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Updating clock time through terminal

In my Fedora 14 desktop I keep losing minutes without knowing how and why (doesn’t the clock update automatically?).
At the beginning I tried to change the file /etc/ntp.conf (edit it and change the parameter server to: ‘server pool.ntp.org’; 1) as perhaps the server did not respond correctly.
I tried to update by:
ntpdate pool.ntp.org

but the result was not the expected one, but an error: “… the NTP socket is in use, exiting”
I stopped (/etc/init.d/ntpd stop) and tried to updated (ntpdate pool.ntp.org) but another error was raised: “… no server suitable for synchronization found” (reasonable though since …ntd was down!).

By looking a little bit around the solution [2] was to update while running as:
ntpdate -u pool.ntp.org

and…that’s it! I removed the extra entry in the /etc/ntp.conf (to keep the original servers only) and it worked again.

Now let’s see if it’s going to keep up or I will need to manually update the clock from time to time.

[1]: Cyberciti.biz – Synchronize the system clock to Network Time Protocol (NTP) under Fedora or Red Hat Linux
[2]: Superuser.com – Socket is in use

Updating Scisoft from 7.5 to 7.7 in Fedora 14

Updating Scisoft in Fedora is rather easy (see the installation details). First if we have already a previous installation we can easily remove it by running (as root):

yum remove scisoft-\*

and check that the directory /scisoft has been totally removed (if something extra has been added the we should still see the scisoft directory with all the extras inside).
Then, we follow the same steps as the first time (for example see this installation notes). Since we are updating then the repository file should already exist. We don’t have anything more to do than just to edit the file /etc/yum.repos.d/scisoft.repo and edit the line containing the baseurl:


Actually we just replace …7.5/… with …7.7/… . Then we install the scisoft normally:

yum clean all
yum install scisoft-\*

and everything should be just fine!

NOTE: during this installation only the scisoft-idllib-7.7.0-0.i386 was not installed due to the lack of scisoft-idl. And that’s … because it is not included (along with SuperMongo) as they are paid versions.
The installation can be skipped by using — skip-broken (after all, no need for IDL since we get Python 2.7.2 and Matplotlib 1.1.0!!!).

VStar conflicts with java used

VStar is a multi-platform variable star visualisation and analysis tool, developed under the CitizenSky project and the AAVSO. Its use is straightforward if java is installed. But you should be carefull what java you are using…

I tried to use VStar in two different machines running Ubuntu 10.10 64bit and Fedora 14 32bit and the first impression was that everything was set. The visualization of the data and the phase plot (epoch folding) were working but the analysis tool DCDFT (date-compensated discrete Fourier transform) was not! After some discussion with the author of the program David Benn it was found that IcedTea (a java environment) was used to run the program which “is not fully 1.6 compliant, possibly in terms of some of the Swing libraries“. So, as only the Oracle Java has been really tested, it is strongly advised to install this version in order to run the program without any issues.

Installing Oracle’s Java is simple, as there is a guide for this. A fast note of this is the following steps:

1. Download the Linux self-extracting file named jre_6u3_linux_i586.bin, or similar  (source page).

2. Make this file executable (type: chmod +x jre_6u3_linux_i586.bin).

3. Create, if it doesn’t exist, the directory /usr/java (type: mkdir /usr/java – for this we need to be root) if we want to install java in the whole system, else place it under the home directory.

4. Run the self-extracting binary (type: ./jre-6u3_linux_i586.bin). After accepting the license, the installation proceeds and finishes when “Done” is displayed.

5. We can verify the installation by checking if jre1.6.0… sub-directory is listed under the /java directory.

Then we can select VStar to open with this java environment and start digging into the light-curves!

matplotlib within Scisoft and file system – Fedora case

While I was working on a script to make multiple plots with matplotlib I found out that it was not possible with the version that Scisoft 7.5 uses (0.99) but a later version can do it (1.0.1)! So a logical though was to go on and upgrade the matplotlib inside scisoft but was not really obvious or successful. Also, I was not able to find a way to combine python modules inside scisoft with modules outside it (ie at the file system under /usr/lib/python2.x/ in Fedora). Although i did ask in mailing lists about this I have not get any answer yet, so I went on to install the latest version of matplotlib, numpy, scipy through the usual repositories under the file system. Then if I want my script to take advantage of the matplotlib 1.0.1 I insert


at the first line of the scripts while

#!/usr/bin/env python

if I want to work with the modules inside scisoft (like pyraf).

Perhaps I have a better solution to post in the future…

Changing passwords and keyring

After updating my Fedora 14 login password I was about to use the Empathy messaging client but this “Unlock Login Keyring” dialog box was keeping opening without accepting the new or older passwords… So, while useful it seemed irritating not to be able to use the system with any kind of password working. Searching a little bit around I found this post which practically solves the problem.

Go to home directory and .gnome2/keyrings and delete the login.keyring (and any other keyring files). This will prompt for a new password and you can select the login password so as not to have to deal with many passwords around.

New installation of Fedora 14 and GNOME configurations

A new installation of Fedora 14 was performed some days ago allowing to fresh up my heavy duty machine at work. Of course this does not come without any troubles but, thankfully, all have been solved quicker than expected.

The first and more serious problem was to install the necessary drivers for the graphics (an nVidia GeForce 9400 GT). By following thoroughly all the steps given in this howto-configure-kmode-nvidia link the problem was solved successfully without any further delays (thank to Paolo B. to point me that link!). A quick check if everything is working ok is to test (type in terminal) ‘glxgears’. If  the rotating gears are there and the output is more than 2000fps then the graphics run correctly (thanks to Thodoris B. for this tip!).

Next step, to organize a little bit the desktop … Yum-install the gconf-editor and then I (personally dislike these icons) removed the computer, trash and home icons from Desktop. From gconf-editor select apps>nautilus>desktop and untick the boxes named *_icon_visible.

Next step was to activate the compiz 3d graphics and add Cairo-Dock, along with some plug-ins which provide all the (cool) stuff that somebody (or at least me) needs. With that I found the panels useless so I removed them completely through gconf-editor again, by selecting desktop>gnome>session>required_components and removing the value “gnome-panel” from panel (it can be restored by putting this value again back).

Now I am enjoying my new fresh and cool machine !

Scisoft 7.5 in Fedora 14 using bash

Scisoft is a great collection of astronomical software (IRAF 2.14-1, IDL 7.1, Python 2.5.4, PyRAF 1.9.0, and more) mainly used at the ESO. Installing the whole package is very easy through yum in Fedora, which is officially supported. Following the instructions you can have Scisoft ready in a few minutes and then what is left is to run the software.

For bash users type (“dot space” at the beginning):

. /scisoft/bin/Setup.bash

and csh/tcsh users:

source /scisoft/bin/Setup.csh

Most probably though the Scisoft will not start at all, as a check message about the SELinux is printed. Fedora comes with SELinux enabled by default which may create problems with some applications (like inmidas and PyRAF). The best solution is to disable this feature and to do so you have to edit the /etc/selinux/config (as root). What you will see is this text:

# This file controls the state of SELinux on the system.
# SELINUX= can take one of these three values:
# enforcing - SELinux security policy is enforced.
# permissive - SELinux prints warnings instead of enforcing.
# disabled - No SELinux policy is loaded.
# SELINUXTYPE= can take one of these two values:
# targeted - Only targeted network daemons are protected.
# strict - Full SELinux protection.

where you change SELINUX= value from enforcing to disabled. Then if you run again the Scisoft will normally start and you can select you application by typing the appropriate keyword (like cl for IRAF, pyraf for PyRAF, etc).

There is still a warning message appearing about nm:
bash: nm: command not found...
Though it seems not to affect, it is better to go on and install the ‘binutils’ package (binutils collection of binary tools) and be sure that everything will be totally safe (go on and install it with yum install).

In order to avoid typing all the time this long command to start Scisoft an alias can be created easily at the .bashrc file, by adding this line:

alias scisoft='. /scisoft/bin/Setup.bash'

Then, just typing ‘scisoft’ is enough to invoke the programs.