Introduction to the SUNs: u80csi2, u80csi3 and u80csi7

Overview | Logging in | Passwords | Files | Running | Parallelism | Busy? | Editing | Printing | Documentation | Compiling | Libraries | Applications | Where is ...? | Wish list 
This page describes the SUN Ultra 80 workstations u80csi2, u80csi3 and u80csi7 and the basics of using them.

Overview

We have access to three SUN Ultra80 workstations, u80csi2, 3 and 7, courtesy of the Computational Science Initiative. They are in the machine room SERF/C-109. Each machine has 4 450MHz processors and 4GB of memory, which is shared by all processors (like Isaac). The SUNs give a performan similar to Isaac (best), but in some cases may me much slower (by a factor of 2), due to compiler and architecture issues.

The machines run Solaris 8, SUN's version of UNIX. i.e. Each machine is (more or less) just another UNIX box with a sufficient number similarities to the SGI and IBMs to be comforting, but a sufficient number of differences to be annoying. Unfortunately, the PATHs to the compilers, libraries etc. are different to isaac - see below for updates.

Isaac's userspace is mounted: accounts (and passwords) are common to both machines - ~swei/PRL.tex is the same file on Isaac and the SUNs.

As these machines are very "bare bones", please inform Volker if you need any software installed.

Logging in

The machines are configured to allow telnet or rlogin from inside of NREL.

The password is the same as for Isaac and the IBMs [provided you have always changed your password correctly (see below)] The shell is the same as on isaac - almost certainly bash.

ssh is installed, allowing direct access from outside of NREL.

Passwords

Your account uses the "network" (NIS) password system. To change your password you should either (i) telnet to syssrv3a, login, then type "passwd", which is the safe and sure approach, or (ii) type "passwd" on Isaac, which should also change your NIS password.

Files

The machines NFS mount Isaac's userspace therefore inheriting all of Isaacs' disk space limits. Files are shared over 100Mb/sec ethernet, so large file transfers will be slow.

18GB of unmetered scratch/temporary space is available in /data. Please use this area for large files or calculations requiring a lot of disk space. This area is not purged automatically; please only make reasonable usage and delete files when not needed.

Running programs

Programs are launched as per any UNIX machine, i.e. ./a.out >nature.data runs a.out and redirects the output to nature.data

How do I run in parallel?

Only OpenMP is currently supported. MPICH is installed for MPI programs - see Volker for details, as there appears to be some issues. (HEROS WANTED: Problems were experienced installing SUN's MPI. Only the heroic or underemployed should attempt, as SUN's automated build system has problems.)

How busy is the system?

A version of the "top" command is installed at /usr/apps/bin/top. top gives the total system load and memory usage. Please always use "top" to check if the machines are "free"

SUN provides more detailed monitoring tools:

"sar 1" will average the system load for 1 second: 

u80csi2:~>sar 1



SunOS u80csi2 5.8 Generic sun4u    11/20/00



12:12:41    %usr    %sys    %wio   %idle

12:12:42      75       0       0      25
This shows that 3 (of the four) processors are busy and 1 is idling. See "man sar" for details of memory and I/O monitoring.

"ps -alu" will give a list of (nearly) all processes, with user names, and CPU usage. Other variants give nice priorities etc. 

u80csi2:/usr/apps/explorer>ps -alu

USER       PID %CPU %MEM   SZ  RSS TT       S    START  TIME COMMAND

ghart     5998 25.0  2.8143384110016 pts/14   O 08:18:30 314:42 vasp.sun

ghart     8867 24.9  0.85555232928 pts/16   O 13:01:28 34:15 vasp.sun

ghart     8948 24.8  1.06279237128 pts/15   R 13:20:24 15:25 vasp.sun

ghart     8986 24.7  0.95968834560 pts/13   O 13:26:50  9:06 vasp.sun

root      9045  0.1  0.1 1528 1112 pts/1    O 13:36:03  0:00 ps -alu

pkent     8568  0.0  0.1 2456 1760 pts/1    S 12:07:58  0:00 -bash
Here, Gus is running 4 vasp jobs.

Editing

Currently only vi and xemacs are installed. xemacs is in /opt/SUNWspro/bin

Printing

No printer queues are currently installed on the SUNs.

Documentation

In addition to the man pages, SUN has a searchable website with all documentation online: http://docs.sun.com

Compiling

Each machine has up to date f77, f90, f95, c, and c++ compilers. However, they are not on the default PATH.
You should: 
export PATH=$PATH:/opt/SUNWspro/bin:/usr/ccs/bin

export MANPATH=$MANPATH:/optSUNWspro/man
Then "f90 -o program_name sourcefile.f" will work as expected. "man f90" gives details of the optimisation settings.

If when attempting to run the c compiler "cc" you see the error 

/usr/ucb/cc:  language optional software package not installed
then you have either not set you PATH correctly (see above), or /usr/ucb/cc is being found ahead of /opt/SUNWspro/bin/cc. Change your path so that the compilers in /opt/SUNWspro/bin are found first

Libraries

BLAS, LAPACK and FFTs are found in SUN's performance library. Note that LAPACK is version 3.0; the version on Isaac is older. Link using f90 -o program sourcefile.f -xlic_lib=sunperf. Documentation can be found at http://docs.sun.com

The HDF5 includes, utilities, and libraries are installed under /usr/apps/hdf5/solaris. The directory structure is the same as on Isaac - only H5ROOT should require changing between the different machines.

Applications

Applications will be installed under /usr/apps as far is as reasonably possible.

IRIS Explorer (1-3D visualisation)

Currently installed under /usr/apps/explorer, you must sit at the console (in the machine room) to run.
The following settings are required: 
export EXPLORERHOME=/usr/apps/explorer

export PATH=$PATH:$EXPLORERHOME/bin

export LM_LICENSE_FILE=7312@sst-pc3.nrel.gov
The executable is "explorer"
 

OpenDX (1-3D visualisation)

C(in the machine room) to run.
The following settings are required: 
export EXPLORERHOME=/usr/apps/explorer



export PATH=$PATH:$EXPLORERHOME/bin



export LM_LICENSE_FILE=7312@sst-pc3.nrel.gov
The executable is "explorer"
 

OpenDX (1-3D visualisation)

Currently installed under /usr/apps/dx, you should sit at the console (in the machine room) to run. Sitting at the console allows the use of hardware rendering for significant speedups (try it - rendering is orders of magnitudes faster than software rending. Fly around your data!).

No special settings are required, but if you have a complex network you may wish to experiment with 

export DXPROCESSORS=4
The executable is "dx". However, to run dx you must:

1. "dx -execonly &"
2. "dx -uionly &"
3. In the user interface, go to the menu "Connection->Start Server". Select "Options", then "Already running server". Click "OK" in the options dialog and in the server dialog. You should now be able to select "Execute->Execute on change" and run a visualisation.
4. Select "Options->Rendering Options" and enable "Hardware" rendering. Force the renderer to redraw by, e.g. resetting or rotating the view. Rendering should be fast, colours may be a little different.

tgif (xfig like drawing tool)

In /usr/apps/bin.

Where is ...?

The chances are that your favourite appplication (e.g. top, TeX) is not installed or is renamed under Solaris. Check with the Solaris documentation, or mail Volker to add something to the wish list.

Wish list

Current list of wanted system software and applications: Previously wished for: Note that although it is intended that all the machines have an identical suite of software, due to IS issues there may be small differences. Let Volker know if any of these are problematic...
Last update: 20th November 2002
gabriel_bester@nrel.gov