Welcome to spacibm!


Recent Updates


2014 July 14

STSDAS and TABLES have been upgraded to version 3.17.


2014 July 07

HEAsoft has been upgraded to the 64-bit version 6.16. Please note the new path needed in your .cshrc/.bashrc. Some older versions are still available.


2014 May 30

Matlab has been upgraded to version 2014a. Older versions are still available (check below for the appropriate command path).


2014 February 04

IDL 8.3 has been installed. It is now the default version. Note that IDL is now owned by Exelis, so there is a new path for the set-up file.


2013 November 28

The operating system has been updated to SLES 11 SP3.


2013 August 16

ds9 has been upgraded to version 7.2.


2013 February 06

Mathematica has been upgraded to version 9.0.1. The previous versions are still available (check below for the appropriate command path). Note: if you are having problems checking out licenses, then remove your .Mathematica/Licensing/mathpass file.


2013 January 24

IRAF has been upgraded to version 2.16. Before using this version for the first time, users should move their login.cl file and uparm directory somewhere else, reinitialize their configuration using mkiraf, and then merge any desired settings from the old version into the new one.


System Overview

spacibm.rice.edu (128.42.200.228) is a dual-opteron (64-bit AMD 246) IBM. It is the departmental server for mail, web, IDL etc. It also has up-to-date data analysis packages (Fortran, IDL, Matlab, Mathematica, HEAsoft, IRAF...), and office programs (LibreOffice, latex, GIMP...).

spacibm runs SuSE Enterprise Linux 11.3. This only has a few subtle differences from Red Hat.

You can search for the location of commands using which or locate. Make sure that e.g. the path and lpath environments in .cshrc and aliases point to the correct program.


Printers

The names of the main print queues are ps2430 (default printer), ps3800 (color printer), and ps4050. Note that the old queues phaser and phaserdouble no longer exist, so if you were using aliases for the phaser in e.g. your .cshrc, please replace "phaser" with "ps3800".

There are extra print queues defined for double-sided printing: ps2430double, ps3800double, and ps4050double. e.g. lpr -Pps4050double

The upgrade to SLES 10 required switching back to the CUPS printing package in place of LPRng. Thus the "-Z" options for selecting the tray, duplexing, etc. no longer work. A complete description of the CUPS options can be found at: http://www.cups.org/documentation.php Some common examples:

Manual feed: lpr -Pps4050 -o media=Manual

Duplex on the short edge: lpr -Pps4050 -o sides=two-sided-short-edge

A4: lpr -o media=A4

Please do not use the color printer as a default for all your printing! Please remember to sign up your color printing usage.

For drivers and installation information about using your computer with ps3800, click here.

On 2009 September 22, the Service Center printers in Herman Brown 335 moved to the following IPs:

128.42.182.69 spac-ps-2430.rice.edu

128.42.182.70 spac-ps-3800.rice.edu

128.42.182.71 spac-ps-4050.rice.edu

128.42.182.72 spac-ps-600.rice.edu


Enscript

If you use enscript and want to continue to use the Bounding Box that was used on spacsun (and thus the number of lines of text on a page), be sure to set the ENSCRIPT environment variable to letter (note the small l). e.g. in .cshrc:

setenv ENSCRIPT --media=letter


Mail

If you use a program such as Thunderbird, SeaMonkey, Evolution, or Outlook to read mail, you should have the mail reading server set to spacibm.rice.edu . Both POP and IMAP should work, although only POP has been tested.

The mail command works similarly to spacsun, but has a number of subtle differences. Please man mail for details. For example, note that r and R are switched, so that r replies to everyone in the original mail whilst R replies to just the sender (you can reverse this by adding set Replyall to your .mailrc).

If you like to use vi to edit mail, you should include setenv EDITOR vim in your .cshrc.

pine is not included in the SuSE distribution. It has been built (with some difficulty) as an add-on (current version 4.64). It appears to work fine, although this is not a program that I use. pine and its related programs (pilot, pico, mailutil) are all located in /usr/local/pine

The mail program elm is not included in the SuSE distribution and is not being maintained by its authors; thus it has not been installed.

An alternative similar mail reader is mutt.

Thunderbird is located at /usr/local/thunderbird/thunderbird

Seamonkey is located at /usr/local/seamonkey/seamonkey


Web Browsing

Netscape and mozilla have been replaced with firefox and seamonkey.


Web Publishing

Files for web display need to go in a directory called public_html in your home directory (not in www). Links to http://spacibm.rice.edu/~yourusername/ will then work.


ftp

ftp is disabled for security. Please use sftp.

In theory, older programs that require ftp can be tunneled using ssh. However, we have not had success in doing this in practice, so it is best to upgrade to a secure version/program.

There is no longer a /home/ftp that you can use to allow people to download your files. Instead, make a simple web page in public_html that includes, for example, the line:

Download copy of paper.pdf

(Generated by <a href="paper.pdf">Download copy of paper.pdf</a>)


ssh/sftp

spacibm uses openssh/sftp, rather than the ssh.com versions used on spacsun. Whilst the sftp in ssh.com is far superior (for example, allowing the downloading of directories all at once), the non-commercial version would not work on spacibm.

Users should therefore remember to tar directories before transferring them.


Fortran/C

Lahey/Fujitsu Fortran 95 Compiler (version 6.20d) provides Fortran 95, 90, and 77. Although this is a 32-bit version that is not optimized for AMD-64, it seems to work fine. To get it to work correctly, you must use the command:

/usr/local/lf9562/bin/lf95 -Wa,--32

If you have problems with libraries not being seen, try:

source /usr/local/lf9562/csh_setup

There is also gcc (/usr/bin/gcc), g++ (/usr/bin/g++), and gfortran (/usr/bin/gfortran).

GNU Fortran version 3.3 is also available at /opt/gcc33/bin/g77 (new location). If you get errors about loading shared libraries, add to your .cshrc

setenv LD_LIBRARY_PATH /opt/gcc33/lib64:${LD_LIBRARY_PATH}

You can check that all your library paths are being seen using echo $LD_LIBRARY_PATH


Mathematica and Wolfram Workbench

Note: if you are having problems checking out licenses, then remove your .Mathematica/Licensing/mathpass file.

Mathematica 9.0.1 - /usr/local/bin/mathematica

Mathematica 8.0.1 - /usr/local/bin/mathematica.801

Mathematica 6.0.3 - /usr/local/bin/mathematica.603

Mathematica 5.1 - /usr/local/bin/mathematica.51

Wolfram Workbench 2.0 - /usr/local/bin/WolframWorkbench

If you have problems with displaying fonts, you will need to install them on your local machine. From your linux machine:

sftp yourusername@spacibm

cd /usr/local/src

get mathematica_fonts.tar.gz

login as root on your linux machine and:

cp mathematica_fonts.tar.gz /usr/share/fonts

cd /usr/share/fonts/

gunzip mathematica_fonts.tar.gz

tar xf mathematica_fonts.tar

xset fp+ /usr/share/fonts/Type1

xset fp+ /usr/share/fonts/BDF

xset fp rehash

Mathematica should now work correctly. You will need to do the three xset commands each time you log in to your linux box.


IDL

IDL 8.3 - /usr/local/bin/idl or /usr/local/bin/idlde

Note that IDL is now owned by Exelis, so there is a new path for the set-up file:

source /usr/local/exelis/idl/bin/idl_setup

Earlier versions are available as e.g. /usr/local/rsi/idl_6.0/bin/idl or /usr/local/rsi/idl70/bin/idl or /usr/local/itt/idl80/bin/idl

The default is to run the 64-bit version. Sometimes it may be necessary to use the 32-bit version; for this use idl -32

spacibm is the license server for IDL.

To be able to use IDL, you need to have the correct address set for spacibm.rice.edu in your LM_LICENSE_FILE environment variable. If this is not done, IDL will go into demo mode.

- In unix-type operating systems, this is set in your .cshrc or .kshrc or .bashrc *and* it may also be set in your .flexlmrc file. You need to check both places.

- In Windows the LM_LICENSE_FILE is set in Control Panel - System - Advanced - Environment Variables.


Matlab

The 64-bit Matlab version 8.3.0 (R2014a) is at: /usr/local/bin/matlab

Version 8.2.0 (R2013b) is at: /usr/local/MATLAB/R2013b/bin/matlab

Version 8.1.0 (R2013a) is at: /usr/local/MATLAB/R2013a/bin/matlab

Version 7.13 (R2011b) is at: /usr/local/MATLAB/R2011b/bin/matlab

Version 7.9 (R2009b) is at: /usr/local/matlab_7.9/bin/matlab

Version 7.7 (R2008b) is at: /usr/local/matlab_7.7/bin/matlab

Version 7.6 (R2008a) is at: /usr/local/matlab_7.6/bin/matlab

Version 7.5 (R2007b) is at: /usr/local/matlab_7.5/bin/matlab

Version 7.4 (R2007a) is at: /usr/local/matlab_7.4/bin/matlab

Version 7.3 (R2006b) is at: /usr/local/matlab_7.3/bin/matlab

Earlier versions of matlab would not work with SLES 10 and have not been saved.


Supermongo

supermongo - /usr/local/supermongo/bin/sm

Be sure to have e.g. in your .cshrc:

set path = ($path /usr/local/supermongo/bin /usr/local/supermongo/lib )

setenv LD_LIBRARY_PATH /usr/local/supermongo/lib

To get TeX to process Greek fonts correctly, you may need to have in your /home/username/.sm

TeX_strings 0


xmgrace

xmgrace - /usr/local/bin/xmgrace

Not currently working. This software has not had any development since 2008.


HEAsoft

The 64-bit HEAsoft version 6.16 is installed.

Versions 6.6.1, 6.13, and 6.15.1 are also still available.

Please note the correct path for the HEADAS environment variable (the directory name changes after an upgrade to a newer version):

For C Shell users (csh, tcsh), include in your .cshrc:

setenv HEADAS /usr/local/heasoft-6.16/x86_64-unknown-linux-gnu-libc2.11.3

source $HEADAS/headas-init.csh

For Bourne Shell users (sh, ash, ksh, bash), include in your .login:

HEADAS=/usr/local/heasoft-6.16/x86_64-unknown-linux-gnu-libc2.11.3

export HEADAS

. $HEADAS/headas-init.sh

NOTE: these environment settings should come after other initializations that use LD_LIBRARY_PATH (such as supermongo).

NOTE: these replaced the previous LHEASOFT environment variables which should be deleted if they are in your .cshrc. Also make sure you are not setting any of the old environment variables FTOOLS or XANADU.


CALDB

Set up environment with e.g. for .cshrc:

setenv CALDBCONFIG /usr/local/caldb/caldb.config

setenv CALDBALIAS /usr/local/caldb/alias_config.fits

setenv CALDB ftp://legacy.gsfc.nasa.gov/caldb


ROOT

ROOT version 5.10 is installed.

You will need to set 3 environment settings in your .cshrc:

set path = ($path /usr/local/root-5.10/root/bin )

setenv ROOTSYS /usr/local/root-5.10/root

setenv LD_LIBRARY_PATH ${ROOTSYS}/lib:${LD_LIBRARY_PATH}


IRAF/ds9/x11iraf

IRAF 2.16 - /usr/local/bin/cl

Before using this version for the first time, users should move their login.cl file and uparm directory somewhere else, reinitialize their configuration using mkiraf, and then merge any desired settings from the old version into the new one.

STSDAS/TABLES version 3.17 is installed.

ds9 v.7.2 - /usr/local/bin/ds9

ds9 v.7.1 - /usr/local/bin/ds9_7.1_64bit

ds9 v.6.2 - /usr/local/bin/ds9.linux.6.2

ds9 v.6.0 - /usr/local/bin/ds9_6.0_32bit

ds9 v.5.6.3 - /usr/local/bin/ds9_5.6.3_32bit

ds9 v.5.2 - /usr/local/bin/ds9_5.2

ds9 v.4.13 - /usr/local/bin/ds9_4.13

x11iraf uses version 2.0BETA; ximtool is now working.


Media Viewers and Manipulators

For viewing pdf files, it is usually better to use okular - /usr/bin/okular - or evince - /usr/bin/evince - rather than Adobe Reader.

Adobe Reader 9.5.3 - /usr/bin/acroread

The default version of GIMP is now 2.6.2 at /usr/bin/gimp . The first time it runs, it will create a .gimp-2.6 directory. You may want to copy over personalized items such as patterns and brushes from your previous .gimp directories. Make sure your Page Setup is set to US Letter before printing.

The previous version of GIMP (1.2.5) is still available at /usr/local/bin/gimp-1.2

xv no longer works with SLES 10 and the package has been removed.


LibreOffice/OpenOffice

OpenOffice has mutated into LibreOffice. The current version is 4.0. The command remains: /usr/bin/soffice

Although not recommended, version 1.1.0 is still available at /usr/local/OpenOffice and then at /home/username/OpenOffice/soffice once you have gone through the setup procedure (do a Workstation Installation: DO NOT do a Local Installation.)


tex/latex/pdflatex/ps2pdf/dvips

Make sure that you are finding the binaries for latex, dvips, etc. These are located in /usr/local/teTeX/bin/x86_64-unknown-linux-gnu . For example, in your .cshrc, add:

set path = ($path /usr/local/teTeX/bin/x86_64-unknown-linux-gnu )

Unless you know what you are doing, you should comment out all the TEX... environment variables in e.g. your .cshrc. The exception is to create a directory such as /home/yourusername/texinputs where you keep your input tex, sty, cls ... macros. Then include e.g. in your .cshrc:

setenv TEXINPUTS .:/usr/local/teTeX/share/texmf/tex//:/home/yourusername/texinputs//:

Since the default in SuSE is to use A4 paper, when converting postscript to pdf, use ps2pdf -sPAPERSIZE=letter

Also use dvips -t letter



Last Updated: 2014 August 04

Mail problems to: amanda AT spacibm.rice.edu