on the CSF is version 3.13.0 (basic\/community edition). <\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v3 <a href=\"\">license<\/a> and all usage must adhere to that license.<\/p>\n<p>Please cite your usage of the software according to the instructions at the <a href=\"https:\/\/ovito.org\/index.php\/about\/how-to-cite-ovito\">Ovito how-to-cite<\/a> page.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>\r\nmodule load apps\/binapps\/ovito\/2.9.0  # no interactive use\r\nmodule load apps\/binapps\/ovito\/3.0.0-dev628\r\nmodule load apps\/binapps\/ovito\/3.13.0  \r\n\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p><strong>Please do not run Ovito on the login node.<\/strong> Jobs should be submitted to the compute nodes via batch (to process python scripts that generate visualization).<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#SBATCH -p serial         \r\n#SBATCH -t 1-0 # Wallclock limit (days-hours). Required!\r\n\r\nmodule purge\r\nmodule load apps\/binapps\/ovito\/3.13.0\r\n\r\n# You <strong>MUST<\/strong> ensure you use the correct number of threads (1 for a serial job).\r\n# $SLURM_NTASKS will be replaced automatically with the correct number.\r\n\r\n# You <strong>MUST<\/strong> also unset the following to prevent a <em>QXcbConnection<\/em> error occuring:\r\nunset DISPLAY\r\n\r\n# Now run ovito <strong>without<\/strong> the GUI to process your python script\r\novito --nogui --nthreads $SLURM_NTASKS --script <em>myviz.py<\/em>\r\n         #                                  #\r\n         #                                  # Supply your python script name\r\n         #\r\n         # Prevent the GUI displaying in batch.\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>sbatch <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore\r\n#SBATCH -n 8         \r\n#SBATCH -t 1-0 # Wallclock limit (days-hours). Required!\r\n\r\nmodule purge\r\nmodule load apps\/binapps\/ovito\/3.13.0\r\n\r\n\r\n# You MUST ensure you use the correct number of threads.\r\n# $SLURM_NTASKS will be replaced automatically with the correct number from above.\r\n\r\n\r\n# You <strong>MUST<\/strong> also unset the following to prevent a <em>QXcbConnection<\/em> error occuring:\r\nunset DISPLAY\r\n\r\novito --nogui --nthreads $SLURM_NTASKS --script <em>myviz.py<\/em>\r\n         #                                  #\r\n         #                                  # Supply your python script name\r\n         #\r\n         # Prevent the GUI displaying in batch.\r\n<\/pre>\n<h2>Interactive Use<\/h2>\n<p>Start an interactive session from the login node using the following command<br \/>\n<code>srun-x11<\/code><br \/>\nSee <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/batch-slurm\/srun\/\">Interactive Jobs (srun, srun-x11)<\/a> for further options. <\/p>\n<p>Once interactive session has started load the Ovito module file<\/p>\n<pre>\r\nmodule purge\r\nmodule load apps\/binapps\/ovito\/3.13.0\r\n\r\n# Start ovito\r\novito\r\n<\/pre>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/ovito.org\/manual\/\">Ovito user manual<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Ovito is a Scientific visualization and analysis software for atomistic simulation data. The latest Version installed on the CSF is version 3.13.0 (basic\/community edition). Restrictions on use There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v3 license and all usage must adhere to that license. Please cite your usage of the software according to the instructions at the Ovito how-to-cite page. Set up procedure.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/ovito\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4419","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4419","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=4419"}],"version-history":[{"count":11,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4419\/revisions"}],"predecessor-version":[{"id":10767,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4419\/revisions\/10767"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=4419"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}