SGI ALTIX 3700 - Inferno

The Inferno systems are SGI Enterprise ALTIX 3700 Superclusters which provides Virginia Tech researchers with access to high performance computing on an SGI hardware platform:

Obtaining an Account

Faculty and Graduate Students may obtain accounts on the SGI ALTIX by completing the web based User Account Application Form. As part of your application request, you will be asked for your name, PID, department,address, phone number, system resource requirements, and for an abstract describing the research for which Inferno will be used. The inclusion of citations to related journal publications is encourage

Unfortunately, the SGI Altix 3700 does not support several significant software applications required by researchers at Virginia Tech. To provide support for these applications, the VT Research Computing Group has purchased a Sun Microsystems server. Dante is a Sun Fire v480 system running Solaris 9 which provides Virginia Tech researchers with access to high performance computing on a Sun Microsystems hardware platform and supports SAS, MATLAB, IMSL, and Gauss which are not currently available on Inferno. The system currently contains four 900 MHz CPUs, 16 GB memory, two 36 GB fiber-channel drives, and external storage on the Virginia Tech NAS.

Note:  By default, an account on Dante will only be created if you require an application (such as SAS or MATLAB) or the IMSL libraries which are not currently available on Inferno; otherwise, an account will be created for you on Inferno. Accounts on both Inferno and Dante will be created if you require applications found on both systems. Shared disk space between the two systems is provided to facilitate file access.

Note: Submitted abstracts may be made available online at some future date via hypertext links from the VT SGI ALTIX webpage.

Accounts will typically be created within one workday of submission, but, occassionally, up to one week may required to complete user verification and account processing.

Support

If you need assistance, contact 4Help by using the Help Request Form (http://4help.vt.edu/info/4help/request/escalate.asp) or by calling (540) 231-HELP (4357).

Usage Overview

This document assumes that you are already familiar with using a UNIX operating system. For a general information about using UNIX systems, see Introduction to VTAIX;   for specific information regarding SGI ALTIX systems, see SGI Technical Publications.

Documentation of many commands is available via the  "info"  command as well as from the  "man" command. For example, to obtain a description of the Intel debugger, enter:

info  idb

To obtain informaiton about the current hardware installed on the system, enter:

hinv

An SSH (Secure Shell) client is required to log onto Inferno. Example SSH clients include ssh for most UNIX systems (i.e., at your UNIX shell prompt, enter:  ssh inferno.cc.vt.edu), SSH Secure Shell for MS Windows Systems, Secure-CRT (for Windows 95/98/NT/2000), or F-Secure's SSH (for Windows 95/98/NT/2000 or Macintosh systems).

Transferring Files: Although you can use the ftp command from Inferno to move files and data to or from the system, it is recommended that you use a secure file copy program, such as as the UNIX "scp" command, instead. If you are using a Windows 95/98/NT/2000/ME system, you are encouraged to use the Secure File Transfer client which is included with SSH Secure Shell.

Disk Space Allocations

Each user account is initially allocated 5 GB of disk space with more space available upon request.

To view current disk availability, enter:

df  -k

To view your current disk utilization, enter:

cd
du  -k

Disconnected Program Processing

A batch queuing system will be available on "Inferno" in the future, but is not yet installed. In the interim, you can use the  "nohup"  to submit jobs for background processing and enable them to continue processing after logoff, i. e., enter:

nohup  command_name_and_options  &

where command_name_and_options is the name of a shell script or a command with options that you wish to execute.

For example, to submit the Mathematica program my_prog.ma for background processing, enter:

nohup  math  <my_prog.ma  &

Note:  it is necessary to press the "Enter" key a second time after the "nohup: appending output to `nohup.out'" message appears in order to regain the command prompt.

For additional information on using the nohup command and general information regarding the use of UNIX systems, see: Background Jobs and Logout -- the "nohup" command

Default File Permissions

When the file system of Inferno was initially installed, the umask was set such that new files are created with user writable and group readable permissions (-rw-r-----), i.e., umask 027. If you desire, you can use the  chmod  command to change the permissions of your existing files or the umask to change the the default permissions which will be assigned to new files. For example, to assign write permission to user and read permission to everyone (-rw-r--r--), add the following command to .profile (Bourne and Korn Shell users) or .login (C Shell users):

umask  022

Installed Software

The following software is currently available on the SGI ALTIX for your use:

Application Programs

ABAQUS

is a software application used for advanced finite element analysis.

To invoke ABAQUS to execute commands contained in the file   "abq_test.inp"   in the current directory, enter:

abaqus  job=abq_test

Mathematica

provides an environment and collection of tools for visualization, computation, and mathematical analysis.

To invoke Mathematica interactively, enter:

math

Exit the command  Quit  to exit from the Mathematica environment.

To invoke the Mathematica to execute the Mathematica program file file_name.m, enter:

math  <file_name.m

Gaussian

is an interconnected system of programs used for performing molecular orbital calculations. Gaussian 03 is now available for your use on Inferno.

To execute your Gaussian program, enter the command g03 followed by the name of your Gaussian program file, followed by the name you wish to assign to the output file. For example, to use the sample water molecule file, test000.com copied to the current directory, you could use the following command:

 g03  <test000.com  >test.out

GASP

AeroSoft's GASP (General Aerodynamic Simulation Program; version 4.2) has been ported to the SGI Altix platform and is available on Inferno. Version 4.2 features a new input format (xml) so that earlier (e.g. 4.1) input files can not be used. There is a gasp41to42 utility to convert input files but the conversion is not entirely robust and is not available for the Altix. If you have 4.1 files then you should run gasp41to42 on the (SGI or linux) machine you have been using.

In order to use GASP, you must be a member of the  "gasp"  group; if you had indicated that you would be using GASP, you were automatically added to the  group; otherwise -----------

Before you begin using GASP, you must first define the AEROSOFT_HOME environment variable and include the directory referenced by this the first element of the directory search path. If you are using GASP on a regular basis, you may wish to add these commands to .profile (Bourne and Korn Shell users) or .login (C Shell users).

First set the AEROSOFT_HOME environment variable; if you are using the Bourne or Korn Shell, the command would be:

AEROSOFT_HOME=/opt/local/repositories/ia64/AeroSoft
export AEROSOFT_HOME

If you are using the C Shell or one of its derivatives, the command would be:

setenv AEROSOFT_HOME /opt/local/repositories/ia64/AeroSoft

Note: by default, under Altix,  'gasp'  is the name of the gnu assembler:

$ which gasp
/usr/bin/gasp

Therefore you should set your search path so that the  "$AERO_SOFT_HOME/bin"  directory occurs before the  "/usr/bin"  directory. If you are using the Bourne or Korn Shell, the command to do this would be:

export PATH=$AEROSOFT_HOME/bin:$PATH

If you are using the C Shell or one of its derivatives, the command would be:

set path = ($AEROSOFT_HOME/bin:$path)

You are now ready to run a GASP program. For example, to use the GASP solver with GASP program information in the file  "my_gap_program.xml", you could enter the following command:

gasp --solve -i my_gasp_program.xml < /dev/null

Note: the  "/dev/null"  is included above to prevent stalling during program execution.

If you plan to use the GASP gui, log onto Inferno from a system running an X Windows System Server. If you are using a UNIX based desktop system that includes an X server, you may be able to use ssh to initiate your X Windows System session. For example, to begin an X session using the account  "my_inferno_id"  on Inferno, try the following command:

ssh  -X  my_inferno_id@inferno.cc.vt.edu

Then set the  "DISPLAY"  environmental variable to send your GASP output back to the X Server. For example if the IP address of your X server is  "aaa.bbb.ccc.ddd", you could use the following command from the Bourne Shell and its derivatives (ex: sh, ksh, and bash):

export DISPLAY=aaa.bbb.ccc.ddd:0.0

Or the following command from the C shell and its derivatives (e.g., csh or tcsh):

setenv  DISPLAY  aaa.bbb.ccc.ddd:0.0

Note:  When you start the GASP gui, you may receive the following message which can be safely ignored:

** WARNING **:
Unable to locate loadable module in module_path: "libraleigh.so"

Compilers

The SGI Intel 8.0 Fortran and C Compilers are now available on Inferno:

To compile a Fortran program "test_prog.f" using the Intel 8.0 compiler, enter:

ifort test_prog.f

To compile the C Language program "test_prog.c" using the Intel 8.0 C compiler, enter:

icc  test_prog.c

Note:  If you prefer to use the GNU C compiler, use  "cc"  instead of  "ecc"  to compile your programs.

Tuning Guide Fortran Reference Manual

Subroutine Libraries

The following subroutine libraries are currently installed on the system:

SCSL

-- Scientific Computing Software Library: provides a set of parallel and scalable functions and tools used widely in scientific and engineering computing. includes BLAS (Basic Linear Algebra Subroutines), LAPACK (Linear Algebra Package), FFT and signal processing routines, and sparse equation solvers plus OpenMP-Parallelized versions of BLAS-2/3.

To link in this libarary, use:   -lscs   or   -lscs_mp

Intel MKL

-- Math Kernel Library

Intel IPP

-- Integrated Performance Primitives Library

SGI MPT

-- Message Passing Libraries for Altix including MPI and SHMEM

Debuggers

gdb

is the GNU debugger for C and C++ code.

For additional information on using this debugger, enter the command:

info gdb

idb

is Intel's proprietary debugger designed for its compilers; supports C, C++, and Fortran. For additional information on using this debugger, enter the command:

info idb

Parallel Processing

The objective of parallel processing is to reduce the wall clock time associated with the execution of program code by distributing the code processing across multiple processors. Note, however, that the total CPU time for the program will increase as a result of the communication between processors. Thus, typically, only long running programs which are to be run multiple times will be written or modified to be executed as parallel applications.