Accessing the Machine

SSH

You should log in to aurora with X11-forwarding via:
[code sh]
ssh -Y [uid]@aurora.multiscale.utah.edu

[/code]
to be able to run any windowed application like totalview and matlab.

Note that from off-campus you will need to use a VPN connection. For your VPN username, use [uid]@chpc.utah.edu to get the CHPC VPN pool.

FastX

This allows you to access the machines using xwindows through a web browser:

• aurora

Using the Desktop Client

1. Download the desktop client.  To do this, point a browser to the appropriate machine (see links above) and rather than logging in, click the link “Looking for the desktop client?” to download it.
2. Configure the client.  Launch the FastX client and click the “+” sign to add a new connection. Enter [host].multiscale.utah.edu as the host (substituting, prism, aurora or anasazi for host as appropriate) and your UNID as “User”
3. Connect to the prism connection you just made.
   • Note that you will need a VPN connection in order to connect through the desktop client if you are connecting from off campus.
4. Click “+”  and then choose “xfce” under the “Suggestions” drop-down menu.  This will launch a xterm desktop environment.  Alternatively, you can select a previous session or launch a specific command rather than clicking the “+” icon.

More Information

Additional information on FastX can be found on the CPHC web page.

Fair Use Policy

These machines are primarily intended for development. If you need to run small cases, feel free, but do not overload the machine.

Also note that aurora runs our Jenkins build/test system, so it will have periodic load spikes associated with code commits.  So you should never load aurora more than 50% for extended periods of time.

---

Machine Description

aurora is a linux desktop machine with the following specs:

• 2 x Intel Xeon 12 Core E5-2670 v3 2.30GHz processors
• 30 MB L3 Cache
• 64 GB RAM
• nVidia Tesla K80 GPU with 24 GB memory

Filesystems

aurora mounts several filesystems:

• CHPC home directory. When you log into prism, you will land in your CHPC home directory. Note that this is SLOW read/write access. You should not run cases or compile code from this directory.

• 700 GB of local SSD scratch disk space located at

/scratch/local/aurora_fast

• This is not backed up, but is persistent (will not be purged) unless you abuse it.
• 5.5 TB of local scratch disk space located at

    /scratch/local/aurora_large
  

  This is not backed up, but is persistent (will not be purged) unless you abuse it.

Mounting Aurora’s Filesystem

Samba mount via:

  smb://ad;<UNID>@aurora.multiscale.utah.edu/Aurora

and when prompted for your user name, use:

  ad\[UNID]

and your campus password.

If you are connected via Uconnect Wifi, make sure that you set the following username for Uconnect:

  <UNID>@chpc.utah.edu

your password should be the same as your campus password.

---

Software installed

It has most software pre-installed. If you need something that is not installed, contact James.

Some software requires you to load modules:

• totalview: module load totalview
• matlab: module load matlab

A recent version of visit is available at:

• visit: /usr/local/visit/bin/visit

Some useful “productivity software”

• LyX (just run lyx& from a command prompt).
• LibreOffice: libreoffice&
• xpdf (pdf reader)
• inkscape for drawing graphics

Cantera

Many of our codes have a dependency on Cantera.  We maintain our own version that has a few modifications to the main cantera development branch.  This has been installed on prism, aurora and anasazi in [code]/usr/local[/code].  Be sure to set the following environment variables:

[code]

setenv PYTHONPATH /usr/local/lib/python2.7/site-packages

[/code]

This is required to convert .cti files to .xml files as cantera starts up.

If you are having trouble with Cantera on prism or aurora, look at

[code]

/usr/local/cantera/bin/setup_cantera

[/code]

which has a number of environment variables that you may want to set.  In fact, it is best to add:

[code]

source /usr/local/cantera/bin/setup_cantera

[code]

to your shell login script.

Building Uintah

Many of you are interested in using aurora to build Uintah. Here’s one approach to do so:

• Create a working directory for yourself under /scratch/local/prism_fast or /scratch/local/aurora_fast. It is best that you call this directory by the first letter of your first name followed by your last name. Lets call this jdoe.
• cd /scratch/local/prism_large/jdoe
• checkout a fresh version of uintah: git clone https://github.com/Uintah/Uintah.git uintah. This will checkout the latest copy of Uintah and store it under ./uintah
• change directories to uintah: cd uintah
• we will start by building an optimized version of uintah: mkdir opt
• change directories to the optimized folder: cd opt
• create a configure script: vi uintah-configure-opt.line
• paste the following:
  [shell]../src/configure
  –with-hypre=/usr/local/hypre_2.11.2
  –with-mpi-include=/usr/include/mpich \
  –with-mpi-lib=/usr/lib/mpich/lib \
  –enable-wasatch_3p \
  –enable-wasatch \
  –without-fortran \
  –with-boost=/usr \
  –enable-64bit \
  –enable-optimize=’-O3′[/shell]
  • make your configure line executable: chmod +x uintah-configure-opt.line
  • execute your configure line: ./uintah-configure-opt.line
  • wait… if unsuccessful, you will see a lot of errors 🙂
  • now build! make -j 10
  • To build in debug, create a directory called dbg and a new configure line uintah-configure-dbg.line.
  • You will need to replace --enable-optimize='-O3' with --enable-debug and you’re good to go.