{"id":2134,"date":"2019-01-25T13:54:14","date_gmt":"2019-01-25T13:54:14","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=2134"},"modified":"2025-11-10T14:20:44","modified_gmt":"2025-11-10T14:20:44","slug":"gpyro","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/gpyro\/","title":{"rendered":"gpyro"},"content":{"rendered":"<p><em>Draft &#8211; not yet ready for general use<\/em><\/p>\n<h2>Overview<\/h2>\n<p>gpyro (Generalized Pyrolysis Model for Combustible Solids) is an open source computer model that describes the thermal response of solid materials exposed to radiative or convective heating, including thermo-oxidative pyrolysis of the condensed phase.<\/p>\n<p>Version is installed on the CSF. It was compiled with Intel Compilers 17.0. using <code>-msse2 -axSSE4.2,AVX,CORE-AVX2,CORE-AVX512<\/code> and openmpi 3.1.3.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>This software is open-source so all CSF users may use it. Please ensure you read the National Institute of Standards and Technology (NIST) disclaimer on the <a href=\"http:\/\/reaxengineering.com\/trac\/gpyro\/wiki\/WikiStart\">gpyro website<\/a>.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>module load apps\/intel-17.0\/gpyro\/0.8186\r\n<\/pre>\n<p>We recommend that this is done in your jobscript as shown in the examples below.<\/p>\n<h2>Running the application<\/h2>\n<ul>\n<li>Please do not run gpyro on the login node.<\/li>\n<li>All Jobs should be submitted to the compute nodes via batch.<\/li>\n<li>It is recommended to run gpyro using multiple cores.<\/li>\n<li>openmp based executables can only be run on a single node.<\/li>\n<li>mpi based executables can be run on a single node or multiple nodes<\/li>\n<li>the <code>$NSLOTS<\/code> in the below examples is important to ensure correct resource utilisation.<\/li>\n<li>For SCE optimization, the number of processors must equal the number of complexes (NGS) plus 1\n<ul>\n<li>So for an NGS of 46, we would specify 48 cores and use <code>-np $((NSLOTS-1))<\/code> to call gpyro under mpirun.<\/li>\n<\/ul>\n<\/li>\n<li>This software will not run on the AMD nodes.<\/li>\n<\/ul>\n<h3>Parallel batch job submission &#8211; max. 32 cores on a (single compute node) &#8211; openmp based executables<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>#!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -pe smp.pe 5\r\nmodule load apps\/intel-17.0\/gpyro\/0.8186\r\n\r\nexport OMP_NUM_THREADS=$NSLOTS\r\ngpyro_openmp MY_SIM.data\r\n<\/pre>\n<p>Submit the jobscript using:<\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<p>Other openmp based executables = <code>fds6_gpyro<\/code><\/p>\n<h3>Parallel batch job submission &#8211; max. 32 cores on a (single compute node) &#8211; mpi based executables<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>#!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -pe smp.pe 5\r\nmodule load apps\/intel-17.0\/gpyro\/0.8186\r\n\r\nmpirun -np $((NSLOTS-1)) --bind-to none fds6_mpi_gpyro MY_SIM.data\r\n<\/pre>\n<p>Submit the jobscript using:<\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<p>Other mpi based executables = <code>gpyro_propest<\/code><\/p>\n<h3>Parallel batch job submission &#8211; multiple nodes &#8211; 48 cores or more in multiples of 24 (max. 120 cores) &#8211; mpi based executables<\/h3>\n<pre>#!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -pe mpi-24-ib.pe 48\r\nmodule load apps\/intel-17.0\/gpyro\/0.8186\r\n\r\n\r\nmpirun -np $((NSLOTS-1)) fds6_mpi_gpyro MY_SIM.data\r\n<\/pre>\n<p>Submit the jobscript using:<\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>Other mpi based executables = <code>gpyro_propest<\/code><\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/reaxengineering.com\/trac\/gpyro\/wiki\/WikiStart\">gpyro website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Draft &#8211; not yet ready for general use Overview gpyro (Generalized Pyrolysis Model for Combustible Solids) is an open source computer model that describes the thermal response of solid materials exposed to radiative or convective heating, including thermo-oxidative pyrolysis of the condensed phase. Version is installed on the CSF. It was compiled with Intel Compilers 17.0. using -msse2 -axSSE4.2,AVX,CORE-AVX2,CORE-AVX512 and openmpi 3.1.3. Restrictions on use This software is open-source so all CSF users may use.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/gpyro\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":7,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2134","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2134","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\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=2134"}],"version-history":[{"count":9,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2134\/revisions"}],"predecessor-version":[{"id":2190,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2134\/revisions\/2190"}],"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=2134"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}