{"id":2522,"date":"2019-03-05T13:58:26","date_gmt":"2019-03-05T13:58:26","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=2522"},"modified":"2019-04-01T12:29:53","modified_gmt":"2019-04-01T11:29:53","slug":"openbabel","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/openbabel\/","title":{"rendered":"Openbabel"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"http:\/\/openbabel.org\/\">Open Babel<\/a> is a chemical toolbox designed to search, convert, analyze, or store data from molecular modelling, chemistry, solid-state materials, biochemistry, or related areas.<\/p>\n<p>Version 2.4.1 is available. It was compiled with the Intel compiler version\u00a0 17.0.7 and python 2.7.<\/p>\n<p>Please note that the GUI is not installed for either version and so Open Babel should be used for batch work only.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing the software. The source code is release under the <a href=\"http:\/\/www.gnu.org\/licenses\/gpl-2.0.html\">GPL v2<\/a> license.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the required modulefile:<\/p>\n<h3>Version 2.4.1<\/h3>\n<pre>module load apps\/intel-17.0\/obabel\/2.4.1        (1-core) jobs\r\n\r\nOR\r\n\r\nmodule load apps\/intel-17.0\/obabel\/2.4.1-omp    # Multithreaded MMFF94 force-field code\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run Open Babel on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Open Babel is mainly a serial code and so should only be run with a serial batch scripts (no <em>PE<\/em> flag). If you wish to run many similar jobs please see the instructions on <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/batch\/job-arrays\/\">job arrays<\/a> for the correct way to do this.<\/p>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\nmodule load apps\/intel-17.0\/obabel\/2.4.1\r\nbabel infile outfile<\/pre>\n<p>Submit the jobscript using:<\/p>\n<pre>qsub <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>The MMFF94 force-field code <em>is<\/em> multicore aware in the 2.4.1-omp version. If you are running OpenBabel and specifying the following flags on the command-line:<\/p>\n<pre>-ff MMFF94\r\n<\/pre>\n<p>then your job may benefit from being run with multiple cores.<\/p>\n<p><strong>Please note: <\/strong>If you are not using the MMFF94 code <em>do not<\/em> use the <code>-pe<\/code> line in your jobscript &#8211; use a serial jobscript. Requesting multiple cores without using the MMFF94 code will simply waste cores because your code will use only one core.<\/p>\n<p>For example:<\/p>\n<p>Make sure you have the 2.4.1 or 2.3.2-omp modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -pe smp.pe 4     # Job will use 4 cores (max 32 allowed)\r\n\r\n# Must set this to use the correct number of cores\r\nexport OMP_NUM_THREADS=$NSLOTS\r\n\r\n# Must be using the MMFF94 force-field code\r\nobminimize -ff MMFF94 <em>other args<\/em> <em>molfile<\/em>\r\n\r\n<\/pre>\n<p>Submit the jobscript using:<\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/openbabel.org\/\">Open Babel website<\/a><\/li>\n<li><a href=\"http:\/\/openbabel.org\/wiki\/Guides\">Open Babel Guides<\/a> describe each command-line program, giving options\/flags to use on the command-lines in your jobscripts.<\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Open Babel is a chemical toolbox designed to search, convert, analyze, or store data from molecular modelling, chemistry, solid-state materials, biochemistry, or related areas. Version 2.4.1 is available. It was compiled with the Intel compiler version\u00a0 17.0.7 and python 2.7. Please note that the GUI is not installed for either version and so Open Babel should be used for batch work only. Restrictions on use There are no restrictions on accessing the software. The.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/openbabel\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2522","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2522","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\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=2522"}],"version-history":[{"count":5,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2522\/revisions"}],"predecessor-version":[{"id":2533,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2522\/revisions\/2533"}],"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=2522"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}