MolCal-MPI<\/a> is a parallelization of the commonly used MobCal suite to calculate ion mobilities and collision cross sections (v1.2). For full documentation, see the MobCal-MPI user guide.<\/a><\/p>\n GNU GENERAL PUBLIC LICENSE Version 3 – (free to use, not for profit).<\/p>\n To access the software you must load one the following modulefile in your jobscript:<\/p>\n Please do not run Mobcal-MPI on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n To run, MobCal-MPI requires an input file, with the extension “.sub”. if you wish to run the jobscript examples below, please take the following preparatory steps: Submit the jobscript using:<\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Make sure you have your input file in the current directory and then create a jobscript in that directory. For example:<\/p>\n Submit the jobscript using:<\/p>\n If you have access to more than 32 cores, you can run multi-node jobs. These take longer to start but can complete the work faster. Submit the jobscript using:<\/p>\n The job example creates <\/p>\n with <\/p>\n output files.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview MolCal-MPI is a parallelization of the commonly used MobCal suite to calculate ion mobilities and collision cross sections (v1.2). For full documentation, see the MobCal-MPI user guide. Restrictions on use GNU GENERAL PUBLIC LICENSE Version 3 – (free to use, not for profit). Set up procedure To access the software you must load one the following modulefile in your jobscript: module load apps\/binapps\/mobcal\/12Jan2022 module load apps\/binapps\/mobcal\/24Oct2018 Running the application Please do not run Mobcal-MPI.. Read more »<\/a><\/p>\n","protected":false},"author":14,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-5721","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5721","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\/14"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=5721"}],"version-history":[{"count":10,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5721\/revisions"}],"predecessor-version":[{"id":6410,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5721\/revisions\/6410"}],"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=5721"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
module load apps\/binapps\/mobcal\/12Jan2022<\/pre>\n
module load apps\/binapps\/mobcal\/24Oct2018\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\n
\nFor batch job submission, this is confusing – as this is not<\/em> a jobscript to submit.<\/p>\n
\n
\nmkdir ~\/scratch\/mobcal
\ncd ~\/scratch\/mobcal
\ncp \/opt\/apps\/apps\/binapps\/mobcal\/24Oct2018\/Test_Files\/Mobcal_Inputs\/AMIFOSTINE_3.mfj .
\necho -e \"AMIFOSTINE_3.mfj\\nAMIFOSTINE_3.mout\" > Amifostine_3.sub
\n<\/code>
\nMake sure you have your input files “AMIFOSTINE_3.sub” and “AMIFOSTINE_3.mfj” in the current directory and then create a jobscript in that directory. For a serial job example:<\/p>\n#!\/bin\/bash --login\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n\r\nmodule load apps\/binapps\/mobcal\/24Oct2018\r\nMobCal_MPI.exe Amifostine_3.sub\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Single-node Parallel batch job submission<\/h3>\n
#!\/bin\/bash --login\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -pe smp.pe 8 # Number of cores (max 32)\r\n\r\nmodule load apps\/binapps\/mobcal\/24Oct2018\r\nmpirun -np $NSLOTS MobCal_MPI.exe Amifostine_3.sub<\/pre>\n
qsub scriptname\r\n\r\n<\/em><\/pre>\n
Multi-node Parallel batch job submission<\/h3>\n
\nMake sure you have your input file in the current directory and then create a jobscript in that directory. For example:<\/p>\n#!\/bin\/bash --login\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -pe mpi-24-ib.pe 48 # multiples of 24 cores\r\n\r\nmodule load apps\/binapps\/mobcal\/24Oct2018\r\nmpirun -np $NSLOTS MobCal_MPI.exe Amifostine_3.sub<\/pre>\n
qsub scriptname<\/em><\/pre>\n
AMIFOSTINE_3.mout<\/pre>\n
output_{1-X}.out<\/pre>\n