EMsoft<\/a> is a program for the computation and visualization of scanning electron microscopy diffraction patterns, notably EBSD, ECP, TKD, and EKP. <\/p>\n Version 5.0.3 is installed on the CSF. The EMsoftSDK and EMsoftData packages have been installed centrally. <\/p>\n There are no restrictions on access EMsoft on the CSF. All usage must adhere to the license<\/a>.<\/p>\n We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n Load one of the following modulefiles:<\/p>\n This will set the The Please do not run EMsoft on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview EMsoft is a program for the computation and visualization of scanning electron microscopy diffraction patterns, notably EBSD, ECP, TKD, and EKP. Version 5.0.3 is installed on the CSF. The EMsoftSDK and EMsoftData packages have been installed centrally. Restrictions on use There are no restrictions on access EMsoft on the CSF. All usage must adhere to the license. Set up procedure We now recommend loading modulefiles within your jobscript so that you have a full.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-5277","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5277","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\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=5277"}],"version-history":[{"count":7,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5277\/revisions"}],"predecessor-version":[{"id":10394,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5277\/revisions\/10394"}],"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=5277"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/gcc\/emsoft\/5.0.3 # A release version (faster)\r\nmodule load apps\/gcc\/emsoft\/5.0.3-debug # Debugging turned on during compiler (slower)\r\n<\/pre>\n
EMSOFTPATHNAME<\/code> environment variable to point to the central installation. All other EMSOFT env vars are unset and so the application should work in your current working directory.<\/p>\nRunning the application<\/h2>\n
Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/gcc\/emsoft\/5.0.3\r\n\r\n# You may need to indicate where to write data and temp files.\r\nexport EMDATAPATHNAME=\/scratch\/$USER\/EMdata\/\r\nexport EMTMPPATHNAME=\/scratch\/$USER\/EMdata\/temp\/\r\nmkdir -p $EMDATAPATHNAME $EMTMPPATHNAME\r\n\r\n# Location where your Xtal data is stored. Change as required.\r\nexport EMXTALFOLDERPATHNAME=\/scratch\/$USER\/XtalFolder\/\r\n\r\n# Example running the EMEBSDDI app. The input .nml file needs modifying\r\n# to say how many cores are in use. Run the CSF helper script that adds\r\n# so lines to the end of the input file:\r\nemsoft-ri-cores-gpus-config $NSLOTS >> input<\/em>.nml\r\n\r\n# Now run the app\r\nEMEBSDDI input.nml\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
GPU batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n#$ -l v100=1 # Use a single GPU\r\n#$ -pe smp.pe 8 # Number of cores per GPU (2--8). Default is 1 if this line is missing.\r\n # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/gcc\/emsoft\/5.0.3\r\n\r\n# You may need to indicate where to write data and temp files.\r\n# [On a GPU node you may want to use $TMPDIR instead of\r\n# \/scratch\/$USER in the commands below to use the fast \r\n# NVMe storage. Files will be deleted from $TMPDIR automatically\r\n# at the end of the job.]\r\nexport EMDATAPATHNAME=\/scratch\/$USER\/EMdata\/\r\nexport EMTMPPATHNAME=\/scratch\/$USER\/EMdata\/temp\/\r\nmkdir -p $EMDATAPATHNAME $EMTMPPATHNAME\r\n\r\n# Location where your Xtal data is stored. Change as required.\r\nexport EMXTALFOLDERPATHNAME=\/scratch\/$USER\/XtalFolder\/\r\n\r\n# Example running the EMEBSDDI app. The input .nml file needs modifying\r\n# to say how many cores are in use. Run the CSF helper script that adds\r\n# so lines to the end of the input file:\r\nemsoft-ri-cores-gpus-config $NSLOTS $NGPUS >> input<\/em>.nml\r\n\r\n# Now run the app\r\nEMEBSDDI input.nml\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Further info<\/h2>\n
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Updates<\/h2>\n