March 2002 - Ifeffit - millenia.cars.aps.anl.gov

Problems running athena/tkatoms
by Norbert Weiher 12 Apr '02

12 Apr '02

Dear friends, seems to be that I'm another guy having problems in setting up athena/tkatoms ;) I browsed the archives but found nothing that helped me to get them running. Here is the story: tkatoms worked well - then I installed the newest version and get: weiher> tkatoms.pl ...(lots of messages like the following)... Bareword found where operator expected at /usr/lib/perl5/site_perl/5.6.0/Xray/lib/atomsrc line 186, near "12 normal" (Missing operator before normal?) Unquoted string "normal" may clash with future reserved word at /usr/lib/perl5/site_perl/5.6.0/Xray/lib/atomsrc line 186, <RC> line 186. couldn't read bitmap file "/usr/lib/perl5/site_perl/5.6.0/Xray/lib/tkatoms.xbm": Datei oder Verzeichnis nicht gefundenerror reading bitmap file "/usr/lib/perl5/site_perl/5.6.0/Xray/lib/tkatoms.xbm" at /usr/lib/perl5/site_perl/5.6.0/i586-linux/Tk/Submethods.pm line 37, <RC> line 186. for athena it seems that it can't find the ifeffit.so libs - although they are installed (as well as the perl wrappers) and pass all test runs. I get: weiher> athena Can't load '/usr/lib/perl5/site_perl/5.6.0/i586-linux/auto/Ifeffit/Ifeffit.so' for module Ifeffit: /usr/lib/perl5/site_perl/5.6.0/i586-linux/auto/Ifeffit/Ifeffit.so: undefined symbol: G77_getenv_0 at /usr/lib/perl5/5.6.0/i586-linux/DynaLoader.pm line 200. at /usr/local/bin/athena line 50 Compilation failed in require at /usr/local/bin/athena line 50. BEGIN failed--compilation aborted at /usr/local/bin/athena line 57. I'd really love to get the packages on their way which has never been a real problem. I don't know why the new versions don't compile on my system. The requirements are all fulfilled (perl > 5.0, new Tk version...). Can anyone help me with my problems? The system is a SuSE linux box (V7.2) with kernel 2.4.4 compiled. Regards, Norbert -- Dipl. Chem. Norbert Weiher (norbertweiher(a)yahoo.de) Institute for Chemistry - Takustr. 3 - 14195 Berlin Phone/Fax: +49 30 838 53750 / 54792

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online help bug in tkatoms
by Bruce Ravel 28 Mar '02

28 Mar '02

Howdy folks, Today I received a bug report regarding the on-line help feature in tkatoms. I belve that this problem only affects unix systems. The problem is that, when selecting "Help with Atoms" from the help menu, you may get an error dialog telling you, among other things "Error: Can't set -file to `tkatoms.pod' for Tk::Pod=HASH(0x8f06fe0)" The cause seems to be an error in one of my installation scripts and it should be fixed in the next release (sometime in the indeterminate future -- I am mostly working on artemis right now). If you don't feel you can live without the online help, I think you can make the problem go away by copying by hand the file `tkatoms.pod' from /usr/lib/perl5/site_perl/5.6.0/i586-linux/Xray/ (or whatever similar directory it ended up in on your system) to /usr/lib/perl5/site_perl/5.6.0/i586-linux/Xray/lib/ which is where it should have gone in the first place, except for the bug in my installation script wherein I left out the "lib/" part. Regards B Carlo, if you haven't already, you may be interested in subscribing to our mailing list http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Update athena problems
by Norbert Weiher 28 Mar '02

28 Mar '02

Dear friends, I tracked down the athena installation problems to the point that it's definitively a bug in the perl wrapper for ifeffit. Even re-compiling my gcc suite didn't solve this problem. All suggestions given by Matt and Bruce have not been successful so far. Maybe someone here got athena running on a linux box (I have SuSE 7.2) and experienced the same? Could it be the gcc version I use (2.95.3)? Include paths, etc seem to be okay. The build of the wrapper works, but the make test still aborts with the message I posted... gifeffit & ifeffit work fine. Any new suggestions on this issue? Regards, Norbert -- Dipl. Chem. Norbert Weiher (norbertweiher(a)yahoo.de) Institute for Chemistry - Takustr. 3 - 14195 Berlin Phone/Fax: +49 30 838 53750 / 54792

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volunteerism....
by Bruce Ravel 27 Mar '02

27 Mar '02

Hi Folks, Matt said: > From a political viewpoint, I think we'd need a volunteer to keep > the scripts in working order for Win95/98/ME. Unless that happens, > I don't consider "upgrade to 2000" to be an unreasonable response. I want to second this request. It's really hard for Matt and I to stay on top of all these different platforms. The 9x/ME series of OS's is sufficiently different from 2000/NT/XP (I run 2000 under VMWare on my linux box) that it is hard for us to keep up. I would be happy to help a volunteer 9x/ME tester/debugger get up and running. The biggest chore is learning how to use the program that Matt and I chose for building the Windows installation package. That's not hard -- I had it mostly figured out in a day. Then Matt said: > Also from a political viewpoint, could we encourage 'A fellow' > to post such problems here? I get lots of email from people about Atoms and, of late, about Athena. I have taken to pointing out the web entry point to our mailing list whenever I answer a question from someone who may not be a subscriber. I encourage all of you to encourage anyone around you who may be interested in our software to subscribe. As ifeffit and friends have been finding a wider audience, more problems have been cropping up. This is a natural part of growth and is very healthy. With the help of all of you on this list, Matt and I will be able to make a much better package. Finally, some suggested reading from freshmeat, the software repository: The Importance of Non-Developer Supporters in Free Software http://freshmeat.net/articles/view/156/ How to Report Bugs Effectively http://freshmeat.net/articles/view/149/ B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: Ifeffit digest, Vol 1 #10 - 1 msg
by Guilhem DEZANNEAU 27 Mar '02

27 Mar '02

Hi, i actually work with Windows 95 (version 97) OS and encountered similar messages : - too many parameters - environment out of memory for all programs of the ifeffit package Nevertheless, even if these messages appear, the programs TkAtoms, Gifeffit run without problems... It is not the case for APT that stays without running... Guilhem DEZANNEAU ___________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en français ! Yahoo! Mail : http://fr.mail.yahoo.com

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ifeffit on Windows ME
by Bruce Ravel 27 Mar '02

27 Mar '02

Howdy folks, I got an interesting bug report a few days ago which I could only partly address. A fellow asked me: > I have installed the IFEFFIT package in my computer (WIN ME). The > installation software seems to work ok. However, when I try to run > the *.bat files, I have the following message, repeated twice: "out > of environment space". Despite these messages athena, gifeffit and > ifeffit are runnig ok. However, tkatoms.bat and apt.bat don't run > at all. I understand that the "out of environment space" problem results from the rather awkward way the old Windows operating systems handled "conventional" memory and the amount of memory dedicated to holding the values of environment variables. It seems reasonable that this message turns up when our .bat files are run since they add to the environment. I suppose that an environment that is already nearly full could be tipped by our .bat files. See, for example, http://www.pcguide.com/ts/x/sys/operrEnvironmentSpace-c.html The second part of the question stumps me. Why do three of the codes work, but tkatoms and the periodic table not run? The tkatoms executable is, in fact, larger than athena, but the periodic table is smaller. And the periodic table does not use Ifeffit, which should make its memory demands even smaller. So does anyone have any wisdom for Windows ME? ("Upgrade" and other snippy comments are not helpful! ;-) Has anyone been able to use these codes on 98 or ME? B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: [Ifeffit] iFEFFit and Tcl
by Bruce Ravel 11 Mar '02

11 Mar '02

John said: jjr> Maybe, I misunderstand, but presently we do have Python-2.0.1 jjr> installed. Does anyone know what version of Python is needed to jjr> have Tkinter? A quick search on google turned this up: http://www.python.org/topics/tkinter/

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Re: [Ifeffit] iFEFFit and Tcl
by John J. Rehr 11 Mar '02

11 Mar '02

Hi Matt, Thanks for the comments: > For G.I.Feffit, I think it's just a matter of getting a version > of python with Tkinter built-in. If perl/Tk were installed, > I'd guess that athena and tkatoms would run fine too. These > are both (python/Tkinter and perl with Tk) a small amount of Maybe, I misunderstand, but presently we do have Python-2.0.1 installed. Does anyone know what version of Python is needed to have Tkinter? Also, both tkatoms and athena appear to run fine on our SGI (at least for the jobs I've run). Only gifeffit seems to be problematic. John

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new Athena release, version 2002.03.08
by Bruce Ravel 11 Mar '02

11 Mar '02

Hi, I just posted a new release of the athena source code. I have not yet made a new windows binary. This version is 2002.03.08. New in this release: ** Phase corrected Fourier transforms (requires ifeffit 1.0069 or later) which make use of tables of central atoms phase shifts as I discussed on the feffdevel list http://cars9.uchicago.edu/feff/feffdevel/msg00082.html ** Spline clamps, both high and low, but with discrete, menu-chosen scaling factors. This is not yet documented, but the basic idea is that you can put restraints at the high and low end of the spline range in the autobk algorithm to coerce the spline to go through the data at those points. Try autobk with the high clamp set to Strong -- very cool! ** a few bug fixes -- as always ;-) Kind of a small list, but PCFTs and spline clamps are both fairly major bits of user functionality, so it seemed worth making a new release. As always, point your browser at http://feff.phys.washington.edu/~ravel/software/exafs/ for the latest. B P.S. Those of you to whom I sent this message by blind carbon copy should go to http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit and subscribe to Matt's great, new ifeffit mailing list. In the future all announcements will be made there. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: [Ifeffit] iFEFFit and Tcl
by John J. Rehr 11 Mar '02

11 Mar '02

Hi Everyone, I'm simply delighted to see all the effort/success in getting gifeffit/ifeffit/ etc. going on OSX. However, I'm curious about the status on SGIs. Although I've gotten ifeffit to build and install using SGI's cc compiler (setenv CC cc), it appears that gifeffit does not work yet even with the latest release of ifeffit. Some symptoms, which may or may not be relevant: 1) from the ifeffit make install: Making install in wrappers Installing python extension Distutils works Testing for Tkinter and Pmw ===== WARNING WARNING WARNING ===== Tkinter is NOT installed, or was not found G.I.FEFFIT will not work. Pmw 0.8.5 is already installed. Great! 2) from wrappers/tcl cd /usr/local/src/ifeffit_1.0b/wrappers/tcl 44# sh Build cc -fpic -g -c -I../../src/lib ifeffit_wrap.c -o ifeffit_wrap.o cc ERROR parsing -fpic: unknown flag *** Error code 2 (bu21) This is not an urgent matter; ifeffit/gifeffit/athena/tkatoms, etc all appears to work fine on my laptop and desktop running various RH LINUX OS. But we still love our SGIs. Cheers, J. Rehr

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