Scisoft 7.6 - An Astronomical Software Collection

Frequently asked questions

The first few questions and answers are general ones relating to Scisoft. Numbers 20 and upwards are more specific technical points related to common problems with installation and running the software. If you have further suggestions for this list please send them to "scihelp@eso.org".

Q1: What is Scisoft?

Scisoft is a project within ESO to provide a collection of astronomical software utilities, mostly public domain tools developed outside ESO, in a uniform way at all four ESO sites. Major data-analysis packages (eg, IRAF/STSDAS and ESO-MIDAS) are included as well as many smaller utilities. An "export" version is available for distribution to external institutes.

Q2: Which platforms/distributions does it run on?

The latest version, Scisoft 7.4 was built on Fedora 11 Linux. In addition there are earlier versions for Fedora Cores 6 & 3, Solaris 8, Linux Redhat 9 and HP-UX 11. Although all packages have been compiled and tested only under Fedora 11, we expect many of them will still working under different Linux distributions (e.g. Ubuntu). However, we do not guarantee the full compatibility of Scisoft under other distributions nor can support be provided.
Users of Solaris, HP-UX, and earlier Linux distributions can still request the older collections. The collection will most probably run on similar systems (eg, SuSE rather than RedHat) but these are the ones on which software has been compiled and tested. Note in particular that Scisoft v4 for HP requires HPUX 11. An initial release for Mac-OSX is also available. There is no Windows version and no plan to develop it.

Note - the current releases do not run on 64 bit platforms. It is intended that Scisoft VIII will support 64 bit.

Q3: What is included?

The contents are very similar on all platforms but only the Linux (and, externally the MacOSX version) are now updated. A list of all the items included, with the version numbers and links to further information, is available here. The contents are biased towards tools of use to the users of ESO facilities. See Q4 & Q8. Note that Supermongo (SM) and IDL are not included in the EXPORT versions as these two packages are commercial.

Starting at Scisoft VII there are also some Virtual Observatory tools included.

Q4: What is NOT included?

Scisoft doesn't include ESO instrument pipelines or proposal and observation preparation tools - these are available through the appropriate ESO web pages. Also excluded are non-astronomical utilities such as ghostview, xv and the like. There are no compilers, debuggers, web browsers etc. There is also little radio or X-ray specific software.

Q5: Where is Scisoft Installed?

It should be installed on all machines within ESO which are available for general-user data analysis activities. It appears in a directory /scisoft in all cases.

Q6: How do I run it?

For most ESO users there is no specific setup required - simply type the normal command name to start it. Eg, "cl" will start IRAF, "inmidas" will start ESO-MIDAS and "idl" will start IDL.

If these commands are not defined it is necessary to invoke the command "source /scisoft/bin/Setup.csh" if you are using the csh or tcsh (which is normally the case under Solaris). If you are using "bash" (which is often the default shell on Linux) then the equivalent command is ". /scisoft/bin/Setup.bash" ("dot space" at the start). In these cases the commands should be added to the appropriate file (.tcshrc/.cshrc or .profile for bash) so that they are automatically invoked at login time.
If there is no /scisoft directory then Scisoft has not been installed. In this case please contact the local administrator or, in Garching, send email to "helpdesk@eso.org".
It is necessary to run either the csh/tcsh or "bash" - other shells are not supported.

Q7: How often are new releases?

We aim to have releases once per year although the gaps between releases have varied a lot. The next one, Scisoft VIII, is expected in late-2009. So far there have been seven releases: June and November 2000, July 2001, April 2002, December 2003, April 2006, June 2007 (and many updates) . We also have occasional patch releases such as Scisoft 7.1 in April 2008, 7.2 in October 2008 and 7.3 in January 2009. Scisoft 7.4 in Septemeber 2009 was the first for Fedora 11 but is quite close to 7.3.

Q8: How can I request something else to be included?

Within ESO there is a board with a representative for each site who decide the content, bearing in mind the requirements of their users and that the collection should be of general use. Please send email to "sciboard@eso.org" or contact the individual board members.
IMPORTANT: please note that we cannot promise to follow-up on external requests for additions to Scisoft or requests for support for new platforms. The content is decided for the organisation. However, a good suggestion may well also be useful for ESO - so please send them!

Q9: How do I get a copy?

The easiest way is to download the distribution (as a tar file, RPMs or using yum). Follow the links to the FTP site on www.eso.org/scisoft.
It is also possible to order a DVD, for a notional handling charge, from the ESO Web shop. This also has a link on the Scisoft page.
Finally we have a distribution site hosted in China which should be used only for requesters in China itself.

Q10: How big is it?

The current core collection fits easily on a DVD in compressed form and takes about 2GB of disk space when installed.

Q11: Can one run it from the DVD?

Unfortunately no - it has to be installed.

Q12: Can one squeeze it into less space?

Yes, after or during the installation you can remove some directories which you don't need (eg, if you are a MIDAS user you could remove IDL and IRAF) and it will still run.

Q13: How is it supported?

In general support for each component of Scisoft is supplied by the originators of the software. If you need help with the installation or aren't quite sure what is wrong please email "scihelp@eso.org". The support effort available here in Garching is small but we will do our best to point you in the right direction. Please read through this FAQ first as most of the common problems are already described here.

Q14: How do I install it?

On the DVD there is a small README which gives installation instructions in some detail and a large, compressed "tar" file containing all the software. There are also RPMs of individual components.

Q15: Do I need "root" access?

Yes. Some parts of the installation (eg, IRAF) involve small additions to system directories and other changes. It is also important that everything is in /scisoft and setting this up normally requires root access too.

Q16: Is there a version for Windows or Macs?

Scisoft requires a UNIX-like system, and so there is no Windows version. An excellent release for Mac-OSX is available but is not an ESO product.

Q17: Is source code provided?

In general yes although not for everything. Programs are provided as ready-to-run executables and do not have to be built during the installation.

Q18: Is any of the software commercial?

There are two commercial items which are only included in the internal version of Scisoft. Firstly Supermongo (SM) which has been purchased by ESO for all four sites and also IDL where licenses have been bought by ESO. Both Supermongo (SM) and IDL are excluded from the EXPORT version although some IDL libraries and tools (eg, ATV) are included.

Q19: Can I copy the DVDs?

The EXPORT version may be copied at will so long as the contents are not changed, the DVDs are not sold and credit is given appropriately.



More technical details...

Q20: When running some applications there are errors similar to "libXm.so.2: cannot open shared object file: No such file or directory". What's wrong?

This is a common problem, particularly on Linux systems. It applies to programs which use the Motif library for X11 graphics - this includes some MIDAS GUIs, XEphem, Grace etc. This library is not included in some installations. The solution is either to find this file and make sure that it is added to your "LD_LIBRARY_PATH" or get it and install it. Motif is a commercial package for some systems and we cannot supply it as part of the Scisoft distribution. There is a public-domain product called Lesstif which works well with many of the packages included here but not with all - MIDAS GUIs for example do not work with Lesstif. Lesstif is available on the Redhat 6.2 and later distribution CDs. Motif should already be available on all ESO Solaris and HPUX installations. Please contact "scihelp@eso.org" if you need further help.

Q21: When starting ximtool there is an error like "X Error of failed request: BadMatch..." and it doesn't start. What's wrong?

Ximtool and SAOimage assume that the X-server running supports 8bit displays. If you instead have a 24 or 16bit server running then you get this error. This problem is most common on Linux machines but can occur on other systems depending on the X configration. There are different solutions. If your machine does support "8bit Pseudocolor" (as many do) you can change your X-server configuration to use that. This works well on SUN workstations but prevents full 24/16bit applications from working at their full capacity. One solution is to download and install the GNU VNC server from http://www.uk.research.att.com/vnc/start.html. It provides an 8-bit world (wrapped into a single window) within a true color X environment. ximtool and any other X application can be started inside this 8-bit framework in parallel to all the other true color applications. This is known to clash with VMware.
An alternative is set up two X-servers running at the same time. This can be done fairly easily on Linux. In this case one will host the 8bit applications (eg, ximtool) and the other "normal" 24/16bit operation.
Finally, and probably the best solution, is not to use ximtool but instead use DS9 the latest display server from SAO which is included in Scisoft. This fully supports 24bit displays and has many other powerful features.

Q22: Some Applications crash on old HP machines. Why?

The CPU architecture is different on older HPs. The Scisoft HPUX applications were built on a modern machine and this may generate code which cannot run on the older machines. Unfortunately it would be a very large effort to re-build the applications to avoid this and, as these machines will be retired in the relatively near future we have decided not to work on this.

Q23: Scisoft causes problems with Latex/xdvi on Linux. Why?

This problem is caused by a name clash. There is a command "access" which is used by tetex (the version of Tex/Latex commonly installed on Linux machines) and also one in /scisoft/saord/bin as part of the SAO RD collection. When you define Scisoft this picks up the latter rather than the former as it is nearer the start of the "path". This really messes tetex up completely and typically leads to errors related to font creation. The easiest solution is to add /usr/bin at the front of your search path again. This will get tetex working again at the expense of SAO RD - probably the lesser of two evils.

Q24: Scisoft causes problems with RCS "co" command. Why?

This is another name clash problem. There is a command "co" in the RCS code management system. There is also a "co" in the Gildas package which is defined by Scisoft. The "workaround" suggested is to use an alias for co which is usually "/usr/server/gnu/bin/co" on Solaris and /usr/bin/co on HP-UX. Alternatively one could modify the path, as mentioned in Q23.

Q25: inmidas fails: "cannot restore segment prot after reloc: Permission denied"

Fedora Core 6 comes with SELInux enabled by default which causes problems with inmidas and PyRAF, and probably other applications. To deactivate SELinux edit /etc/selinux/config make sure you have SELINUX=disabled and reboot (of course you will need to have root access). If you don't want to disable SELinux completely you can modify access control in a more fine-grained way using the chcon command, but this is much more complicated, please contact your local administrator for more information.
Scisoft's Setup script will check if SELinux is enabled and will warn you if it's the case, to disable the warning you will need to add the following in your shell startup file:
  • For bash (usually ~/.bashrc):
    export SCISOFT_IGNORE_SELINUX_WARNING=1
  • For tcsh (usualy ~/.tcshrc):
    setenv SCISOFT_IGNORE_SELINUX_WARNING 1

Q26: The imhead and setpix command from wcstools don't work as expected

Both Miriad and wcstools provide commands called imhead and setpix, to prevent them from conflicting the wcstools ones have been renamed to imhead_wcstools and setpix_wcstools.

Q27: How do I run the Virtual Observatory tools provided with Scisoft?

Most of the VO tools in this version of Scisoft are written in Java and can be run using the Java web start facility. In this case the latest version of the tool will be downloaded from its originating site and cached locally.

Tools in this category, and the command that should be typed to run them are: aladin-ws, vospec-ws, voplot-ws, splat-ws and plastic-ws.

These tools are run from the local Scisoft installation in the usual way: virgo, stilts and specview.

And finally TOPCAT can be either run locally (topcat) or using web start (topcat-ws).

Q28: scisoft-gaia fails to upgrade to 7.2: "error: unpacking of archive failed on file"

The reasons for this are not very clear to us but we have seen it; it seems something to do with a symlink in the old RPM being replaced by a file in the new RPM or vice versa, and the way that rpm unpacks the new RPM before it removes the old one (it has to do this in order that if something goes wrong it can roll back).
The fix is to remove scisoft-gaia (yum erase scisoft-gaia) and then to reinstall it (yum install scisoft-gaia).

Q29: How do I run the "double" version of supermongo?

Two version of supermongo are provided, one compiled with vector type 'float' and one with vector type 'double'.
In order to have both versions installed in parallel the 'double' version is suffixed by '_d', so to start the 'double' version of supermong run:
 /scisoft/bin/sm_d
or to compile some code using the 'double' version of supermongo use e.g.:
 -L/scisoft/lib -ldevices_d -lplutsub_d -lutils_d