[Ifeffit] [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 [EMAIL PROTECTED] PhD student - GILDA BM08 c/o ESRF (Grenoble, FR) ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source
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 [EMAIL PROTECTED] PhD student - GILDA BM08 c/o ESRF (Grenoble, FR) ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source
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: 312.567.3498Fax: 312.567.3494 [EMAIL PROTECTED] http://www.iit.edu/~segre [EMAIL PROTECTED] ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Sealed Sample Cell
Dear Bhoopesch, a typical design for a liquid sample cell is shown in the 2006 HASYLAB annual report, p. 76 (E. Welter et al.): http://hasyweb.desy.de/science/annual_reports/2006_report/part1/contrib/25/18872.pdf The cell consists of teflon spacers with stainless steel plates on both ends. These plates hold some kind of X-ray transparent window in place. A syringe can be used for filling and emptying the cell. Now, for your special application, the choice of the window is critical. However, at 10 keV you are not really limited to special materials like Be or BN, with ultralow scattering cross sections. The absorption length of a typical carbon-based polymer at 10 keV is already around 0.2 cm, which means that you could just use a regular polyethylene vessel with 1 mm wall thickness as sample cell. I wouldn't use Beryllium, due to several reasons. With organomercury compounds, the chemical stability of Be could be an issue. I could imagine the formation of Beryllium amalgames, which are unstable in air and decompose to powders, as in JACS 1957, 3925. Also, Be windows are an inherent safety issue and should be avoided whereever possible. Have you investigated the applicability of Teflon-coated Kapton foil, like the FN type of DuPont ? We've used this type of foil (150FN019, teflon side towards the reaction cell) as window for many different reative gas atmospheres, like ammonia, acrolein, CO/CO2,... at elevated temperatures and never had problems with chemical stability or permeability of these foils. You could for example use some thicker variants like the 250FN029, with 50µm Polyimide / 13µm Teflon, or the 400FN022. Best regards, dominik Bhoopesh Mishra wrote: Dear All, I am planning to conduct an EXAFS experiment which involves dealing with methyl mercury. Obviously, I want to be as cautious as I can in sealing the sample. In that connection, I am wondering if anyone on this forum can advise me regarding the best way to have a completely sealed (air tight) sample holder. My requirements are given below. Third requirement is not as important as the first two. 1. Sample cell (or the front and rear exit) should be made of low scattering material that would not attenuate photons too much at ~ 10-12 keV. 2. The sample cell should be a perfectly sealed, as gaseous phase methyl mercury or even di-methyl mercury could be produced in the cell. 3. I would like to inject solution using syringe in the sealed sample holder (if possible, this requirement is not necessary). Among several possibilities, I am thinking of designing a cuvette shaped rectangular box with a thin bottom section, and probably using some sort of polypropylene such that scattering is as low as possible. It should be easy to put two silicon rubber septa on the top. Other possibility could be using a thick Beryllium window (and please forgive my naivete' here - isn't there some restriction in using Be) on both the front and back of a rectangular or cylindrical box with rubber stopper at the top. The easiest and probably the best would be to have a commercially available sample cell that can serve my purpose. I don't know any commercially available product like that. But I suspect, people who work with volatile material and/or radioactive material might know a lot about it. If you know anything, please write me back. Any comments, suggestions, or criticism would be highly appreciated. PS: Sealing with kapton tape (or any other thin film) might not be enough in this case as gaseous phase methyl mercury might diffuse through kapton, and also air might diffuse through kapton making the inside of the cell environment aerobic while I need to do this experiment anaerobically. Thanks for your help! Bhoopesh ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Dr. Dominik Samuelis [EMAIL PROTECTED] Max-Planck-Institut für Festkörperforschung Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on Ubuntu from source
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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
