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Category: Installed software

fixing problems with pgplot and cpgplot: building them and linking them to our own pgms

Published by jweisber on 2017-01-22

See updates at bottom from building pgplot and cpgplot on phasshare virtual 64 bit machine

First, recall that there is a pgplot-32bits (obsolete as of 2021 Feb ) and a pgplot (now 64) directory

On Aug 2, 2016, Yuping suggested putting cpgplot.h into /usr/include  .  Note this is NOT a shared directory so will need to be done on whatever host one is working on. If it is not there and one tries to build cpgplot, it will fail.

Another possible problem could occur when trying to link pgplot or cpgplot to a program.

e.g; the (64 bit) linking command

gfortran -o LKBorig LKBorig.o -L/usr/share/astro/psrhome/pgplot -lpgplot -lcpgplot -L/usr/lib64 -lX11 -lm -lstdc++ -lpng -lz

(cpgplot is just a c wrapper for pgplot and Yuping says it was actually pgplot that was damaged or missing.) (But see below 2021 Feb 3 update for a related prob- there we need to type ‘make cpg’  to make libcpgplot.a   . I dont think we use lib….so any more)

–Joel (with help from Yuping)

Update 2021 Feb 3 JMW: Creating pgplot and cpgplot on phasshare 64 bit virtual machine:

First, don’t ignore above advice about certain special files and their placement.

Second, Bruce and Joel could only get cpgplot programs to work by seeing how libcpgplot.a was created and linked , in psrchive  directory(much more below)!

To create a fresh pgplot and cpgplot that work, execute pgplot.csh in the bowels of psrchive:

/usr/share/astro/psrhome/src/psrchive/packages>
./pgplot.csh | tee /usr/share/astro/psrhome/pgplot/pgplot.csh.out
(tee sends the text  output to the named file  in addition to standard output). See a fuller description of what pgplot.csh does below.

(User must move the previous pgplot out of the way before running this script; ie
mv /usr/share/astro/psrhome/src/pgplot/ /usr/share/astro/psrhome/src/pgplot.older/)

(And I worry that maybe I need to move other random carcasses out of the way too.)

Some of the things done by pgplot.csh:
1. create a mother directory to put all necessary pgplot files into:
/usr/share/astro/psrhome/src/pgplot, after first moving aside the current tree there (see above).Actually it creates /usr/share/astro/psrhome/src/ and then will pour everything below it.)
2. Also create /usr/share/astro/psrhome/pgplot/ (I wonder if we should have moved old one out of way here too?)
3. get if necessary and gunzip and de-tar the pgplot 5.2  distribution (!)  and put it into and under newly created mother dir.
4 patch the png routines: Interestingly, there is a file
/usr/share/astro/psrhome/src/psrchive/packages/pndriv.patch which seems to suggest that there might indeed be probs with standard png driver, and it is pulled in by pgplot.csh and does seem to enable the use of png routines with pgplot and I assume cpgplot.
5. fix psrchive.conf
6. enable good output drivers
7. run /usr/share/astro/psrhome/src/pgplot/makemake with appropriate flags, creating master makefile, and ‘make’ -ing it and ‘make cpg’ -ing it.  As far as I can tell, the makefile made from this process is essentially identical to the earlier one(s), except that the earlier ones could not link in the png routines because they were broken, but the current ones are patched by pgplot.csh  (perhaps not in makefile itself but rather in something it calls.)

But for now consider the following:

lots of pgplot source files are in
/usr/share/astro/psrhome/src/pgplot/src/
cpgplot files are in
/usr/share/astro/psrhome/src/pgplot/cpg/  (see cpgplot.doc here for important help and note that pgbind.c ,which is run by ‘make cpg’, actually makes the libcpgplot.a I believe)

Note that the two above directories are not parallel nor do they have any other logical relative location!!!

pgplot executable etc dir is /usr/share/astro/psrhome/pgplot/  One can find things like makefile (manually placed there), libpgplot.a, libcpgplot.a cpgdemo, pgplot.csh.out (the text output of the proper building  of cpgplot (and pgplot) via running pgplot.csh as follows:
/usr/share/astro/psrhome/src/psrchive/packages>
./pgplot.csh | tee /usr/share/astro/psrhome/pgplot.csh.out  (tee sends the output to the file  in addition to   standard output)

Note makefile can be created by makemake in /usr/share/astro/psrhome/pgplot/src/pgplot and in fact running makemake in that dir places makefile there too, so I manually moved it up two directories.

makemake /usr/share/astro/psrhome/src/pgplot/ linux psrchive   [the latter three ‘words’  are the arguments of the makmake command], which erroneously dumped makefile into the above specified dir (upon its own reccomendation) so I had to manually mv it to /usr/share/astro/psrhome/pgplot/     .  In the end I had to make from the above  psrchive version in order successfully to create cpg or at least the png parts of it, and to successfully link cpgdemo.

then ‘make’ makes libpgplot.a  and ‘make cpg’ makes libcpgplot.a  (see steps near bottom of that file)!  There is a problem with png routines though that crashes? (or at least reports errors in) the make cpg  but the psrchive-generated makefile fixes this!

 

More serious problem with cpgplot (fixed by Bruce and Joel 20210204):
If I try to build any c (.c) or c++ (.C)  program and link it with cpgplot up thru Feb 3, it failed because it couldn’t find ANY of the cpgplot routines that the program tries to call. (eg the creation of cpgdemo inside the make cpg part of the makefile, or the pglink64plkc.C script for compiling and linking plkc.C in usr4/lk-lookey). Note that cpgplot is just a c wrapper to fortran pgplot routines and that is what is failing.  Long ago we had this problem and it was fixed by adding a trailing “_” to any fortran routine name.  I see that that is being done now but it doesn’t fix the problem (maybe it exacerbates it?). One example of failure (there are many, one for each unique call of a cpgplot routine):

{phasshare.physics.carleton.edu}:{jweisber}:/data/psrdata/usr4/lk-lookey> pglink64plkc.C
/usr/share/astro/psrhome/pgplot/libcpgplot.a(cpgbeg.o): In function `cpgbeg’:
cpgbeg.c:(.text+0x34): undefined reference to `pgbeg_’

The fix of Feb 4 was to model our 64bit compile and link scripts
(like /usr/share/astro/pglink64cpgdemo.C), on the (more automated) steps that
successfully create it in the makefile.  So now /usr/share/astro/pglink64cpgdemo.C is
my template for making other 64 bit, c compile and link scripts. . . .

I found on Feb 5 that .C (ie capital C) files like usr4/lk-lookey plkc.C can not use the same script as .c (ie lower case c) files because the .C files are c++.  After a (too long) while, I got working a script to do so.

So for a c file <filename.c> one types pglink64.c  <filename>  (with extension stripped off), and

for a c++ file <filename.C> one types pglink64.C  <filename>  (with extension stripped off)

( There may be slight path issues. )  Both scripts are in /usr/share/astro on phasshare

 

building python 2.7 & related stuff on astronet

Published by admin-joel on 2016-10-05

Yuping:

references:

https://www.digitalocean.com/community/tutorials/how-to-set-up-python-2-7-6-and-3-3-3-on-centos-6-4

https://www.digitalocean.com/community/tutorials/common-python-tools-using-virtualenv-installing-with-pip-and-managing-packages

——————————————————–

I decided for now to install python 2.7 instead of python 3.0  because that’s what most astronomy python libraries are compatible with (e.g. psrchive). If someone wants to build python 3.0 just substitute the following 2.7.12 with 3.0.* and that should work. Note that I install it in /usr/local/ for each of the computers (i’m not sure what exactly willhappen if multiple hosts try to run the same python) so the following is repeated for each computer we have.

——————————————————

prereqs: make sure you do

sudo yum install tcl tcl-devel tk tk-devel

and check to make sure that all prereqs specified in

https://www.digitalocean.com/community/tutorials/common-python-tools-using-virtualenv-installing-with-pip-and-managing-packages

are satisfied.

install:

First download python from https://www.python.org/ and untar it

>xz -d Python-2.7.12.tar.xz

>tar -xvf Python-2.7.6.tar
>sudo cp -r Python-2.7.6 /usr/local/src/

now we can cd into /usr/local/src/Python-2.7.6 and run

>sudo ./configure --prefix=/usr/local
>sudo make

make will complain about not having the following

>Python build finished, but the necessary bits to build these modules were not found:
>bsddb185           dl                 imageop
>sunaudiodev

These four we can live without (see http://www.kelvinwong.ca/2010/08/02/python-2-7-on-dreamhost/) but if you are missing more than that, google it up.

Now do the following (altinstall is very important otherwise you are gonna break CentOS)

> sudo make altinstall

Now python should be built with executable under /usr/local/bin/python2.7

Now build pip which does package management and virtualenv which lets
you install python library without sudo-ing and makes complicated
dependencies easier to handle (see reference article 2)

 

First you need setuptool because pip depends on it

You can download it from https://pypi.python.org/packages/source/s/setuptools/, untar it and copy it over to /usr/local/src/

then do

> cd setuptools-1.4.2

> sudo /usr/local/bin/python2.7 setup.py install

then you download pip from https://bootstrap.pypa.io/get-pip.py into /usr/local/src/ and do

> sudo /usr/local/bin/python2.7 get-pip.py

and pip should be installed.

Finally you can do the following to get some common libraries installed:

> sudo /usr/local/bin/pip2.7 install numpy scipy matplotlib astropy ipython

you can do this on a single computer, go to some nfs mounted directory (e.g. your home directory) and do

> /usr/local/pip freeze > package_list.txt

which pipes the current installed packages to the file package_list.txt. Then you can hop (ssh) onto other computers and just do

> sudo /usr/local/bin/pip2.7 install -r package_list.txt

And done!

more to come on installing python libraries without being sudo.

When the IDL license manager halts for no good reason on canopus…

Published by admin-joel on 2016-03-17

Updated by Bruce and Joel July 2019

So apparently the license manager for idl on canopus loses connection to the server from time to time and Bruce found out that the best way to deal with it was just to power cycle it. Yuping encountered the problem again today and tried the following and it worked.

sudo su – (puts one into root and bash shell – must have sudo privileges)

$ cd /usr/local/exelis/idl83

This is where the IDL installation is

$./bin/lmutil lmdown

This will kill all of the license managers.

$ps aux|grep lm

Make sure that all lm’s are killed

$ ./bin/lmgrd > lmgrd-201Y-MM-DD.log

imgrd starts the license managers.

This appears to fix the problem.

-Yuping

On 2016-05-26, joel found that the above did not quitre work without some help.  I had to first create the log file with a sudo touch filename command, and then CONCAT to the log file in the above sh command by adding a second > to the first one.

psrchive build notes

Published by admin-joel on 2016-02-25

PSRCHIVE BUILD NOTES

This file is also located /usr/share/astro/psrhome/PsarchiveBuildNotes.txt
Yuping Huang
02/25/2016

psrchive is built under 64bit and with gfortran as the fortran compiler. Note that they require a 64bit gfortran compiled pgplot. I will start by building psrchive since it well build its dependencies automatically.

—–PSRCHIVE—————
Set $PSRHOME to /usr/share/astro/psrhome/ this is the directory for all the softwares.

Add $PSRHOME/bin to your $PATH variable

$ cd $PSRHOME

Unzip psrcat in the directory (psrcat available at http://www.atnf.csiro.au/people/pulsar/psrcat/download.html). Then add in .cshrc setenv PSRCAT_FILE $PSRHOME/psrcat/psrcat.db

$ mkdir src && cd src

$ git clone git://git.code.sf.net/p/psrchive/code psrchive

$ cd psrchive

$ ./bootstrap

$ ./configure –prefix=$PSRHOME F77=gfortran

Then psrchive will complain about not having required packages. It generetes csh scripts under packages for installation and we will use those

$ cd packages

$./pgplot.csh

Remember to add to .cshrc $PGPLOT_DIR and $PGPLOT_FONTS as the script suggests. In my case it is

setenv PGPLOT_DIR $PSRHOME/pgplot/

setenv PGPLOT_FONTS $PGPLOT_DIR/grfont.dat

You should also add $PGPLOT_DIR to your LD_LIBRARY_PATH in .cshrc.

$./fftw.csh

$./cfitsio.csh

$PSRHOME/x86_64-linux/src/cfitsioTake notes of where the cfitsio source is located. We will need it later. In my case it is under $PSRHOME/src/cfitsio

$source ~/.cshrc

this step validates the changes made to the environmental variables.

$./tempo2.csh

This will install tempo2 but likely pgplot will not be linked and henceforth this is not yet a fully functional tempo2. But it does have the components
that psrchive needs. The tempo2 linked with pgplot will be built seperately later.

You should set your $TEMPO2 variable to the tempo2 runtime directory. In my case it is $PSRHOME/tempo2

$ cd ..

This should bring you back to the psrchive folder where configure is located. Now rerun ./configure. It should not complain about fftw, cfitsio, tempo2 or pgplot

./configure –prefix=$PSRHOME F77=gfortran –with-cfitsio-dir=$PSRHOME/src/cfitsio

If you are still having trouble, look at http://psrchive.sourceforge.net/third/packages.shtml. When I did it it can find everything but cfitsio so I fed in the
–with-cfitsio-dir directory. Now we are ready to build it.

$ make

$ make check

$ make isntall

Done! the binaries should locate in $PSRHOME/bin . You should add it to your $PATH variable.

How to configure Oklular to show a document’s file name in its titlebar instead of the document’s “title property”

Published by jweisber on 2015-10-07

By default, the version of Okular available to CentOS 6 does not show the viewed document’s filename in the Okular window titlebar, but rather the value of the “Document Title” property embedded in the document being viewed. This is bad news because the Document Title property is usually set to the name of the app that created the document, making it difficult to tell multiple documents generated by the same app apart.

You can force Okular to set it’s window titlebar value to the name of the file being viewed by editing the file ~/.kde/share/config/okularpartrc and appending this line to the ‘[General]’ section:

DisplayDocumentTitle=false

When you finish, the file will end up looking like this:


[General]
UseKTTSD=false
DisplayDocumentTitle=false

 

Thanks Bruce!

compile pgplot in 32bits

Published by admin-joel on 2015-06-09

Since we decided to compile the computing programs in 32 bits to ensure consistencies, pgplot should be compiled in 32 bit as well so that those programs can call it. The build notes are in

/usr/share/astro/psrchive/00READMECarleton

 

The compatibility libraries (with the yum commands) that I had to pull in (which Bruce had a copy):

yum install compat-libgfortran-41.i686
yum install libICE-devel.i686

yum install glibc-devel.i686

yum install zlibrary-devel.i686

yum install libpng-devel.i686

yum install xorg-x11-server-devel.i686

yum install compat-libstdc++-33.i686

yum install compat-libstdc++-296.i686

yum install libxcb-devel.i686

yum install libxcb-devel.i686

yum install zlib-devel.i686

yum install libX11-devel.i686

 

-Yuping

mingw64-pkg-config.x86_64

Published by admin-joel on 2015-06-09

I installed mingw64-pkg-config.x86_64

It seems like it need to pull in its sister package e2fsprogs before compiling dump by typing in the /root/ directory

$ git clone git://git.kernel.org/pub/scm/fs/ext2/e2fsprogs.git

$./configure –enable-elf-shlibs

$ make

$ make check

$ make install

$ make install-libs

which puts the binary file in /usr/bin or /usr/local/…

then go to the dump source file, type

http://surf.ml.seikei.ac.jp/~nakano/dump-restore/dump-restore-mini-HOWTO.en.html

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

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.