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Author: admin-joel

tempo2,fftw3 and cfitsio setup

Published by admin-joel on 2014-08-13

TEMPO 2 is the newer pulsar timing package. FFTW3 is a fast fourier transformation library. CFITSIO is the NASA library for reading FITS format images. All of them are installed under $PSRHOME.  there’s another installation documenting file 00READMECarleton under that folder. FFTW3 and cfitsio are the dependencies for some of the tempo2 plugins and psrchive.

1. FFTW 3.3.4 is obtained from http://www.fftw.org/download.html,  unzip the tar file then

./configure –prefix=$PSRHOME/FFTW3/
sudo make
sudo make check
sudo make install

This will install the double precision FFTW3 library for TEMPO 2. However, the single-precision fftw
library that psrchive might require is not installed yet.

2.CFITSIO 3.370 is obtained from http://heasarc.gsfc.nasa.gov/fitsio/, unzip, cd, then

./configure –prefix=$SOFTWARE_DIR
sudo make shared
sudo make install

3. TEMPO2 is obtained by CVS anonymous checkout
cvs -z3 -d:pserver:anonymous@tempo2.cvs.sourceforge.net:/cvsroot/tempo2 co tempo2

The installation requires an amount of modification of config files (pgplot compilation flag, fixing bugs).
See 00REAMECarleton for details. But basically you do

./bootstrap
 setenv TEMPO2 $PSRHOME/tempo2/
 ./configure --prefix=$PSRHOME/tempo2/ --with-cfitsio-dir=$PSRHOME/cfitsio/ --with-fftw3-dir=$PSRHOME/FFTW3/ F77=f77
 sudo make && sudo make install
 sudo make plugins && sudo make plugins-install

-Yuping

xfig

Published by admin-joel on 2007-07-17

OUT OF DATE as of 2008-11-01.

xfig, a figure drawing program, is now installed at /usr/share/astro . The executable is called xfig. The Imakefile I used to compile and install this program can be found a /etc/secret/Imakefile.xfig

If this ever needs to be compiled again, download the source and follow the directions to compile located in the README, using my Imakefile

sudoer list

Published by admin-joel on 2007-07-17

As of this post date 2007, the Astro network syncs thuban’s sudoers file to the other workstations, just as it does with user accounts. Please contact fullerj with any problems regarding sudo.

IDL 6.4 upgrade

Published by admin-joel on 2007-05-23

This is an entry to explain how IDL 6.4 was installed.

First we received an email telling us to upgrade our licensing to IDL 6.4. We followed the website instructions to upgrade our 3 licenses from 6.3 to 6.4. The newly upgraded license files were then emailed to Joel who forwarded them onto me(Josh).

I downloaded the tar file from the ITT website through Joel’s login.

I then went to /usr/local and created a directory called itt. I unpacked the 6.4 software in this directory using the command: tar -xvzf idl_linux.x86.tar.gz

Next, run the install binary by typing ./install if you are in the ITT directory or /usr/local/itt/install if you need the absolute path. You will be prompted a few times, just hit yes to install the software and yes to create the symbolic links. Ignore the web server questions just by hitting enter. IDL 6.4 is now installed.

However, in order to use the software, you must now do the licensing correctly.

I placed a copy of all 3 licenses in one flat file in /etc/secret/license.txt.

Copy license.txt and edit it so that the license for the machine you are installing to is the only entry in the file. Then rename the file license.dat.

Move this file to /usr/local/itt/license/

Then restart the license manager on the machine by typing:

/usr/local/itt/idl64/bin/lmdown

followed by:

/usr/local/itt/idl64/bin/lmgrd -c /usr/local/itt/license/license.dat

This will then restart the license manager with the new license for IDL 6.4

Now, make sure the license manager is starting at boot time. To do this, simply look in /etc/rc.d/rc.local.

If this command is not there, add it to the end of the rc.local script: /usr/local/itt/idl64/bin/lmgrd -c /usr/local/itt/license/license.dat

Added by JMW 07/2007: Note that idl without the goddard routines is like a fish without a bicycle.  As of July 2007, they must be manually copied on all three computers from the old idl’s lib directory to the new idls lib directory.  crude!  (See goddard libe entry below for more details, but basically root has to do a cp -r.)

Finally test and finish.

———————————————————————————————–

The final step is to make sure you have overwritten any environment variables you have set up in your .tcshrc or .cshrc.

To do this, look in your .cshrc and if you have the line:

source /usr/local/rsi/idl_6.3/bin/idl_setup

Make sure you change it to:

source /usr/local/itt/idl/bin/idl_setup

(Joel supplied the above July 29, 2007. note that rsi->itt and idl_6.3->idl (assuming idl dir is linked to idl64 and future ones) )
———————————————————————————————

Where to set up Environment variables etc for ALL users on login

Published by admin-joel on 2006-10-03

OUT OF DATE as of 2008-11-01.

Here is how to set the path or add to the path for all users when they log in. The procedure depends on whether the users’ shell is tcsh (usual case) or bash.  (To determine if your shell is tcsh, type ‘printenv SHELL’.)

———————

TCSH:

For tcsh users, the file to modify is /etc/csh.login. (Also note that other startup conditions can be set for all users in /etc/csh.cshrc).  To add an environment variable simply type

setenv JAVA_HOME /usr/java/1.3.1

To append to the Path in say YOUR OWN .cshrc, type:

setenv PATH “${PATH}:/path/to/be/added”

(This will append your new desired path to the path set for everyone in /etc/csh.login)

————————————————-

BASH:

For users that like bashrc, you can modify /etc/bashrc to add the necessary path or variable. To add a variable, for instance java’s home directory, simply type

export JAVA_HOME=”/usr/java/jdk1.3.1″

If you wanted to add an extra path to sys set up path in YOUR OWN bashrc, type:

export PATH=$PATH:path/to/be/added

Date and Time Configuration

Published by admin-joel on 2006-09-15

OUT OF DATE as of 2008-11-01.

For our systems, we want to use the network time protocol put in place by the college. Therefore, we do not set the time manually but rather, have it sync from the Carleton Network Time server. To do this follow these easy steps.

As root, under the Applications menu to the right of the little red hat, click on System Settings/Date and Time.

Click on the Network Time protocol tab. Under this tab you should see a place to add and delete network time servers. Delete any servers that are there.

Then type ntp.carleton.edu and click the add button. ntp.carleton.edu should then appear as a server on the list. Click OK and wait a few moments for the machine to sync with the server.

Double check the time to make sure it is accurate. Your system should now have the correct date and time.

User Login Problem and Fix

Published by admin-joel on 2006-08-18

This week we experienced some login failures with the astro network. The symptoms were as follows. The user could not log in as himself/herself under our linux boxes. However, root login continued to be successful. Errors in /var/log/messages indicated an error which suggested the ldap server could not be contacted.

To fix this problem, we first looked at /etc/ldap.conf which had a line like “host 127.0.0.1″ which was not the proper configuration for our network(the ldap server is ldap.carleton.edu”.

To fix this we reinstalled the carletonldapauth rpm located in /etc/secret/RPMS/.

However, this did not fix our error. The error we were now getting in /var/log/messages was an invalid credentials error when trying to bind with the ldap server. After calling ITS admins to see the logs on the server side of things we noted that our astro machines were trying to bind to the ldap server as root. This is incorrect. After discussing the matter further we determined that a newer version of carletonldapauth had been created which was not on the astro network.

This should have been installed automatically by our scripts that we run on the astro network. However, ITS had recently changed the cert on the server which broke our updates. After installing the new cert(located in /etc/secret/RPMS), installing some missing packages on some of the machines(openssl-perl) and installing the new carletonldapauth everything is back to normal.

Algol tape drives

Published by admin-joel on 2006-08-02

We have two tape drives now attached to Algol. The first is an exabyte tape drive listed under

/dev/st0 (or /dev/nst0 depending on if you are using no rewind or not)

The SDLT 320 tape drive is listed under /dev/st1 (/dev/nst1).

To read data from the exabyte. Simply CD into the directory you want to put your data in. Then use the command:(must be run as root)
>>tar xvf /dev/st0

If this fails, try setting the bock size and density using these two commands and then try again.

>>mt setdensity 0x00

>>mt setblk 0

To extract from the SDLT tape drive, the tar command should work as well.

WARNING: When retrieving data from tape, make sure the directory you are in is empty as you can overwrite data files without even realizing it.

Converting RAID to LVM-on-RAID

Published by admin-joel on 2006-05-05

OUT OF DATE as of 2008-11-01.

We decided to convert the Raid1 array to LVM instead of a monolithic partition. This will make life easier.

Commands:

  1. pvcreate /dev/md0
    makes a physical volume out of the RAID array device
  2. vgcreate VolGroup01 /dev/md0
    creates a new volume group to which we can add logical volumes
  3. Use Redhat Logical Volume Management tool to create partitions on the new device
    • /docs (5 gigs)
    • /home (50 gigs)
    • /etc/secret (10 gigs)
    • /data (399 gigs)
  4. Modified /etc/exports on Algol to export the new partitions
  5. Modified /etc/fstab on the client computers to use the new partitions
  • mkdir /docs
  • mkdir /data
  • added lines to /etc/fstab:
    algol:/data /data nfs defaults 1 1
    algol:/docs /docs nfs defaults 1 1
  1. Un-tarred the backups from /bkup, which I created with the command:
    cd /bkup & tar -czvpf home.tgz /home
  2. Untar by going to desired directory and running:
    tar -xzvpf /bkup/secret.tgz
    Both of these commands put the directory INTO the desired directory. Once unpacked, it’s necessary to move the contents to the proper location.
  3. Modified /etc/cron.weekly/quotacheck.cron to be:
    #!/bin/bash
    # Update the database that keeps track of quotas
    # Created by Mark Knight (4.13.06)
    # Modified by Mark Knight (5.06.06)
    quotaoff -a
    quotacheck -agum
    quotaon -a

    exit 0

  4. Also, had to modify /etc/fstab to add quotas back on to the new mount line for /home

All in all, not that hard. The permissions are all correct, so hopefully this was just as easy & painless as I think it was.