{"id":4404,"date":"2018-02-09T16:08:55","date_gmt":"2018-02-09T16:08:55","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4404"},"modified":"2018-02-12T09:56:21","modified_gmt":"2018-02-12T09:56:21","slug":"plumed","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/plumed\/","title":{"rendered":"Plumed"},"content":{"rendered":"

Overview<\/h2>\n

PLUMED<\/a> PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines.<\/p>\n

Version 2.4.0 is installed on the CSF. It was compiled with the Intel 15.0.3 compiler and uses the Intel MKL for blas and lapack functions.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing this software on the CSF. It is released under the GNU Lesser GPL v3.0<\/a> and any usage must adhere to that license.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load one of the following modulefile:<\/p>\n

\r\nmodule load apps\/intel-15.0\/plumed\/2.4.0            # Serial or Single-node OpenMP parallel\r\nmodule load apps\/intel-15.0\/plumed\/2.4.0-mpi        # Single-node MPI parallel\r\nmodule load apps\/intel-15.0\/plumed\/2.4.0-mpi-ib     # Multi-node MPI parallel using Infiniband network\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run plumed on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
Plumed provides a list of commands \/ tools that are run via the main plumed<\/code> executable. To see a list of available commands \/ tools you may run the following on the login node:<\/p>\n
\r\nplumed -h\r\n<\/pre>\n
The tools are:<\/p>\n
\r\ndriver\t\tkt\t\tsimplemd\tmklib\r\ndriver-float\tmanual\t\tsum_hills\tpartial_tempering\r\ngentemplate\tpathtools\tnewcv\t\tvim2html\r\ninfo\t\tpesmd\t\tconfig\t\tpatch\r\n<\/pre>\n
Serial batch job submission<\/h3>\n
Make sure you have the OpenMP plumed modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n# Inform plumed how many cores to use (1 for serial)\r\nexport OMP_NUM_THREADS=$NSLOTS\r\nplumed toolname<\/em> list of input flags for that tool<\/em>\r\n         #\r\n         # See above for list of tool names. \r\n         # Example: To display the plumed version use:\r\n         # plumed info --version\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
OpenMP Parallel batch job submission<\/h3>\n
Make sure you have the OpenMP plumed modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Number of cores (2-23 for single-node multi-core jobs)\r\n\r\n# Inform plumed how many cores to use\r\nexport OMP_NUM_THREADS=$NSLOTS\r\nplumed toolname<\/em> list of input flags for that tool<\/em>\r\n         #\r\n         # See above for list of tool names. \r\n         # Example: To display the plumed version use:\r\n         # plumed info --version\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
MPI Parallel batch job submission<\/h3>\n
Make sure you have one of the MPI plumed modulefiles loaded (the -ib version should be used when running multi-node parallel jobs) then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n#### Choose one of the following\r\n#$ -pe smp.pe 8           # Number of cores (2-23 for single-node parallel jobs)\r\n### OR\r\n#$ -pe orte-24-ib.pe  48  # Number of cores (48 or more in multiples of 24 for multi-node jobs)\r\n\r\n# Run the requested number of parallel instances of plumed\r\nmpirun -n $NSLOTS plumed toolname<\/em> list of input flags for that tool<\/em>\r\n                            #\r\n                            # See above for list of tool names. \r\n                            # Example: To display the plumed version use:\r\n                            # plumed info --version\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n