{"id":1879,"date":"2014-10-16T08:38:18","date_gmt":"2014-10-16T08:38:18","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=1879"},"modified":"2016-07-22T13:18:53","modified_gmt":"2016-07-22T13:18:53","slug":"gulp","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/gulp\/","title":{"rendered":"GULP"},"content":{"rendered":"

Overview<\/h2>\n

GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.<\/p>\n

Version 4.2 is installed on the CSF. It was compiled with Intel Compilers 14.0.3 and openmpi 1.6 (optimisation flags -O3 -msse4.2 and -axAVX <\/code>were used). This installation will only work on Intel nodes (due to some flags used in the openmpi compilation).<\/p>\n

Restrictions on use<\/h2>\n

GULP is available only for Staff and Students of the University to use (no visitor access permitted). It must not be used for commercial purposes or research. Use of the software must be cited in publications. All users must agree to abide by these conditions before being added to the relevant software group.<\/p>\n

There is no access to source code on the CSF.<\/p>\n

Set up procedure<\/h2>\n

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

To run on a single node (1 core jobs and multi-core jobs up to 16 cores)<\/p>\n

\r\nmodule load module apps\/intel-14.0\/gulp\/4.2\r\n<\/pre>\n
To run on more than one node (24 cores or more in multiples of 12)<\/p>\n
\r\nmodule load module apps\/intel-14.0\/gulp\/4.2-ib\r\n<\/pre>\n
The GULP utilities (arc2his<\/code>, mc2arc<\/code>, mdb2a<\/code> and reaxff2lib<\/code>) have been compiled without MPI or optimisation and must be run as serial jobs.<\/p>\n
Running the application<\/h2>\n
Please do not run GULP on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the 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\ngulp < input.gin\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
Parallel batch job submission - 2 to 24 cores<\/h3>\n
Make sure you have the appropriate 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 12\r\n\r\nmpirun -np $NSLOTS gulp < input.gin\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission - 48 cores or more in multiples of 24<\/h3>\n
Make sure you have the appropriate modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V \r\n#$ -pe orte-24-ib.pe 48\r\n\r\nmpirun -np $NSLOTS gulp < input.gin\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