{"id":659,"date":"2013-05-14T17:22:57","date_gmt":"2013-05-14T17:22:57","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=659"},"modified":"2013-05-16T10:05:35","modified_gmt":"2013-05-16T10:05:35","slug":"gerris","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/gerris\/","title":{"rendered":"Gerris2D &#038; Gerris3D"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"http:\/\/gfs.sourceforge.net\/wiki\/index.php\/Main_Page\">Gerris<\/a> is a program for the solution of the partial differential equations describing fluid flow.<\/p>\n<p>Version snapshot 13.01.12 is installed on the CSF, compiled for AMD Bulldozer. The compilation includes<\/p>\n<ul>\n<li>GTS snapshot 12.11.30<\/li>\n<li>gfsview-batch2D and gfsview-batch3D<\/li>\n<li>OSMesa 7.8.2<\/li>\n<li>FFMPEG 0.6.5<\/li>\n<li>Hypre 2.0.0 has <strong>NOT<\/strong> been compiled in to this version<\/li>\n<\/ul>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on user access. However, this software has only been compiled for the AMD Bulldozer nodes and so you must have access to these nodes.<\/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\/amd-4.5.2\/Gerris\/13.01.12\r\n<\/pre>\n<p>This will set up your path to run the tools in Gerris, including <code>gfsview-batch2D<\/code> and <code>gfsview-batch3D<\/code>. It will also set the environment variable <code>GERRIS_HOME<\/code> which can be used in your own <code>Makefile<\/code>s if compiling code against the Gerris libraries. See the page on <a href=\"\/csf-apps\/software\/applications\/compilersamd\/openmpibd\/\">compiling OpenMPI applications on AMD Bulldozer nodes<\/a> for more information.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run Gerris on the login node. Jobs should be submitted to the compute nodes via batch and should use the <code>orte-64bd-ib.pe<\/code> parallel environment.<\/p>\n<p>Gerris will <strong>not<\/strong> run on the Intel nodes and will <strong>not<\/strong> run serially (i.e., without <code>mpirun<\/code>)<\/p>\n<p>It is highly recommended that you run your jobs from the scratch file system (especially when generating large .mpg files).<\/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\r\n#$ -S \/bin\/bash\r\n#$ -cwd\r\n#$ -V\r\n#$ -pe orte-64bd-ib.pe 64      # Multiples of 64 must be used\r\n\r\nmpirun -n $NSLOTS gerris2D input.gfs\r\n  #\r\n  # Can also run gerris3D for example\r\n  #\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub scriptname<\/pre>\n<p>All Gerris command must be run via <code>mpirun<\/code>. Hence If you need to run <code>gerris2D<\/code> or <code>gerris3D<\/code> to do pre-processing (e.g., to split your domains) before running the solver, add the following to the jobscript above (check the docs for your required flags)<\/p>\n<pre>\r\n# Example commands to split and parallelise a domain for use with 4 processors.\r\n# Preprocessing is done serially (i.e., using 1 MPI process)\r\nmpirun -n 1 gerris2D -s 2 -m input.gfs > input-s2.gfs\r\nmpirun -n 1 gerris2D -p 2 -m input-s2.gfs > input-p2.gfs\r\n# Now run the simulation in parallel with 4 processors (set the PE to this many processors)\r\nmpirun -n $NSLOTS gerris2D input-p2.gfs\r\n<\/pre>\n<p>In the above example the input.gfs file contains the commands to process the results through <code>gfsview-batch2D<\/code>. For example, it may contain the following lines:<\/p>\n<pre>\r\nppm2mpeg -s 800x100 > pid.mpg \r\ngfsview-batch2D pid.gfv end.gfs\r\n<\/pre>\n<p>See the <em>parallel<\/em> example at <a href=\"http:\/\/gerris.dalembert.upmc.fr\/gerris\/examples\/examples\/cylinder.html#htoc5\">http:\/\/gerris.dalembert.upmc.fr\/gerris\/examples\/examples\/cylinder.html#htoc5<\/a> for a complete parallel example.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/gfs.sourceforge.net\/wiki\/index.php\/Main_Page\">Gerris<\/a> website.<\/li>\n<li>See the section on <a href=\"http:\/\/gfs.sourceforge.net\/wiki\/index.php\/Gerris_in_parallel\">preparing your input files<\/a> for running Gerris in parallel.\n<li>After loading the Gerris modulefile you can use <code>man gerris2D<\/code> or <code>man gerris3D<\/code> to access the manual pages.\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Gerris is a program for the solution of the partial differential equations describing fluid flow. Version snapshot 13.01.12 is installed on the CSF, compiled for AMD Bulldozer. The compilation includes GTS snapshot 12.11.30 gfsview-batch2D and gfsview-batch3D OSMesa 7.8.2 FFMPEG 0.6.5 Hypre 2.0.0 has NOT been compiled in to this version Restrictions on use There are no restrictions on user access. However, this software has only been compiled for the AMD Bulldozer nodes and so.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/gerris\/\">Read more &raquo;<\/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-659","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/659","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=659"}],"version-history":[{"count":7,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/659\/revisions"}],"predecessor-version":[{"id":669,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/659\/revisions\/669"}],"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=659"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}