Re: [Ifeffit] Artemis error message
Hi Stefano, Did you try using /Applications/Ifeffit/bin/feff6 as the preferred feff executable in Artemis? That's what the error message was suggesting you try. Can you verify that you have /Applications/Ifeffit/bin/feff6? --Matt
Hi Matt,
Did you try using /Applications/Ifeffit/bin/feff6 as the preferred feff executable in Artemis? That's what the error message was suggesting you try.
I had inserted the /Applications/Ifeffit/bin/feff6 path instead of just feff6 in the Artemis preferences, but the error persists
Can you verify that you have /Applications/Ifeffit/bin/feff6?
I do have it there. 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"
Hello Matt and Paul, I verified the following: 1) here is the error message in the echo window Preparing to run FEFF ... Performing autosave ... Saving feff.inp file Performing autosave ... done! Running feff (this could take a few minutes, please be patient) ... Uh oh! That Feff calculation did not run successfully. 2) when I run the command "feff6" from the terminal, I get the following message: stefano% feff6 Feff 6L.02 Fatal Error: cannot open file "feff.inp" in module rdinp I interpret this message with the conclusion that I can just type 'feff6' in the Artemis preferences, as the command is actually seen and of course it is missing the feff.inp file if I run the command from the terminal. In the end, I have not been able to pinpoint the problem. Maybe a fault in the installer??? I am stuck. 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"
rdinp is the input routine for feff -- the error message means that for some reason feff6 could not open the input file (e.g. feff is running correctly and cannot find the input file). Now in the echo area, artemis claims the feff.inp file is being created. feff will attempt to open an "feff.inp" file from the directory in which it is invoked (e.g. something like: ls -l ~/.horae/stash/artemis.project.1/data0.feff3: total 776 drwxr-xr-x 41 paulfons paulfons 1394 Sep 5 19:07 ./ drwxr-xr-x 13 paulfons paulfons 442 Sep 5 19:07 ../ -rw-r--r-- 1 paulfons paulfons 701 Sep 5 19:07 atoms.inp -rw-r--r-- 1 paulfons paulfons 6388 Sep 5 19:07 feff.inp -rw-r--r-- 1 paulfons paulfons 7228 Sep 5 19:07 feff.run -rw-r--r-- 1 paulfons paulfons 4666 Sep 5 19:07 feff0001.dat -rw-r--r-- 1 paulfons paulfons 4666 Sep 5 19:07 feff0002.dat You must be in this directory for feff to work (e.g. from the terminal). You might try this and see what happens. Otherwise, the error message for feff is correct -- there probably was no feff.inp in the directory you ran it from. I am still not clear on the cause though. Paul On Sep 9, 2006, at 11:37 PM, Stefano Ciurli wrote:
Hello Matt and Paul,
I verified the following:
1) here is the error message in the echo window
Preparing to run FEFF ... Performing autosave ... Saving feff.inp file Performing autosave ... done! Running feff (this could take a few minutes, please be patient) ... Uh oh! That Feff calculation did not run successfully.
2) when I run the command "feff6" from the terminal, I get the following message:
stefano% feff6 Feff 6L.02 Fatal Error: cannot open file "feff.inp" in module rdinp
I interpret this message with the conclusion that I can just type 'feff6' in the Artemis preferences, as the command is actually seen and of course it is missing the feff.inp file if I run the command from the terminal.
In the end, I have not been able to pinpoint the problem. Maybe a fault in the installer??? I am stuck.
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" _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Paul, no, there was no feff.inp file in the directory from which feff6 was invoked, but I ran the command just to see whether the program would start from any directory, so as to remove the doubt that the Artemis preferences (in which I use the default "feff6" to call the executable) would work correctly So, the reason why the program does not run correctly (see the uh oh message in the echo window) is not the settings of the Artemis preferences for feff6, and I still do not know what the reason might be. 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"
Hello Matt,
Did you try using /Applications/Ifeffit/bin/feff6 as the preferred feff executable in Artemis? That's what the error message was suggesting you try.
I did try, no success
Can you verify that you have /Applications/Ifeffit/bin/feff6?
verified, I do have it. In the meantime I made an interesting discovery that some of you will certainly be able to explain: If I launch Artemis using the double click on the application icon I DO get the error message and feff does not run, regardless of which application I choose for the graphics However: If I launch the program from the terminal window, I do not get the question on whether to choose Xwindow or Aquaterm, the default being apparently Xwindow PGPLOT, and everything runs smoothly. So, what is the origin of the error message that I get when I launch the program from the icon? 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"
The program icon for artemis and athena is a short applescript application (that in turn calls a unix script). The source code is in the Ifeffit/applescript folder (the top level artemis is a compiled applescript applescript). It goes like this: display dialog "Please pick an output device" buttons {"X11 graphics", "Aquaterm"} default button "X11 graphics" set mydevice to the button returned of the result if mydevice contains "Aquaterm" then do shell script "/Applications/Ifeffit/bin/runprog -q -m -x -a artemis" else do shell script "/Applications/Ifeffit/bin/runprog -q -x -a artemis" end if As you can see depending on the answer received the script / Applications/Ifeffit/bin/runprog is invoked (with different options). The shell script runprog is a bourne shell script (written by Matt and hacked by me). The -m option just sets the environment variable PGPLOT_DEV to the value /AQT before ifeffit is invoked. The option list is: -a) app=$2 ; shift ;; -x) $open_x ;; -q) show_out=0 ;; -d) show_dir=1 ;; -m) device='/AQT' ;; *) files="$files $1" ;; It should be possible to invoke artemis with an aquaterm graphics output by using the line "/Applications/Ifeffit/bin/runprog -q -m -x - a artemis" (without the quotes) in an X11 window. Does this command work? I should add that some of the linking is dynamic (at runtime) and by installing other dynamic libraries, it is conceivable that aquaterm could get confused (but of course, I should say that I have never seen this on my machines and I install a lot of stuff). Hope this helps, Paul On Sep 14, 2006, at 9:34 PM, Stefano Ciurli wrote:
Hello Matt,
Did you try using /Applications/Ifeffit/bin/feff6 as the preferred feff executable in Artemis? That's what the error message was suggesting you try.
I did try, no success
Can you verify that you have /Applications/Ifeffit/bin/feff6?
verified, I do have it.
In the meantime I made an interesting discovery that some of you will certainly be able to explain:
If I launch Artemis using the double click on the application icon I DO get the error message and feff does not run, regardless of which application I choose for the graphics
However:
If I launch the program from the terminal window, I do not get the question on whether to choose Xwindow or Aquaterm, the default being apparently Xwindow PGPLOT, and everything runs smoothly.
So, what is the origin of the error message that I get when I launch the program from the icon?
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" _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Paul,
The program icon for artemis and athena is a short applescript application (that in turn calls a unix script). The source code is in the Ifeffit/applescript folder (the top level artemis is a compiled applescript applescript). It goes like this:
display dialog "Please pick an output device" buttons {"X11 graphics", "Aquaterm"} default button "X11 graphics" set mydevice to the button returned of the result if mydevice contains "Aquaterm" then do shell script "/Applications/Ifeffit/bin/runprog -q -m -x -a artemis" else do shell script "/Applications/Ifeffit/bin/runprog -q -x -a artemis" end if
I checked. In my case the Artemis.scpt file looks like this (and indeed the strange symbols are present in all the scripts in the directory, so maybe it is OK): I am worried about the red symbols: is the file corrupted? And if so, why is it? I just installed the package I downloaded, nothing else.
As you can see depending on the answer received the script /Applications/Ifeffit/bin/runprog is invoked (with different options). The shell script runprog is a bourne shell script (written by Matt and hacked by me). The -m option just sets the environment variable PGPLOT_DEV to the value /AQT before ifeffit is invoked. The option list is:
-a) app=$2 ; shift ;; -x) $open_x ;; -q) show_out=0 ;; -d) show_dir=1 ;; -m) device='/AQT' ;; *) files="$files $1" ;;
It should be possible to invoke artemis with an aquaterm graphics output by using the line "/Applications/Ifeffit/bin/runprog -q -m -x -a artemis" (without the quotes) in an X11 window. Does this command work?
It does. And if I launch the program in this way, feff6 is invoked and runs without the error message, the same way as when I launch Artemis with the artemis command from the iTerm window, but differently from when I lauch the program double clicking the Artemis icon. Not that I am stuck at this poin (I can run my fits using artemis launched from the Xwindow) but I wonder whether this little bug can be sorted out. 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"
Probably nothing to worry about. I opened the file in an editor and copied it into the mail program to show you how the system worked. Paul On Sep 16, 2006, at 6:02 AM, Stefano Ciurli wrote:
Hi Paul,
The program icon for artemis and athena is a short applescript application (that in turn calls a unix script). The source code is in the Ifeffit/applescript folder (the top level artemis is a compiled applescript applescript). It goes like this:
display dialog "Please pick an output device" buttons {"X11 graphics", "Aquaterm"} default button "X11 graphics" set mydevice to the button returned of the result if mydevice contains "Aquaterm" then do shell script "/Applications/Ifeffit/bin/runprog -q -m - x -a artemis" else do shell script "/Applications/Ifeffit/bin/runprog -q -x - a artemis" end if
I checked. In my case the Artemis.scpt file looks like this (and indeed the strange symbols are present in all the scripts in the directory, so maybe it is OK): <P1CD30D32> I am worried about the red symbols: is the file corrupted? And if so, why is it? I just installed the package I downloaded, nothing else.
As you can see depending on the answer received the script / Applications/Ifeffit/bin/runprog is invoked (with different options). The shell script runprog is a bourne shell script (written by Matt and hacked by me). The -m option just sets the environment variable PGPLOT_DEV to the value /AQT before ifeffit is invoked. The option list is:
-a) app=$2 ; shift ;; -x) $open_x ;; -q) show_out=0 ;; -d) show_dir=1 ;; -m) device='/AQT' ;; *) files="$files $1" ;;
It should be possible to invoke artemis with an aquaterm graphics output by using the line "/Applications/Ifeffit/bin/runprog -q -m - x -a artemis" (without the quotes) in an X11 window. Does this command work?
It does. And if I launch the program in this way, feff6 is invoked and runs without the error message, the same way as when I launch Artemis with the artemis command from the iTerm window, but differently from when I lauch the program double clicking the Artemis icon.
Not that I am stuck at this poin (I can run my fits using artemis launched from the Xwindow) but I wonder whether this little bug can be sorted out. 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" <P1CD30D32> _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Ahh, I do recall one thing that had to do with permissions (I think). When I installed (via the installer) on another mac once, I got a error permission about the applescript not being able to write (to itself). As there was no obvious reason why it should do so and no harm in not letting it do so (the program worked fine except for the error message), I left it that way. I don't think this is related to the feff problem though. What did the error message say? Paul
Paul,
Ahh, I do recall one thing that had to do with permissions (I think). When I installed (via the installer) on another mac once, I got a error permission about the applescript not being able to write (to itself). As there was no obvious reason why it should do so and no harm in not letting it do so (the program worked fine except for the error message), I left it that way. I don't think this is related to the feff problem though. What did the error message say?
It is reported in my previous message. I do not see any message related to permissions. 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 Stefano (Bruce/Matt), Looking over your comments, I must admit I am a little confused as to what could be causing the problem. If you can invoke aquaterm complete with functioning graphics, the only difference that I can guess could exist is a difference in shell paths. The runprog program with its attendant shell variable changes seems to work fine. The AppleScript program is pretty minimalist, so the only viable explanation I can think of is somehow the shell environment getting corrupted. As the AppleScript that invokes artemis works fine here (and apparently elsewhere as well), a possible cause is the difference in startup initialization at the shell script level. Bruce, Matt, what do you think about this? If a shell is started by AppleScript, it would be a non-interactive shell, whereas if it is started manually via X11 and the default shell is bash, the startup initialization file ~/.bashrc would be read in. If it were invoked via the AppleScript program, it would not. Sounds like something is screwy with the PATH environment variable. Of course, this implies that it is something unique to Stefano's system and not general (never mind the fact that the user can switch shells -- I am using bash on one system and tcsh on another!). If a path was set incorrectly (e.g. affecting a perl library or otherwise), could this cause the symptoms that Stefano is seeing? I might add that I notice the default path for feff6 is "feff6" so this would seem to implicitly assume that feff6 is on the users path (and it obviously isn't in this case, although it is for me). One fix would be to hardwire all of the paths needed into the runprog shells script by appending to the PATH variable (e.g. the location of artemis is wired). Any suggestions? p.s. I noticed there is a dump paths option in the help menu (which is broken in that at least on my system apparently tries to dump to root and fails). I hacked the artemis.dump path to dump to /tmp/ artemis.dump and it worked, however, there is no information on the feff executable variable.
Hi Paul,
Looking over your comments, I must admit I am a little confused as to what could be causing the problem. If you can invoke aquaterm complete with functioning graphics, the only difference that I can guess could exist is a difference in shell paths. The runprog program with its attendant shell variable changes seems to work fine. The AppleScript program is pretty minimalist, so the only viable explanation I can think of is somehow the shell environment getting corrupted. As the AppleScript that invokes artemis works fine here (and apparently elsewhere as well), a possible cause is the difference in startup initialization at the shell script level.
if you need my .cshrc file, here it is below, maybe you can guess if something is wrong: bindkey -k up history-search-backward bindkey -k down history-search-forward if (! $?DISPLAY) then setenv DISPLAY :0.0 endif source ~/Library/Scripts/iterminal_custom.tcsh source /Applications/XtalView/XtalView.env source /sw/bin/init.csh setenv PATH `echo $PATH`:/Applications/Sparky.app/Contents/Resources/bin:/usr/local/sparky/bin:/usr/local:/usr/local/molscript:/usr/local/bin:/Applications/XtalView/bin/powermacDarwin:/Applications/vnmrj1.1d/bin:/Applications/cyana-2.1:/Applications/cara_1.2_osx:/Users/stefano/AutoAssign2.3.0:/Users/stefano/bin defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 no_quit_alert true setenv PGPLOT_DIR /etc setenv PGPLOT_DEV /AQT setenv SPARKYHOME /Users/stefano/Programs/Sparky setenv EDENHOME /usr/local/eden setenv ODAT /Users/stefano/Programs/o/data setenv MARSHOME /Applications/mars-1.1.3_OSX setenv CCPNMR_TOP_DIR /usr/local/ccpnmr setenv PYTHONPATH .:$CCPNMR_TOP_DIR/ccpnmr1.0/python setenv LD_LIBRARY_PATH /sw/lib:/sw/lib:/usr/X11R6/lib setenv LD_LIBRARY_PATH ${CCPNMR_TOP_DIR}/tcl8.3/lib:${CCPNMR_TOP_DIR}/tk8.3/lib setenv TCL_LIBRARY /sw/lib/tcl8.4 setenv TK_LIBRARY /sw/lib/tk8.4 alias runmars $MARSHOME/bin/runmars alias ono osx_ono alias cara /Applications/cara_1.5.2_osx if (-e /Applications/NMRPipe/com/nmrInit.mac.com) then source /Applications/NMRPipe/com/nmrInit.mac.com endif if (-e /Applications/NMRPipe/dynamo/com/dynInit.com) then source /Applications/NMRPipe/dynamo/com/dynInit.com endif # this line was added by Ifeffit Installation Script source /Applications/Ifeffit/bin/iff_init.csh ~
Bruce, Matt, what do you think about this? If a shell is started by AppleScript, it would be a non-interactive shell, whereas if it is started manually via X11 and the default shell is bash, the startup initialization file ~/.bashrc would be read in.
my default shell is tcsh
If it were invoked via the AppleScript program, it would not. Sounds like something is screwy with the PATH environment variable. Of course, this implies that it is something unique to Stefano's system and not general (never mind the fact that the user can switch shells -- I am using bash on one system and tcsh on another!).
let me know which configuration file I should look at
If a path was set incorrectly (e.g. affecting a perl library or otherwise), could this cause the symptoms that Stefano is seeing? I might add that I notice the default path for feff6 is "feff6" so this would seem to implicitly assume that feff6 is on the users path (and it obviously isn't in this case, although it is for me). One fix would be to hardwire all of the paths needed into the runprog shells script by appending to the PATH variable (e.g. the location of artemis is wired). Any suggestions?
will see what Matt and Bruce have to say 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 Stephano, I don't see the directory /Applications/Ifeffit/bin on your search path. It should be there. It is usually automatically included via a script installed by the Ifeffit installer, but it seems to be missing here (perhaps another installer deleted it by mistake). Add the following line to your .cshrc file in your home directory and see if it fixes things. Be careful to use a text editor that understands unix line endings (like the free editor smultron from http:// smultron.sourceforge.net). source /Applications/Ifeffit/bin/iff_init.csh Paul On Sep 19, 2006, at 6:00 PM, Stefano Ciurli wrote:
Hi Paul,
Looking over your comments, I must admit I am a little confused as to what could be causing the problem. If you can invoke aquaterm complete with functioning graphics, the only difference that I can guess could exist is a difference in shell paths. The runprog program with its attendant shell variable changes seems to work fine. The AppleScript program is pretty minimalist, so the only viable explanation I can think of is somehow the shell environment getting corrupted. As the AppleScript that invokes artemis works fine here (and apparently elsewhere as well), a possible cause is the difference in startup initialization at the shell script level.
if you need my .cshrc file, here it is below, maybe you can guess if something is wrong:
bindkey -k up history-search-backward bindkey -k down history-search-forward if (! $?DISPLAY) then setenv DISPLAY :0.0 endif source ~/Library/Scripts/iterminal_custom.tcsh source /Applications/XtalView/XtalView.env source /sw/bin/init.csh setenv PATH `echo $PATH`:/Applications/Sparky.app/Contents/ Resources/bin:/usr/local/sparky/bin:/usr/local:/usr/local/ molscript:/usr/local/bin:/Applications/XtalView/bin/powermacDarwin:/ Applications/vnmrj1.1d/bin:/Applications/cyana-2.1:/Applications/ cara_1.2_osx:/Users/stefano/AutoAssign2.3.0:/Users/stefano/bin defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 no_quit_alert true setenv PGPLOT_DIR /etc setenv PGPLOT_DEV /AQT setenv SPARKYHOME /Users/stefano/Programs/Sparky setenv EDENHOME /usr/local/eden setenv ODAT /Users/stefano/Programs/o/data setenv MARSHOME /Applications/mars-1.1.3_OSX setenv CCPNMR_TOP_DIR /usr/local/ccpnmr setenv PYTHONPATH .:$CCPNMR_TOP_DIR/ccpnmr1.0/python setenv LD_LIBRARY_PATH /sw/lib:/sw/lib:/usr/X11R6/lib setenv LD_LIBRARY_PATH ${CCPNMR_TOP_DIR}/tcl8.3/lib:$ {CCPNMR_TOP_DIR}/tk8.3/lib setenv TCL_LIBRARY /sw/lib/tcl8.4 setenv TK_LIBRARY /sw/lib/tk8.4 alias runmars $MARSHOME/bin/runmars alias ono osx_ono alias cara /Applications/cara_1.5.2_osx
if (-e /Applications/NMRPipe/com/nmrInit.mac.com) then source /Applications/NMRPipe/com/nmrInit.mac.com endif if (-e /Applications/NMRPipe/dynamo/com/dynInit.com) then source /Applications/NMRPipe/dynamo/com/dynInit.com endif # this line was added by Ifeffit Installation Script source /Applications/Ifeffit/bin/iff_init.csh ~
Bruce, Matt, what do you think about this? If a shell is started by AppleScript, it would be a non-interactive shell, whereas if it is started manually via X11 and the default shell is bash, the startup initialization file ~/.bashrc would be read in.
my default shell is tcsh
If it were invoked via the AppleScript program, it would not. Sounds like something is screwy with the PATH environment variable. Of course, this implies that it is something unique to Stefano's system and not general (never mind the fact that the user can switch shells -- I am using bash on one system and tcsh on another!).
let me know which configuration file I should look at
If a path was set incorrectly (e.g. affecting a perl library or otherwise), could this cause the symptoms that Stefano is seeing? I might add that I notice the default path for feff6 is "feff6" so this would seem to implicitly assume that feff6 is on the users path (and it obviously isn't in this case, although it is for me). One fix would be to hardwire all of the paths needed into the runprog shells script by appending to the PATH variable (e.g. the location of artemis is wired). Any suggestions?
will see what Matt and Bruce have to say 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" _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Paul,
I don't see the directory /Applications/Ifeffit/bin on your search path.
the line source /Applications/Ifeffit/bin/iff_init.csh is present at the end of my .cshrc In any case, thanks a lot for the Smultron editor. I am used to vi, but this is much easier :-) 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 Monday 18 September 2006 20:48, Paul Fons wrote:
p.s. I noticed there is a dump paths option in the help menu (which is broken in that at least on my system apparently tries to dump to root and fails). I hacked the artemis.dump path to dump to /tmp/ artemis.dump and it worked, however, there is no information on the feff executable variable.
The purpose of that is to provide a diagnostic (useful mostly to me) about the internal state of the data structures defined in Artemis. It wasn't intended to be especially relevant to the porblem that Stefano is having. 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/
Having now looked at your message, I must admit I am a little confused. If you allow me to paraphrase, I believe you say that if you run artemis from an X11 window using the command line, feff runs normally. On the other hand, if you run artemis using the double click application (the applet) to run artemis, feff doesn't work. This is very hard to understand as the only thing that is different (as you might have been able to see in my last post) is the environment variable, PGPLOT_DEV set in the runprog script is different (e.g. set to use aquaterm output). There is nothing that could ostensibly effect whether or not feff launches (it certainly doesn't use graphics). Paul On Sep 14, 2006, at 9:34 PM, Stefano Ciurli wrote:
Hello Matt,
Did you try using /Applications/Ifeffit/bin/feff6 as the preferred feff executable in Artemis? That's what the error message was suggesting you try.
I did try, no success
Can you verify that you have /Applications/Ifeffit/bin/feff6?
verified, I do have it.
In the meantime I made an interesting discovery that some of you will certainly be able to explain:
If I launch Artemis using the double click on the application icon I DO get the error message and feff does not run, regardless of which application I choose for the graphics
However:
If I launch the program from the terminal window, I do not get the question on whether to choose Xwindow or Aquaterm, the default being apparently Xwindow PGPLOT, and everything runs smoothly.
So, what is the origin of the error message that I get when I launch the program from the icon?
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" _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Paul,
Having now looked at your message, I must admit I am a little confused. If you allow me to paraphrase, I believe you say that if you run artemis from an X11 window using the command line, feff runs normally. On the other hand, if you run artemis using the double click application (the applet) to run artemis, feff doesn't work.
exactly. The error message I get when I run Artemis using the double click on the icon (and that I do NOT get if I run Artemis from the X11 (or iTerm) window is explained here again:
This is very hard to understand as the only thing that is different (as you might have been able to see in my last post) is the environment variable, PGPLOT_DEV set in the runprog script is different (e.g. set to use aquaterm output). There is nothing that could ostensibly effect whether or not feff launches (it certainly doesn't use graphics).
I get the error independently of the graphics window used (X11 or Aquaterm). I understand that it may be difficult to sort out the source of the error. However, I am reporting just the facts. 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 (4)
-
Bruce Ravel -
Matt Newville -
Paul Fons -
Stefano Ciurli