cd into your FLASH directory (e.g., FLASH2.2).
Next, use the "setup" command (which is a python script) to setup the Brio Wu test problem:
./setup briowu -auto -maxblocks=1000
This copies files and creates links to files in the object/ directory (by default; if you want to use a different directory, use the "-objdir=" flag). The default setting is for a 2D run (for 3D use "-3D" flag). "-maxblocks=" sets the maximum number of grids per processor (this must be done at the setup, and can't be changed later).
cd to the object directory.
Complile the code with gnu make:
gmake
(Optional) To keep things cleaner, make a new directory (wherever) to contain the executable and output files. Copy the executable ("flash2") and parameter file ("flash.par") to that directory and cd into it.
In general, you should run the code with:
prun -n 4 flash2
This runs the code on four processors, and it should take only a couple of minutes to finish, though it could wait a while in the queue before it runs (depending on idra usage). Adding a "-I" flag to the prun command forces the run to execute immediately (if resources are available) or not at all (i.e., it will not be queued). The output files will be written to the current directory. The files with a name containing "chk" are checkpoint data files and contain all of the data at a given output time. Files with "plt" in the name contain a pre-specified subset of the data at a given ouput time.
The FLASH user's guide and FAQ describe the "setup" command and many options in detail.
On idra, read the man pages for prun. Other useful commands: xrinfo