Hi folks, I just made a new release of Athena (0.8.049) and Artemis (0.8.006). A new source tarball is at SourceForge and at my website. An updater for Windows is on Matt's server. There is nothing big in this release, just some bug fixes and a few small usability improvements. See the release notes http://cars9.uchicago.edu/iffwiki/HoraeVersion061 for details. Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
I have built Debian packages and they are available on my repository. Carlo On Tue, 28 Mar 2006, Bruce Ravel wrote:
Hi folks,
I just made a new release of Athena (0.8.049) and Artemis (0.8.006). A new source tarball is at SourceForge and at my website. An updater for Windows is on Matt's server.
There is nothing big in this release, just some bug fixes and a few small usability improvements. See the release notes
http://cars9.uchicago.edu/iffwiki/HoraeVersion061
for details.
Enjoy, B
-- 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 Carlo.Segre@iit.edu http://www.iit.edu/~segre
Hi Bruce, any idea on why this happens while installing 061? Does it have to do with the OSX 10.4 issue? Stefano stefano# perl Makefile.PL === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is Mac OSX. Checking dependencies ... Dependencies ok. Cool! Reading configuration file: Ifeffit/lib/athena/athena.config Wrote Ifeffit/lib/athena/athenarc Ifeffit/lib/athena/athenarcw Ifeffit/lib/athena/athena.ini athena_parts/rc.pl Reading configuration file: Ifeffit/lib/artemis/artemis.config Wrote Ifeffit/lib/artemis/artemisrc Ifeffit/lib/artemis/artemisrcw Ifeffit/lib/artemis/artemis.ini artemis_parts/rc.pl Assembled athena.pl from its parts (athena_parts/). Assembled artemis.pl from its parts (artemis_parts/). Assembled hephaestus.pl from its parts (hephaestus_parts/). Fixing execution path in the Athena, Artemis, and Hephaestus executables... Changing athena.pl to /usr/bin/perl Changing artemis.pl to /usr/bin/perl Changing hephaestus.pl to /usr/bin/perl Changing ifeffit_shell.pl to /usr/bin/perl Changing rdaj.pl to /usr/bin/perl Changing atoms.pl to /usr/bin/perl dyld: Library not loaded: /usr/local/lib/libpgplot.dylib Referenced from: /Applications/Ifeffit/bin/ifeffit Reason: image not found Ifeffit's installations directory is (found by capturing `ifeffit -i`) Could not open /config/Config.mak file for reading stefano# -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
On Thursday 30 March 2006 07:38, you wrote:
dyld: Library not loaded: /usr/local/lib/libpgplot.dylib Referenced from: /Applications/Ifeffit/bin/ifeffit Reason: image not found Ifeffit's installations directory is (found by capturing `ifeffit -i`)
Stefano, One of the folks who actually uses the Mac is going to have to give the specifics, but these messages indicate that the pgplot library is being found. It would seem that ifeffit failed because it could not link to the pgplot library. Why that is the case while building my codes today but not while using my codes yesterday is not at all clear to me. Maybe Paul or Matt will have more wisdom. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
I have updated the binary installer for Mac OS 10.4 to include the latest horae (061). There should hopefully be no problems. To simplify some problems that have occurred in the past, the installer now refuses to work if the /usr/X11R6 folder is not present (e.g. if X11 is not installed). If there are any problems, please let me know. Paul p.s. Matt, the links on the ifeffit home page point to an old installer. The newer (mac) installer now has the horae version incorporated into its name, the latest being "ifeffit-1.2.8- Mac10.4_horae61_pkg.dmg"
Hi Paul,
I have updated the binary installer for Mac OS 10.4 to include the latest horae (061). There should hopefully be no problems. To simplify some problems that have occurred in the past, the installer now refuses to work if the /usr/X11R6 folder is not present (e.g. if X11 is not installed). If there are any problems, please let me know.
I installed the package from ifeffit-1.2.8-Mac10.4_horae61_pkg.dmg. I get Artemis to exit (crashing) when I run a fit from the examples folder (copper). Also, if I run the ifeffit command from any unix shell window I get the following message: stefano% ifeffit dyld: Library not loaded: /usr/local/lib/libpgplot.dylib Referenced from: /Applications/Ifeffit/bin/ifeffit Reason: image not found Trace/BPT trap stefano% Any clues? The ifeffit-1.2.8-Mac10.4_pkg.dmg installer causes the same identical problem. Stefano PS: my OSX is 10.4.6, but also 10.4.5 did not work -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
Hi Stefano, I tried reproducing the problem and my copy of artemis (from the 61 installer) works without a hitch. I tried one of my multiple edge fit projects as well as the Cu single shell fit and both worked. I don't have a /usr/local/libpgplot.dylib on my system as well. The problem is thus something different between the machine environments (as the installer just puts the binary files in their proper places). I will look into it. I have been using Bruces compile scripts for the compilation of each version of horae and they are a little crusty (and I don't understand all of their details) so the problem may be in a dynamic lookup specification. As a quick check -- Do you have any DYLDLIB related environment variables set that might force the system to look in particular places for dynamic libraries? I will bounce this off Bruce (as we are both at the APS here at Argonne) and see if he has a similar problem. Right now all I have is my powerbook with me and horae works so to track down the problem, we are going to have to figure out what is different between our systems. The simplest possible difference (I have a /usr/local/ lib/libpgplot.dylib file and you don't) isn't the case. The pgplot library in question should be in /Applications/Ifeffit/pgplot/ libpgplot.a. Paul On Apr 7, 2006, at 2:13 AM, Stefano Ciurli wrote:
Hi Paul,
I have updated the binary installer for Mac OS 10.4 to include the latest horae (061). There should hopefully be no problems. To simplify some problems that have occurred in the past, the installer now refuses to work if the /usr/X11R6 folder is not present (e.g. if X11 is not installed). If there are any problems, please let me know.
I installed the package from ifeffit-1.2.8-Mac10.4_horae61_pkg.dmg. I get Artemis to exit (crashing) when I run a fit from the examples folder (copper). Also, if I run the ifeffit command from any unix shell window I get the following message:
stefano% ifeffit dyld: Library not loaded: /usr/local/lib/libpgplot.dylib Referenced from: /Applications/Ifeffit/bin/ifeffit Reason: image not found Trace/BPT trap stefano%
Any clues? The ifeffit-1.2.8-Mac10.4_pkg.dmg installer causes the same identical problem. Stefano PS: my OSX is 10.4.6, but also 10.4.5 did not work -- ____________________________________________
Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203
"Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI
"Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high" _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Stefano, Paul - Unless Paul changed something with the 10.4 build, ifeffit links with pgplot statically, so there should never be a case where ifeffit looks for a dynamic library for pgplot. You can check this with ~> otool -L /Applications/Ifeffit/bin/ifeffit This should list libX11, a curses / termcap library, and system libraries, but not pgplot. If it does list the dynamic pgplot library, the build is broken. I believe that athena / artemis etc would have a related, but slightly different issue. Here, you'll need to use 'otool -L' on the Ifeffit.bundle under the /Library/Perl tree, probably /Library/Perl/5.8.6/darwin-trhead-something/auto/Ifeffit/Ifeffit.bundle Can anyone else confirm / deny if the installer works on OS X 10.4? --Matt
First off, here is the otool result: Quark:/Applications/Ifeffit/pgplot paulfons$ otool -L /Library/Perl/ 5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/ Ifeffit.bundle: /System/Library/Frameworks/Foundation.framework/Versions/C/ Foundation (compatibility version 300.0.0, current version 567.26.0) /System/Library/Frameworks/AppKit.framework/Versions/C/ AppKit (compatibility version 45.0.0, current version 824.33.0) /Library/Frameworks/AquaTerm.framework/Versions/A/AquaTerm (compatibility version 1.0.0, current version 1.0.0) /usr/X11R6/lib/libX11.6.dylib (compatibility version 6.2.0, current version 6.2.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.5) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 92.0.0) As you can seen, there is no reference to a dynamic library for pgplot (I just used the standard build sequence) -- and besides it works on my machine and no such dynamic library, so something must be different on Stefano's machine. Bruce (who is working on the bending magnet at sector 20 right nearby) mentioned that it may be the case that Stefano could have built his own version of the library and this is being used. He implied this could also be a path difference. Stefano, can you find another instance of the Ifeffit.bundle library on your system using "locate ifeffit.bundle"? On my machine this gives: Quark:/Applications/Ifeffit/pgplot paulfons$ locate Ifeffit.bundle /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/ Ifeffit.bundle /Users/paulfons/Ports/BuildInstaller/Package_Contents/Library/Perl/ 5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle (the second instance is from the Installer Builder and isn't on any search path). My Ifeffit.bundle shows: -r-xr-xr-x 1 root admin 2784400 Apr 6 20:12 /Library/Perl/5.8.6/ darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle The md5 hash (unique signature) on my Ifeffit bundle is: md5 /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/ Ifeffit.bundle MD5 (/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/ Ifeffit.bundle) = 44b898c68c2ede8a05cfd74e807bf32e One other quick thing to try is to delete the package receipt and reinstall the 61 horae version. Paul On Apr 7, 2006, at 10:30 AM, Matt Newville wrote:
Stefano, Paul -
Unless Paul changed something with the 10.4 build, ifeffit links with pgplot statically, so there should never be a case where ifeffit looks for a dynamic library for pgplot. You can check this with ~> otool -L /Applications/Ifeffit/bin/ifeffit
This should list libX11, a curses / termcap library, and system libraries, but not pgplot. If it does list the dynamic pgplot library, the build is broken.
I believe that athena / artemis etc would have a related, but slightly different issue. Here, you'll need to use 'otool -L' on the Ifeffit.bundle under the /Library/Perl tree, probably /Library/Perl/5.8.6/darwin-trhead-something/auto/Ifeffit/ Ifeffit.bundle
Can anyone else confirm / deny if the installer works on OS X 10.4?
--Matt
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Paul,
Stefano, can you find another instance of the Ifeffit.bundle library on your system using "locate ifeffit.bundle"? On my machine this gives:
Quark:/Applications/Ifeffit/pgplot paulfons$ locate Ifeffit.bundle /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle /Users/paulfons/Ports/BuildInstaller/Package_Contents/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle
on mine, I get nothing: stefano% pwd /Library/Perl/5.8.6 stefano% locate ifeffit.bundle stefano%
(the second instance is from the Installer Builder and isn't on any search path). My Ifeffit.bundle shows:
-r-xr-xr-x 1 root admin 2784400 Apr 6 20:12 /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle
mine shows: stefano% pwd /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit stefano% ls -la total 5504 drwxr-xr-x 15 root admin 510 Apr 7 09:06 . drwxr-xr-x 19 root admin 646 Apr 6 19:40 .. -rw-r--r-- 1 root admin 32221 Jan 3 09:44 .packlist drwxr-xr-x 3 root admin 102 Apr 7 09:06 Elements drwxr-xr-x 3 root admin 102 Apr 7 09:06 Files drwxr-xr-x 3 root admin 102 Apr 7 09:06 FindFile drwxr-xr-x 3 root admin 102 Apr 7 09:06 Group -r--r--r-- 1 root admin 0 Aug 11 2005 Ifeffit.bs -r-xr-xr-x 1 root admin 2783188 Jan 3 09:43 Ifeffit.bundle drwxr-xr-x 3 root admin 102 Apr 7 09:06 Parameter drwxr-xr-x 3 root admin 102 Apr 7 09:06 ParseFeff drwxr-xr-x 3 root admin 102 Apr 7 09:06 Path drwxr-xr-x 3 root admin 102 Apr 7 09:06 PathDev drwxr-xr-x 3 root admin 102 Sep 7 2005 Plugins drwxr-xr-x 3 root admin 102 Apr 7 09:06 Tools
The md5 hash (unique signature) on my Ifeffit bundle is:
md5 /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle MD5 (/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle) = 44b898c68c2ede8a05cfd74e807bf32e
mine is: stefano% md5 /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle MD5 (/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle) = 4751c85d37d4113f5bd5fc633287f739
One other quick thing to try is to delete the package receipt and reinstall the 61 horae version.
Paul, before making further possible mistakes, please give me an exact procedure for this (monkey training...) Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
Hi Matt,
Unless Paul changed something with the 10.4 build, ifeffit links with pgplot statically, so there should never be a case where ifeffit looks for a dynamic library for pgplot. You can check this with ~> otool -L /Applications/Ifeffit/bin/ifeffit
this is what I get: stefano% otool -L /Applications/Ifeffit/bin/ifeffit /Applications/Ifeffit/bin/ifeffit: /usr/local/lib/libpgplot.dylib (compatibility version 0.0.0, current version 0.0.0) /usr/X11R6/lib/libX11.6.dylib (compatibility version 6.2.0, current version 6.2.0) /sw/Library/Frameworks/AquaTerm.framework/Versions/A/AquaTerm (compatibility version 1.0.0, current version 1.0.0) /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation (compatibility version 300.0.0, current version 567.21.0) /usr/lib/libncurses.5.4.dylib (compatibility version 5.4.0, current version 5.4.0) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 92.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.2) stefano%
This should list libX11, a curses / termcap library, and system libraries, but not pgplot. If it does list the dynamic pgplot library, the build is broken.
I think it does, as far as I can tell
I believe that athena / artemis etc would have a related, but slightly different issue. Here, you'll need to use 'otool -L' on the Ifeffit.bundle under the /Library/Perl tree, probably /Library/Perl/5.8.6/darwin-trhead-something/auto/Ifeffit/Ifeffit.bundle
stefano% otool -L /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle: /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation (compatibility version 300.0.0, current version 567.21.0) /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit (compatibility version 45.0.0, current version 824.23.0) /Library/Frameworks/AquaTerm.framework/Versions/A/AquaTerm (compatibility version 1.0.0, current version 1.0.0) /usr/X11R6/lib/libX11.6.dylib (compatibility version 6.2.0, current version 6.2.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.2) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 92.0.0) HTH
Can anyone else confirm / deny if the installer works on OS X 10.4?
maybe I am the only one using it? :-) Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
Hi Paul,
The simplest possible difference (I have a /usr/local/lib/libpgplot.dylib file and you don't) isn't the case. The pgplot library in question should be in /Applications/Ifeffit/pgplot/libpgplot.a.
this is what I have in that directory: stefano% pwd /Applications/Ifeffit/pgplot stefano% ls -la total 2480 drwxr-xr-x 13 root admin 442 Apr 7 09:06 . drwxrwxr-x 24 root admin 816 Apr 7 09:06 .. -rw-r--r-- 1 root admin 247 Jan 3 10:48 drivers.list -rw-r--r-- 1 root admin 66020 Jan 3 10:48 grfont.dat -rw-r--r-- 1 root admin 3911 Jan 3 10:48 grpckg1.inc -rwxrwxr-x 1 root admin 613560 Jan 3 10:48 libpgplot_iff.a -rw-r--r-- 1 root admin 211532 Jan 3 10:48 libpng_iff.a -rw-r--r-- 1 root admin 82380 Jan 3 10:48 libz_iff.a -rw-r--r-- 1 root admin 35230 Jan 3 10:48 makefile -rw-r--r-- 1 root admin 162651 Jan 3 10:48 pgplot.doc -rw-r--r-- 1 root admin 6287 Jan 3 10:48 pgplot.inc -rwxr-xr-x 1 root admin 49528 Jan 3 10:48 pgxwin_server -rw-r--r-- 1 root admin 16059 Jan 3 10:48 rgb.txt It appears that I do not have any libpgplot.a in this directory HTH Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
participants (5)
-
Bruce Ravel -
Carlo Segre -
Matt Newville -
Paul Fons -
Stefano Ciurli