SC Linux Workstations
- Access requirements
- Locations and availability
- Obtaining help
- Usage policy and guidelines
- Logging in
- Disk space management (Warning!)
- Locally installed software
- Launching remote software
The Supercomputing Facility provides its users with access to several specially configured Linux workstations at two separate locations (see below) on campus. The primary function of such workstations is to provide stand-alone platforms for interactive pre- and post-processing tasks, including visualization, that are directly related to larger-scale computation on the supercomputers themselves. This manner of handling such tasks is more convenient and effective than the direct use of supercomputers for them.
We require the use of AMS to activate logins on the workstations. To obtain access:
- Apply for an account on any of the Supercomputing servers, if you have not already done so.
- Send a request to firstname.lastname@example.org, requesting access to the SCLAB workstations.
- When you have been notified that you are approved, activate the SCLAB resource in AMS. Read our instructions on using AMS for more details. Allow up to 30 minutes for your account to be accessible.
Locations and availability
Four Linux workstations (hostnames: sclab2.tamu.edu, sclab3.tamu.edu, sclab4.tamu.edu, sclab5.tamu.edu) have been installed in the Open Access Lab at Zachry in room 104 (ZACH 104). Additional information about the lab may be found here. Three additional workstations (hostname: sclab1.tamu.edu,sclab6.tamu.edu,sclab7.tamu.edu) have also been installed at the Student Computing Center (SCC). This lab is typically open 24 hours during the weekdays and for a more limited time on the weekends. Note: The SCLAB workstations were renamed from perkX.tamu.edu to sclabX.tamu.edu on September 18th, 2013. At present, each workstation is available at either name but users should switch to using sclabX.tamu.edu. The daily schedule for both labs can be found here.
The support staff at both labs mentioned above should be the initial point of contact for obvious hardware problems. All other issues (including hardware problems) should be reported to the Supercomputing Helpdesk by calling 845-0219 or by sending email to email@example.com. When sending email, be sure to follow these recommendations so we can help you in a prompt and efficient manner.
Usage policy and guidelines
The Linux workstation accounts are not to be used for work that is unrelated to the purpose for which a user was granted a supercomputing account. These machines are meant primarily for interactive tasks (post-processing or visualization work). Users who need to work primarily through the batch systems on the supercomputers (submitting batch jobs and running programs on the command line) may do so using any of the windows machines in the open access labs. They simply need a secure shell window to log in to one or more of the supercomputers. When both types of users wish to use the Linux workstations, those with non-interactive needs must yield use of the machines to those who have interactive/graphical/visualisation tasks to perform. Furthermore, no user may occupy a workstation for more than 2 hours in a single sitting, unless there is no one else waiting to use a workstation.
Users may login to these workstations either at the console (while sitting in front of the workstation), or remotely over the network using a secure shell connection (SSH). In either case, the user must supply a username and password to gain access to the account. You must activate your username/password for the Linux workstations via AMS. The Linux workstations are represented by the SCLAB AMS resource.
Disk space management
There are several directories on each workstation where users may store files. It is important to understand the characteristics of each directory. Storing your data in the "wrong" place could mean that you will need to expend time and effort to find it again, and in certain cases, it may mean losing your data altogether!
Backed up? 1
Shared 3 Over
16 GB max
- Backed up data is that which is written to tape so that it may be recovered in the event the copy on disk storage is corrupted/destroyed. None of the directories listed above are backed up to tape.
- Persistent storage means that data will not be deleted across system re-boots, or by automated administrative scripts. In some systems, certain directories such as
/tmpcan be "cleaned out" automatically by the OS when the system comes back up after a re-boot. Data in such "temporary" directories may also be deleted by administrative scripts which try to ensure sufficient empty space by periodically deleting older files in these shared disk areas. The
/scratchfilesystem on each workstation is automatically cleaned up by an automated script whenever it fills up to 80% capacity. The script keeps deleting files (oldest first) until the filesystem is only 20% full.
- Directories which are not shared, like
/home/aggiefor instance, represent separate and independent disk storage that is local to each workstation. Saving a file in
/scratch/aggieon the workstation sclab2.tamu.edu means that you cannot access it in
/scratch/aggieon any workstation other than sclab2.tamu.edu. You might find that even when you later return to sclab2.tamu.edu to access the file, it may have been deleted by the automated cleanup script (see note 2). You have been warned!
Locally installed software
The following software packages have been installed on each of the Linux workstations to enable users to offload postprocessing and visualization tasks from the heavily loaded (and therefore interactively less responsive) supercomputers.
In the course of maintaining these packages on the workstations, whenever we become aware of problems/issues with any package, we will post solutions/work-arounds to the problems in the section below.
The following commericial (licensed) applications are presently installed.
Software Command Abaqus 6.12 CAE abq6121 cae (1) Matlab 2013a matlab
- NOTE: for users that are running Abaqus CAE and Viewer on a SCLAB workstation and using X11 forwarding to display the GUI on their Windows PC. The -mesa command line option should be used if your X11 emulator does not support OpenGL (eg. Xming).
In addition to commercial applications, there is a plethora of open-source software installed on these systems. These include:
Software Command Grace xmgrace GROMACS (see: rpm -ql gromacs | grep bin) LAMMPS lmp_g++ LibreOffice ooffice NAMD namd Ncview ncview OpenFOAM (see: rpm -ql OpenFOAM | grep /bin/) Paraview paraview RStudio rstudio TexLive latex, dvips, bibtex, etc.
and many more. For a complete listing of installed software, see this page (sclab0.tamu.edu as of 26sep2013).
Launching remote software
If there is a need to launch software that resides on one of the supercomputers but have it display it's graphical interface on the Linux workstation where the user is sitting, the following instructions can be used: Assume the program name is "xemacs" and that it resides on and will be executed on the machine "eos". At the prompt in a unix shell window (on your workstation), type:
ssh -X eos
Enter your (eos) password in response to the password prompt generated by the ssh program. Once you are logged in to eos, type:
Component Specification System Dell Optiplex 960 CPU Intel Core2 Duo E8500, 3.16Ghz Architecture x86_64 Operating System Fedora 19 64Bit Kernel Version 3.10.10-200.fc19.x86_64 (as of 12sep2013) Main Memory 4GB Hard Disk 250GB Network 100Mbps Ethernet For a detailed listing of the types of hardware provided, see this page (sclab0.tamu.edu as of 18sep2013)