VisIt on BH
There is a binary installation of LLNL's VisIt visualization program at /bd3/visit on the BH cluster. If you have an account on BH, you can download VisIt to your local machine to view files on BH in 3D, and manipulate them as if they were local.
Download VisIt binaries from here. Compiling for yourself is not recommended, it is an extraordinarily painful build process. Be sure to download version 3.1.2 as this is what is on BH and the protocol is not stable between even minor versions.
VisIt and its component programs need to be in your execution PATH on BH. This involves adding the following to .bashrc:
export PATH=$PATH:/bd3/visit/bin:/bd3/visit/3.1.2/bin:/bd3/visit/3.1.2/linux-x86_64/binAfter adding this, you should be able to login with X forwarding (ssh -X bh.astro.illinois.edu), type visit at the command line, and see the VisIt loading screen pop up. The GUI will be very, very slow in this mode except maybe if you're on campus.
On your local machine, open visit and go to Options -> Host Profiles..., create a new profile for BH, and enter the following (replacing the username with your own username on BH):
Each dumps folder in the library on bh:/bd3 should have a folder inside it called xmf, containing a file for each dump ending in .xmf. These are by far the preferred files to work with in VisIt, as they are geometry-aware, so scalars are plotted in r,th,phi, vectors point the right direction, etc.
You can generate xdmf files from normal HARM output with the script xdmf_output.py in this repository. VisIt can plot many different derived variables as well (vector quantities, field strength, etc), using the expressions in visit-expressions.xml, also in this repository, which can be loaded in the VisIt UI under Controls -> Expressions... by pressing Load.
- VisIt does not save your settings unless you select
Options -> Save Settings. Don't ask me why. - VisIt groups all
.h5or.xmffiles in a directory together by default. Don't open them all or the mdserver on BH will crash due to file handle limits and you will have to restart VisIt.
Usually the GUI is pretty clear about errors. Failing to tunnel data connections will cause a "cannot connect" error when first listing a directory, and opening too many files will cause a "file handles" error followed by a silent inability to do anything until the GUI is restarted.
If your error is more subtle than those, detailed logs are available by running visit -debug 5. However, these are client-side only. To get debug logs on the server side, create a new "launch profile" in the host profile for BH, and add "-debug 5" to the additional arguments field.