[PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source
Dear all,
I decided to upgrade ifeffit-1.2.11 on my Ubuntu 8.10 (Intrepid Ibex)
desktop machine. Well, up to now I have always worked with PGPLOT &
Ifeffit binaries from Carlo that are just working fine but seen that
they are still not ready for the new version I decided to build them by
source.
First of all let me say that Ifeffit builds fine if I use the "pgplot5"
binary package, BUT, as stated by Matt in the README.PGPLOT, Ifeffit
will compile without plotting support in this case.
So the only way is to build also PGPLOT from source. Unfortunately the
experience has failed both with the "PGPLOT_install" script and
following steps in the "install-unix.txt".
I have tried many possibilities but the make process interrupts on the
drivers compilations. Seen that following "install-unix.txt" gives the
same error (but on another driver!) of "PGPLOT_install", let's focus on
this last procedure to try debugging the situation:
$sudo ./PGPLOT_install
...
[all fine until the PGPLOT make]
[long list of errors + warnings like:]
...
/home/mauro/local/ifeffit-1.2.11/pgplot/drivers/xwdriv_iff.c:4445:
error: ‘XWdev’ has no member named ‘gc’
...
make: *** [xwdriv_iff.o] Error 1
...
[then the final error due to the bad compilation]
collect2: ld returned 1 exit status
make: *** [pgdemo1] Error 1
OK, I have described more or less the situation but I would not flood
the list with technical mails, so if someone would help me with this
issue we can continue in private and then send just the solution to the
list.
Anyway, the problem is not "urgent" seen that I can work with the 1.2.10
binary installation.
Have a nice day!
Mauro
--
Mauro Rovezzi
Hi Mauro, Firstly, I should note that I'm still using Ubuntu 8.04, Horae 067 and Ifeffit 1.2.10a (I had a problem with Ifeffit 1.2.11 described in another post: "Ifeffit 1.2.11b terminal output"; I don't know if PGPLOT was the cause). I've always built Horae and Ifeffit from source rather than use binary packages.
First of all let me say that Ifeffit builds fine if I use the "pgplot5" binary package, BUT, as stated by Matt in the README.PGPLOT, Ifeffit will compile without plotting support in this case.
Interesting, I'd never even noticed README.PGPLOT... Ifeffit "./configure --with-pgplot-link=-lpgplot" using Ubuntu's PGPLOT package has always* worked for me, at least well enough for using Horae (I use gnuplot to save plots to files). I don't know then what's broken in the binary packages from Ifeffit's point of view, so hopefully someone more knowledgeble can clarify that, but if you just want plots in Athena and Artemis the --with-pgplot-link method seems to work. [* Some Ubuntu versions needed "-lpng" and "-lX" too, from memory, so if ld complains about missing symbols try adding these.] Gareth
Hi Gareth, Thank you for the answer! Gareth Jones wrote:
Ifeffit "./configure --with-pgplot-link=-lpgplot" using Ubuntu's PGPLOT package has always* worked for me, at least well enough for using Horae (I use gnuplot to save plots to files). I don't know then what's broken in the binary packages from Ifeffit's point of view, so hopefully someone more knowledgeble can clarify that, but if you just want plots in Athena and Artemis the --with-pgplot-link method seems to work.
Your solution works! Now I have PGPLOT installed from the binary package
"pgplot5", Ifeffit 1.2.11b compiled using -lpgplot and everything seems
to work fine.
M.
--
Mauro Rovezzi
Hi Marco: I apologize for being behind the curve on the new ifeffit. Too much work here at IIT. I think I will be able to put out a new ifeffit version in the next week or so. Carlo On Wed, 12 Nov 2008, Mauro Rovezzi wrote:
Dear all,
I decided to upgrade ifeffit-1.2.11 on my Ubuntu 8.10 (Intrepid Ibex) desktop machine. Well, up to now I have always worked with PGPLOT & Ifeffit binaries from Carlo that are just working fine but seen that they are still not ready for the new version I decided to build them by source.
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org
Hi Mauro: I have now produced a package of ifeffit 1.2.11b. It is in Debian unstable and available for Ubuntu intrepid and jaunty in my repository deb http://debian-xray.iit.edu intrepid main contrib non-free deb http://debian-xray.iit.edu jaunty main contrib non-free The version for jaunty will be replaced by the ubuntu version once it propagates into the archives. I have not built it for hardy but will if anyone has a need for it. Cheers, Carlo On Wed, 12 Nov 2008, Mauro Rovezzi wrote:
Dear all,
I decided to upgrade ifeffit-1.2.11 on my Ubuntu 8.10 (Intrepid Ibex) desktop machine. Well, up to now I have always worked with PGPLOT & Ifeffit binaries from Carlo that are just working fine but seen that they are still not ready for the new version I decided to build them by source.
First of all let me say that Ifeffit builds fine if I use the "pgplot5" binary package, BUT, as stated by Matt in the README.PGPLOT, Ifeffit will compile without plotting support in this case.
So the only way is to build also PGPLOT from source. Unfortunately the experience has failed both with the "PGPLOT_install" script and following steps in the "install-unix.txt".
I have tried many possibilities but the make process interrupts on the drivers compilations. Seen that following "install-unix.txt" gives the same error (but on another driver!) of "PGPLOT_install", let's focus on this last procedure to try debugging the situation:
$sudo ./PGPLOT_install ... [all fine until the PGPLOT make] [long list of errors + warnings like:] ... /home/mauro/local/ifeffit-1.2.11/pgplot/drivers/xwdriv_iff.c:4445: error: ‘XWdev’ has no member named ‘gc’ ... make: *** [xwdriv_iff.o] Error 1 ... [then the final error due to the bad compilation] collect2: ld returned 1 exit status make: *** [pgdemo1] Error 1
OK, I have described more or less the situation but I would not flood the list with technical mails, so if someone would help me with this issue we can continue in private and then send just the solution to the list.
Anyway, the problem is not "urgent" seen that I can work with the 1.2.10 binary installation.
Have a nice day! Mauro
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org
Carlo Segre wrote:
Hi Mauro:
I have now produced a package of ifeffit 1.2.11b. It is in Debian unstable and available for Ubuntu intrepid and jaunty in my repository
deb http://debian-xray.iit.edu intrepid main contrib non-free
Carlo, Thank you very much for the package. Actually, I was able to build/install ifeffit 1.2.11b from source but not able to build than the Perl/Python wrappers and so no Horae&Friends from Bruce SVN. Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" built from source (Bruce SVN). Everything seems fine but I still do not understand why ifeffit 1.2.11 has all these "IFF str = *" output as stated also by Gareth in his "Ifeffit 1.2.11b terminal output" post. Is it normal? Cheers, Mauro
Hi Mauro: On Mon, 17 Nov 2008, Mauro Rovezzi wrote:
Carlo Segre wrote:
I have now produced a package of ifeffit 1.2.11b. It is in Debian unstable and available for Ubuntu intrepid and jaunty in my repository
deb http://debian-xray.iit.edu intrepid main contrib non-free
Thank you very much for the package.
Actually, I was able to build/install ifeffit 1.2.11b from source but not able to build than the Perl/Python wrappers and so no Horae&Friends from Bruce SVN.
Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" built from source (Bruce SVN).
yeah, I have not completed packaging the new horae. Because of the way Bruce has restructured it, I have had to package several new perl modules and change the build system on the horae programs. I ust need to spend a bit more time on it to get it it right. maybe next weekend :-)
Everything seems fine but I still do not understand why ifeffit 1.2.11 has all these "IFF str = *" output as stated also by Gareth in his "Ifeffit 1.2.11b terminal output" post. Is it normal?
I don't know why this is happening but it looks to me simply like a dump of the ifeffit commands which are being executed. It is annoying but I haven't seen any problems because of it. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org
Hi,
This is my fault... and I apologize for the sloppiness and for being
late in fixing this. I've been mixing 'development/testing' and
'production' versions, and haven't been very good at keeping them
cleanly separated. I think I have this mostly under control now,
but I will have to work on a decent "test suite".
I think I found another reason to make a 1.2.11c version too, that the
mixing of "devel" and "production"
caused an experiment in how fitting was done to be the default, so
that the reported chi-square doesn't actually match the documentation
(instead of summing real and imaginary parts, it sums real and
magnitude components of the misfit, which is part of an experiment to
see how Feff8.5 worked for XAFS. Using Magnitude as well Phase for
another way to report chi-square and misfits is potentially a useful
approach, but it's not what is documented. Anyway, mixing devel and
production versions like this (for the past couple years, really) is
very sloppy on my part, and I apologize again.
I actually have an ubuntu box now, though I built pgplot from source,
and have never made a .deb file.
There is a new source kit at
http://cars.uchicago.edu/~ifeffit/src/ifeffit-1.2.11c.tar.gz I'll
post this to sourceforge this afternoon, and I'll also make a new DLL
for Windows and post all of these on the download page. I'll also make
a new updater for Windows.
--Matt
On Mon, Nov 17, 2008 at 10:07 AM, Mauro Rovezzi
Carlo Segre wrote:
Hi Mauro:
I have now produced a package of ifeffit 1.2.11b. It is in Debian unstable and available for Ubuntu intrepid and jaunty in my repository
deb http://debian-xray.iit.edu intrepid main contrib non-free
Carlo,
Thank you very much for the package.
Actually, I was able to build/install ifeffit 1.2.11b from source but not able to build than the Perl/Python wrappers and so no Horae&Friends from Bruce SVN.
Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter" built from source (Bruce SVN).
Everything seems fine but I still do not understand why ifeffit 1.2.11 has all these "IFF str = *" output as stated also by Gareth in his "Ifeffit 1.2.11b terminal output" post. Is it normal?
Cheers, Mauro _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (4)
-
Carlo Segre -
Gareth Jones -
Matt Newville -
Mauro Rovezzi