Skip to content

Carleton Astronet Admin Log Posts

Compiling Old fortran programs(&link pgplot) on 64-bit system

Published by admin-joel on 2015-05-21

This post is for the old fortran computing programs (except TEMPO)

The moral of the story to compile those old programs in 32-bit on the 64-bit machines, because I could not find any documentation online re how f77 compiles differently in 64-bit and 32-bit. However, we do know that programs compiled in 64 bit behave differently from those compiled in 32-bit (for example the size of some data type are different). Therefore, on the 64-bit machines we should force compile these old programs in 32-bit to ensure consistency. The steps are as follows.

1. Make sure that your $PGPLOT_DIR environmental variable points to /usr/share/astro/psrchive/pgplot_32bits

2. Look at the make file. Add “-m32” to FFLAGS (meaning force compile in 32 bit for fortran) and make sure that the f77 step says f77 $(FFLAGS)     in order that the FFLAGS be invoked.

Make sure that the LIBS line have all of the following especially $(PGPLOT_DIR)

LIBS = -L$(PGPLOT_DIR) -lpgplot -L/usr/X11R6/lib -lX11 -lpng

Then we should be fine

–Yuping

—————————————————————————-

Pulling in additional 32-bit compat library when the compiler complains about not having it:

Do a google search to see what packages provide those libraries (theoretically “yum provides filename” should work but I never succeed on our computer. Useful stuff is “yum search keyword” which search through the available packages. Always pick the package ending with i686 (which stands for 32-bit) and devel if available

for example I see -lz and google tells me zlib is what I need. I run “yum search zlib” and just pick the one with “devel” and “i686″(meaning 32 bit). So I will type “sudo yum install zlib-xxxx-devel-i686

determine the libraries / files that an executable is using!!

Published by jweisber on 2014-11-26

ldd   <path/executablename>  lists what libraries it is looking for (or currently using)

ltrace <executablename programarguments>   traces what executable is doing with libs and other stuff and if it gets stuck there’s your problem.  (Note this actually runs program which is why input params are needed)

strace <executablename programarguments> show files opening and closing. This also requires running the program. Since the output is extremely lengthy you might want to save it to blablabla.txt by

$strace -o blablabla.txt <executablename programarguments>

If you want to just trace specific system calls (for example open,read since you are interested in what the program is using) you can type

$strace -e open,read <executablename programarguments>

This will give only open and read calls.

-Yuping Huang

Firefox: Run it on a host even if it you have it open on another – Bruce

Published by jweisber on 2014-08-25

Firefox setting for users who’s home dir lives on NFS – Bruce Duffy May 2013

Here’s how to tell Firefox that your homedir is sitting on an NFS filesystem:

This update (10.8) also fixes the following bug:

* In certain environments, storing personal Firefox configuration files
(~/.mozilla/) on an NFS share, such as when your home directory is on a
NFS share, led to Firefox functioning incorrectly, for example, navigation
buttons not working as expected, and bookmarks not saving. This update
adds a new configuration option, storage.nfs_filesystem, that can be used
to resolve this issue.

If you experience this issue:

1) Start Firefox.

2) Type “about:config” (without quotes) into the URL bar and press the
Enter key.

3) If prompted with “This might void your warranty!”, click the “I’ll be
careful, I promise!” button.

4) Right-click in the Preference Name list. In the menu that opens, select
New -> Boolean.

5) Type “storage.nfs_filesystem” (without quotes) for the preference name
and then click the OK button.

6) Select “true” for the boolean value and then press the OK button.
(BZ#809571, BZ#816234)

All Firefox users should upgrade to these updated packages, which contain
Firefox version 10.0.8 ESR, which corrects these issues. After installing
the update, Firefox must be restarted for the changes to take effect.

IDL COLOR PLOTTING WITH FANNING ROUTINES – YUPINGS 2014 UPDATE

Published by jweisber on 2014-08-25

On June 11, 2014, Yuping Huang said:

 

I just realized that fsc_color is no longer available because the shared Coyote library was updated a couple weeks ago. So yes the library was updated from its previous early 2000s version. The development for fsc_color stopped at 2011 so now it is not in the library any more, with CGPlot as its successor.

Hence, if you are calling Coyote stuff in idl and found idl telling you that it does not exist, you might want to check the latest Coyote source code online to see if it has been expelled from the library.

Make Evince Display IDL PS Filename on Banner: JUST USE EVINCE!

Published by admin-joel on 2014-08-19

AS OF 2020 Sep (and I believe much earlier), using the graphics displayer EVINCE automatically puts filename on banner, and furthermore the following did not work with other viewers. Therefore consider the following to be “deprecated” (withdrawn) –jmw

To  actually use evince from the command line, type evince <filename> &

To actually use evince in a nautilus file manager, select (click on) the desired file, and go to
file>>open with>>evince

Commonly when one prints plots to a postscript from IDL and open it with evince(as we always do), the banner of the evince window perennially shows “Graphics Produced By IDL”, which is not helpful at all especially when you’re plotting a thousand plots and trying to compare them.

Hence a pair of IDL routines (OPENPS and CLOSEPS )can be called now to make the output PS file display the file name at the banner and to make the plotting to file process slightly less complicated. The way to call them is as follows:

OPENPS, blablabla.ps      //Before you plot anything. This will set the output device to blablabla.ps and by default color plot

[ DEVICE, FONT_SIZE=9]  //This is the optional part if you want anything about the graph beyond color, see IDL documentation on DEVICE for more

//information. Note that you may overwrite the color attribute here by saying DEVICE,/COLOR=PS

plot,bla

overplot.bla //Plot and add labels and do whatever as you like

CLOSEPS //When you’re done with one graph, simply call CLOSEPS, it will save the file for you and set the plotting device back to xwindows

WARNING: DO CLOSEPS BEFORE YOU OPENPS A NEW FILE. IN OTHER WORDS, EACH PLOT FILE MUST BE ENCLOSED BY A PAIR OF

OPENPS-CLOSEPS statement.

For more information, the code locates at /usr/share/astro/idlshare/locallib, or email huangy@carleton.edu.

 

-yuping

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

printing postscript images to printer with gv (ghostview) as backup to evince

Published by jweisber on 2014-02-06

Bruce installed the gv package for viewing and printing postscript.  It works great for viewing.  For printing, it has problems.  Bruce developed this workaround (with a few mods by Joel):

‘gv’ uses the ‘lpr’ command, and if a printer as set as the default in CUPS it will use that printer automatically.  You can hear the printer warm up, but nothing comes out of the printer.

Fortunately ‘gv’ is packaged with a set of file conversion utilities,
including ‘ps2pdf’.  On the command line you can issue this command:

# ps2pdf xxx.ps – | lpr

and that will convert the ps file to pdf (version 1.4) before sending it to lpr.  (You can also convert in place – ie turn your postscript file into a pdf on disk with ps2pdf, and then send the pdf to the printer whenever you want.)

To print a ps on the fly, though:
gv’s print command dialog window has a typein labeled ‘print command’
and it’s automagically populated with the string ‘lpr’.  However you
can change that string to ‘ps2pdf %s – | lpr’.  You can also change
the default print string from ‘lpr’ to whatever you want in
GhostScript options, but that would break printing of non .ps Here’s.

To change the default print string in ‘gv’, select:

State->Setup Options

… Look for the Print Command field, and change the value from
‘lpr’ to ‘ps2pdf %s – | lpr’ (w/o the single quotes).

The change is saved to ~/.gv as the line:

GV.printCommand:        ps2pdf %s – | lpr

 

–bruce via joel