1. NOISELAB COMPUTING RESOURCES
2. GUIDELINES FOR USAGE
3. DISK SPACE AND DATA DIRECTORIES
6. FILE MANAGEMENT
8. USING 'SCREEN'
9. LONG MATLAB JOBS
10. MATLAB BENCHMARKING
11. MATLAB FOR PERSONAL MACHINES
1. NOISELAB COMPUTING RESOURCES
||Dual Intel Xeon E5-2683 v4 2.1 GHz, 40MB cache, 16 cores/32 threads ea. (Total 64 threads available)
||Dual Intel Xeon X5570 2.93 GHz, 8MB cache, 4 cores/8 threads ea. (Total 16 threads available)
The Noiselab computing clusters are listed above. Velella and Pupa are located in the UCSD network and require special accounts for access. The UCSD network can be accessed off-campus via VPN .
Both Velella and Pupa contain numerous scientific computing software packages, acoustic propagation codes, and inversion codes. Available software is listed in Section 5.
- 2x400 GB Solid State Drives STAT Mix Use MC 6 Gbps (system disks, mirrored)
- 7x2 TB 7200 RPM NLSAS 512n Hot-plug Hard Drives in RAID-z2 configuration (with hot spare)
- 9 TB usable disk space
- 7 empty slots for more disk drives (capacity for future doubling disk space)
2. GUIDELINES FOR USAGEWe have no hard restrictions on CPU usage! Please be reasonable!
a) The load on both systems can be monitored with the top command.
b) If you have many jobs to run, execute them sequentially using scripting.
c) Run snippets of code to verify output before running the full (and potentially long) job.
d) A job should not take more than a day to run. Long jobs should be split into sequences that can be tested before continuing.
e) For long jobs write the results out with regular intervals (e.g. once an hour).
3. DISK SPACE AND DATA DIRECTORIESAll Noiselab acoustic experimental data is linked as /project/ in Velella and Pupa.
The folder /project/Noiselab with some data and past papers by the group.
You can see how much disk space is used by the command
You can see how much disk space you use in a directory and subdirectories
4. GRAPHICSExpanDrive is a file managment GUI which may provide easier interfacing between local machines and remote linux machines.
XQuartz provides a GUI environment for software launched remotely from linux terminal (e.g. Matlab)
5. SOFTWAREThe following software packages are installed on the Noiselab clusters:
(1) Matlab R2016b
(2) Python (Anaconda, include the path '/usr/local/anaconda3/bin' in your search path to use it.)
To query whether particular software or packages are installed, you may search for all or part of a filename with the command: 'rpm -qa | grep -i <part of name>'
If you would require a particular software package, you may request it via firstname.lastname@example.org.
6. FILE MANAGEMENTFiles can be transferred between your local machine to the computer clusters in several ways.
One way is to use the secure copy (scp) commands:
(1) To copy a file from one machine to another via scp use: 'scp <directory/filename to copy> <destination_directory>'
...for example, to copy from your local machine to Velella use: 'scp <username>@velella.ucsd.edu:<directory/filename to copy from> <local_directory>'
(2) To copy a directory use the '-rp' (recursive, preserving other file attributes) option: 'scp -rp <directory_to_copy> <destination_directory>'
A nicer way is to use a GUI program. One program that works well is FileZilla. It provides a GUI file management interface between your local machine and ftp (sftp) servers. It works across macOS/linus/unix/windows platforms and is free and open source. To communicate with the clusters, you use SFTP (port 22).
There are also a number of intra-server (linux) GUI’s, and at least one is already installed on Velella: Nautilus, though this requires graphics rendering (xQuartz).
6. PRINTERSThe following Noiselab printers are located in Spiess Hall:
(1) Color printer: HP LaserJet 600 color MFP M775: Web address: mpl-lwwaklabd.ucsd.edu, IP Address:172.16.128.18
printer name on linux systems: lwwaklabd
(2) B/W printer: HP LaserJet Enterprise M609: mpl-lwwaklab.ucsd.edu, IP Address:172.16.128.16
7. USING 'SCREEN'By using 'screen' you can have a termial running even after you have disconnected. When you login again you can reattach the screen. http://www.rackaid.com/resources/linux-screen-tutorial-and-how-to/
To start a new screen, simply type 'screen' at the prompt. You can start a new process in here and detach the screen by pressing Ctrl-a-d. You can logout of the main shell and screen will still be open. To see all open screens, type 'screen -ls'. If you're attached to the screen, it displayes [Attached], else it displays [Detached]. To reattach a detached screen, type ' screen -r <screen name>' You can complete screen name by tab. To exit a screen, just type 'exit' inside the screen.
8. LONG MATLAB JOBSBefore you start a long job remember to make many small tests--- It is a lot easier to find bugs in small runs!
For a long job you can save the output to mat file and then later read that into matlab for post-processing (recommended). Alternatively you you can print your figures to a file.
9. MATLAB BENCHMARKINGmean(bench(10))
LU FFT ODE Sparse 2D 3D
Pupa 0.1918 0.1383 0.1300 0.1533 3.1288 5.3459 (Aug 2017)
Velella 0.0654 0.1102 0.0656 0.1223 2.6750 4.9456 (Aug 2017)
10. MATLAB FOR PERSONAL MACHINESThe University of California San Diego has a Total Academic Headcount license for Matlab. Multiple Matlab versions, toolboxes, and licenses are
available for download for UCSD students, faculty, and staff for both univerity-owned and personal computers.