Amber (Assisted Model Building with Energy Refinement) is a general purpose molecular mechanics\/dynamics suite which uses analytic potential energy functions, derived from experimental and ab initio data, to refine macromolecular conformations.<\/p>\n
There are two installations of Amber 12 version available on the CSF:<\/p>\n
This software is licensed for University of Manchester users. All users should familiarise themselves with the License Agreement<\/a> before using this software. A copy is also available on the system in Please see ‘Running the Application’ below for detailed job submission examples.<\/p>\n Note 1: the modulefiles load additional modules required to run amber, for example the correct openmpi, therefore unloading the amber module will also unload these additional modules.<\/p>\n Note 2: Amber 12 and the associated AmberTools will not run on AMD nodes.<\/p>\n 1. Make sure you have the correct modulefile from the table above loaded.<\/p>\n 2. An example batch submission script:<\/p>\n 3. Submit with the command: By default SMP jobs will run on either a Westmere, Sandybridge, Ivybridge or Haswell nodes depending on what is available at the time. If the job gets a Sandybridge node (max 12 cores) or Ivybridge node (max 16 cores) or Haswell node (max 24 cores) it will perform better. If you wish to ensure that your job runs on one of Sandybridge, Ivybridge or Haswell see the example further down the page. Otherwise the system will choose a node for you – whichever becomes free.<\/p>\n 1. Make sure you have the correct modulefile from the table above loaded.<\/p>\n 2. An example batch submission script:<\/p>\n 3. Submit with the command: By default SMP jobs will run on either a Westmere, Sandybridge, Ivybridge or Haswell node depending on what is available at the time. If you wish to ensure that your job can take advantage of the Sandybridge, Ivybridge or Haswell nodes specifically you need to add an option to your job – see below.<\/p>\n 1. Make sure you have the correct modulefile from the table above loaded.<\/p>\n 2. An example batch submission script:<\/p>\n 3. Submit with the command: To request an Ivybridge node (max 16 cores) use:<\/p>\n instead of<\/p>\n and specify up to 16 cores.<\/p>\n For Haswell nodes (max 24 cores) use<\/p>\n 1. Make sure you have the correct modulefile from the table above loaded.<\/p>\n 2. An example batch submission script:<\/p>\n 3. Submit with the command: Note 1: Serial only<\/p>\n Note 2: You need to request being added to the relevant group to access GPUs before you can run amber on the GPUs.<\/p>\n 1. Make sure you have the correct modulefile from the table above loaded.<\/p>\n 2. An example batch submission script:<\/p>\n 3. Submit with the command: None since install in early Nov 2012.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Amber (Assisted Model Building with Energy Refinement) is a general purpose molecular mechanics\/dynamics suite which uses analytic potential energy functions, derived from experimental and ab initio data, to refine macromolecular conformations. There are two installations of Amber 12 version available on the CSF: Version 12 patched to bugfix level 20 with AmberTools 13 patched to bugfix level 21— detailed below Version 12 patched to bugfix level 13 with AmberTools 12 patched to bugfix level.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":731,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1984","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1984","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=1984"}],"version-history":[{"count":6,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1984\/revisions"}],"predecessor-version":[{"id":3232,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1984\/revisions\/3232"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/731"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=1984"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}$AMBERHOME\/amber12.license<\/code> .<\/p>\nSet up procedure<\/h2>\n
\n
at13<\/code> at the end are Amber12 with AmberTools 13.<\/li>\nmodule load<\/code> with one of the below modulefiles as the option to the command<\/li>\n<\/ul>\n\n
\n Modulefile<\/strong> <\/td>\n SGE\/batch information<\/strong> <\/td>\n<\/tr>\n \n apps\/intel-12.0\/amber\/12-at13 <\/td>\n For serial jobs and parallel jobs up to 24 cores. Uses AmberTools 13<\/td>\n smp.pe, orte.pe<\/td>\n<\/tr>\n \n apps\/intel-12.0\/amber\/12-ib-at13 <\/td>\n For parallel job which are 48 cores or more and a multiple of 24. Uses Infinband nodes and gives better performance. Uses AmberTools 13<\/td>\n orte-24-ib.pe<\/td>\n<\/tr>\n \n apps\/intel-12.0\/amber\/12-cuda-at13 <\/td>\n For pmemd.cuda jobs. Uses AmberTools 13 <\/td>\n -l nvidia <\/td>\n<\/tr>\n \n apps\/intel-12.0\/amber\/12 <\/td>\n For serial jobs and parallel jobs up to 24 cores.<\/td>\n smp.pe<\/td>\n<\/tr>\n \n apps\/intel-12.0\/amber\/12-ib <\/td>\n For parallel job which are 48 cores or more and a multiple of 24. Uses Infinband nodes and gives better performance.<\/td>\n orte-24-ib.pe<\/td>\n<\/tr>\n \n apps\/intel-12.0\/amber\/12-cuda <\/td>\n For pmemd.cuda jobs. <\/td>\n -l nvidia <\/td>\n<\/tr>\n<\/table>\n Running Serial Amber<\/h2>\n
\r\n### SGE Job Stuff\r\n### Set the directory you submit from to be the working directory\r\n#$ -cwd\r\n### Inherit the user environment settings from the login node (important so the job can find all commands)\r\n#$ -V\r\n\r\nsander -O \\\r\n -i file.in\r\n -o file.out\r\n -c file.restart\r\n -r file.rst\r\n -p file.prmtop\r\n -x file.cmd\r\n -inf file.inf\r\n<\/pre>\n
qsub scriptname<\/code><\/p>\nRunning Parallel Amber<\/h2>\n
Important notes for all parallel jobs<\/h3>\n
\n
SMP example – maximum of 24 cores<\/h3>\n
\r\n#!\/bin\/bash\r\n### SGE Job Stuff\r\n### Set the directory you submit from to be the working directory\r\n#$ -cwd\r\n### Inherit the user environment settings from the login node (important so the job can find all commands)\r\n#$ -V\r\n### Submit to the pe and tell SGE how many processors are required. $NSLOTS is set to be this number.\r\n#$ -pe smp.pe 6\r\nmpiexec -n $NSLOTS sander.MPI -O \\\r\n -i file.in\r\n -o file.out\r\n -c file.restart\r\n -r file.rst\r\n -p file.prmtop\r\n -x file.cmd\r\n -inf file.inf\r\n<\/pre>\n
qsub scriptname<\/code><\/p>\nSMP specifically Sandybridge, Ivybridge or Haswell example – maximum of 12, 16 or 24 cores<\/h3>\n
\r\n#!\/bin\/bash\r\n### SGE Job Stuff\r\n### Set the directory you submit from to be the working directory\r\n#$ -cwd\r\n### Inherit the user environment settings from the login node (important so the job can find all commands)\r\n#$ -V\r\n### Submit to the pe and tell SGE how many processors are required. $NSLOTS picks up this number.\r\n#$ -pe smp.pe 12\r\n#$ -l sandybridge\r\n\r\nmpiexec -n $NSLOTS sander.MPI -O \\\r\n -i file.in\r\n -o file.out\r\n -c file.restart\r\n -r file.rst\r\n -p file.prmtop\r\n -x file.cmd\r\n -inf file.inf\r\n<\/pre>\n
qsub scriptname<\/code><\/p>\n\r\n#$ -l ivybridge\r\n<\/pre>\n
\r\n#$ -l sandybridge\r\n<\/pre>\n
\r\n#$ -l haswell\r\n<\/pre>\n
Infiniband MPI example<\/h3>\n
\r\n#!\/bin\/bash\r\n### SGE Job Stuff\r\n### Set the directory you submit from to be the working directory\r\n#$ -cwd\r\n### Inherit the user environment settings from the login node (important so the job can find all commands)\r\n#$ -V\r\n### Submit to the pe and tell SGE how many processors are required. $NSLOTS picks up this number.\r\n#$ -pe orte-24-ib.pe 48\r\n\r\nmpiexec -n $NSLOTS sander.MPI -O \\\r\n -i file.in\r\n -o file.out\r\n -c file.restart\r\n -r file.rst\r\n -p file.prmtop\r\n -x file.cmd\r\n -inf file.inf\r\n<\/pre>\n
qsub scriptname<\/code><\/p>\npmemd.cuda example<\/h2>\n
\r\n#!\/bin\/bash\r\n### SGE Job Stuff\r\n### Set the directory you submit from to be the working directory\r\n#$ -cwd\r\n### Inherit the user environment settings from the login node (important so the job can find all commands)\r\n#$ -V\r\n#$ -l nvidia\r\n\r\npmemd.cuda -O -i mdin -o out.$JOB_ID\r\n<\/pre>\n
qsub scriptname<\/code><\/p>\n\n
Further info<\/h2>\n
\n
Updates<\/h2>\n