Scripts

The following scripts (which can also be found in the repository of the code under “trunk/tools/scripts” can be used for submitting jobs or visualisation)

For visualizing data in VisIt
visnek

Basic Scripts

nek
run nek5000 interactively, in the foreground
Usage – nek

nekb
run nek5000 in the background
Usage – nekb

nekd
run nek5000 with gdb
To use gbd you must edit the makenek script setting “G = -g”. Then recompile (makenek clean; makenek ).
Usage – nekd then type ‘run’ to begin running in gdb

mvn
moves all relevant nek5000 data files to a new name.
Usage – mvn

cpn
copies all relevant nek5000 data files
Usage – cpn

Scripts for parallel runs

Some of these scripts might need to be tailored to each specific system, depending on the MPI environment. In the usage descriptions below, NP refers to the number of processors.

nekmpi
runs nek5000 interactively using mpirun
Usage – nekmpi NP

nekbmpi
runs nek5000 in background using mpirun, redirecting all standard output to the logfile, casename.log.NP
Usage – nekmpi NP

nekqsub
create a nek5000 command script and submit using qsub
Usage – nekqsub NP

nekpbs
run nek5000 in a batch script environment
Usage – nekpbs NP

NekNek Scripts

Running NekNek requires the makenek to be edited to turn the NekNek flag on. In the usage descriptions below, NP1 and NP2 refer to the number of processors specified for and

neknek
runs neknek code, redirecting the output into logfile named according to the first mesh
Uses the MPI environment
Usage – neknek NP1 NP2

neknekb
runs neknek code in the background
Usage – same as neknek

Short Run Scripts

Sometimes it is useful to test code for a short, predetermined number of steps.

nek10s
nek200s
nek1000s

runs nek5000, in serial, for 10, 200, or 1000 steps. Redirects all output to a logfile.
Usage – nek10s

nek10steps
nek200steps
nek1000steps
reuns nek5000 in parallel for 10, 200, or 1000 steps. Redirects all output to a logfile.
Usage – nek10steps NP