(D)Artemis and (D)Athena crash - perl not responding
Dear all, Several days ago, I was using (D)Artemis of the Demeter with Strawberry Perl package version 0.9.13.1 on a Windows 7 64-bit Operating System. Suddenly, the software crashed when opening (D)Artemis. Ever since, (D)Artemis and (D)Athena do not respond anymore when I open them. The windows pop up, but the buttons inside the window do not appear anymore and the software gets stuck. When trying to check for a solution, "perl.exe does not respond" is given as a comment. (D)Hephaestos works fine. (D)Atoms functions until I load an .inp file, then it gets stuck too. I already tried to reinstall and to update to the newest version (9.14), but nothing helps. I tried to install Strawberry Perl's newest version, but since the necessary modules are included in the Demeter software this is probably useless. Does someone know what to do? Thanks a lot, Matthias Filez _____________________ Ir. Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: http://helpdesk.ugent.be/e-maildisclaimer.php http://helpdesk.UGent.be/e-maildisclaimer.php
As I have said many, many times before, there's not much I can do without a proper bug report. http://bruceravel.github.com/demeter/pods/bugs.pod.html#Capturing_error_mess... B ________________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Matthias Filez [Matthias.Filez@ugent.be] Sent: Tuesday, January 15, 2013 11:52 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding Dear all, Several days ago, I was using (D)Artemis of the Demeter with Strawberry Perl package version 0.9.13.1 on a Windows 7 64-bit Operating System. Suddenly, the software crashed when opening (D)Artemis. Ever since, (D)Artemis and (D)Athena do not respond anymore when I open them. The windows pop up, but the buttons inside the window do not appear anymore and the software gets stuck. When trying to check for a solution, "perl.exe does not respond" is given as a comment. (D)Hephaestos works fine. (D)Atoms functions until I load an .inp file, then it gets stuck too. I already tried to reinstall and to update to the newest version (9.14), but nothing helps. I tried to install Strawberry Perl’s newest version, but since the necessary modules are included in the Demeter software this is probably useless. Does someone know what to do? Thanks a lot, Matthias Filez _____________________ Ir. Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.phphttp://helpdesk.ugent.be/e-maildisclaimer.php
Hello, I looked inside the dartemis.log file before, but nothing was inside. Sorry for not mentioning that! Now, I waited for 20 minutes during the startup of (D)Artemis and the software seemed to work. I opened a project file (see attachment), but then Artemis gets stuck again. This time, a bug report could be obtained (see attachment). Matthias _____________________ Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Ravel, Bruce Sent: dinsdag 15 januari 2013 18:03 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding As I have said many, many times before, there's not much I can do without a proper bug report. http://bruceravel.github.com/demeter/pods/bugs.pod.html#Capturing_error_mess ages_from_Demete B ________________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Matthias Filez [Matthias.Filez@ugent.be] Sent: Tuesday, January 15, 2013 11:52 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding Dear all, Several days ago, I was using (D)Artemis of the Demeter with Strawberry Perl package version 0.9.13.1 on a Windows 7 64-bit Operating System. Suddenly, the software crashed when opening (D)Artemis. Ever since, (D)Artemis and (D)Athena do not respond anymore when I open them. The windows pop up, but the buttons inside the window do not appear anymore and the software gets stuck. When trying to check for a solution, "perl.exe does not respond" is given as a comment. (D)Hephaestos works fine. (D)Atoms functions until I load an .inp file, then it gets stuck too. I already tried to reinstall and to update to the newest version (9.14), but nothing helps. I tried to install Strawberry Perl's newest version, but since the necessary modules are included in the Demeter software this is probably useless. Does someone know what to do? Thanks a lot, Matthias Filez _____________________ Ir. Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php<http://helpdesk.ugent.be/e-mai ldisclaimer.php> _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Matthias, The Artemis log file that you sent opens and runs its fit to completion in a reasonable way on the Windows 7 machine here at my beamline. As you no doubt saw, the message in the log fle is "Out of memory". I suspect that this gives a hint about the problem. One of the shortcomings of the current software is that it is based on Ifeffit, a library of exafs-related routines which is written in Fortran and which is related to code that Matt wrote way back (in some previous century) when he and I were in grad school. One of the problems with the dialect of Fortran that Ifeffit is written in is that it does not have dynamic memory allocation. This means that Ifeffit is not able to request memory from the operating system as needed. Instead, it requests a rather large block of memory at start-up and holds it in reserve in case it is needed. Eventually, it will run out of memory. If you search the mailing list, you will find many example of problems related to people attempting to load many dozens of data sets into Athena and eventually exhausting Ifeffit's memory store. If your computer has rather little on-board memory, or if you are running lots of other memory-intensive program, or if you are running several instances of Ifeffit, you may exhaust your computer's capacity. Because of the "out of memory" message in the log file, I suspect that is what is happening to you. The very long time that it took Artemis to give up the ghost and die, suggests that large amounts of memory were being swapped to disk as Ifeffit was trying to start and then trying to fail because memory had been exhausted. Do you think you are in one of those situations? Do you observe this behavior on another computer? (I suspect not, because your project file runs just fine on my computer here at my beamline.) Do you observe this behavior if you manually halt all the other things running on your computer? Or right after rebooting (when, presumably, lots of other stuff isn't running)? B PS: Among the many advantages to Matt's Larch project, which will eventually replace Ifeffit in my software and elsewhere, is that it is written in a way that does dynamic memory allocation. ________________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Matthias Filez [Matthias.Filez@ugent.be] Sent: Wednesday, January 16, 2013 5:32 AM To: 'XAFS Analysis using Ifeffit' Subject: Re: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding Hello, I looked inside the dartemis.log file before, but nothing was inside. Sorry for not mentioning that! Now, I waited for 20 minutes during the startup of (D)Artemis and the software seemed to work. I opened a project file (see attachment), but then Artemis gets stuck again. This time, a bug report could be obtained (see attachment). Matthias _____________________ Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Ravel, Bruce Sent: dinsdag 15 januari 2013 18:03 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding As I have said many, many times before, there's not much I can do without a proper bug report. http://bruceravel.github.com/demeter/pods/bugs.pod.html#Capturing_error_mess ages_from_Demete B ________________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Matthias Filez [Matthias.Filez@ugent.be] Sent: Tuesday, January 15, 2013 11:52 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding Dear all, Several days ago, I was using (D)Artemis of the Demeter with Strawberry Perl package version 0.9.13.1 on a Windows 7 64-bit Operating System. Suddenly, the software crashed when opening (D)Artemis. Ever since, (D)Artemis and (D)Athena do not respond anymore when I open them. The windows pop up, but the buttons inside the window do not appear anymore and the software gets stuck. When trying to check for a solution, "perl.exe does not respond" is given as a comment. (D)Hephaestos works fine. (D)Atoms functions until I load an .inp file, then it gets stuck too. I already tried to reinstall and to update to the newest version (9.14), but nothing helps. I tried to install Strawberry Perl's newest version, but since the necessary modules are included in the Demeter software this is probably useless. Does someone know what to do? Thanks a lot, Matthias Filez _____________________ Ir. Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php<http://helpdesk.ugent.be/e-mai ldisclaimer.php> _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hello, First of all, thanks al lot for your reply. Our in-laboratory technician looked at the 'Out of memory' issue and detected apparently a conflict in perl versions installed on my computer which may induce this 'Out of Memory' message. I uninstalled the appropriate version and now it works again (so no automatic crashes anymore at the start up). I have 4 GB of RAM space on my computer so it seemed surprising to me, being a layman in computer science, that all of the initially estimated free space would be consumed. However, I encounter another crash of the software when I load an artemis project file (1 specific, other projects function perfectly). The log file is included in attachment. Could someone please have a look and give any suggestion about what goes wrong and what can be done to resolve this problem? Thanks in advance! Matthias _____________________ Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Ravel, Bruce Sent: woensdag 16 januari 2013 23:26 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding Matthias, The Artemis log file that you sent opens and runs its fit to completion in a reasonable way on the Windows 7 machine here at my beamline. As you no doubt saw, the message in the log fle is "Out of memory". I suspect that this gives a hint about the problem. One of the shortcomings of the current software is that it is based on Ifeffit, a library of exafs-related routines which is written in Fortran and which is related to code that Matt wrote way back (in some previous century) when he and I were in grad school. One of the problems with the dialect of Fortran that Ifeffit is written in is that it does not have dynamic memory allocation. This means that Ifeffit is not able to request memory from the operating system as needed. Instead, it requests a rather large block of memory at start-up and holds it in reserve in case it is needed. Eventually, it will run out of memory. If you search the mailing list, you will find many example of problems related to people attempting to load many dozens of data sets into Athena and eventually exhausting Ifeffit's memory store. If your computer has rather little on-board memory, or if you are running lots of other memory-intensive program, or if you are running several instances of Ifeffit, you may exhaust your computer's capacity. Because of the "out of memory" message in the log file, I suspect that is what is happening to you. The very long time that it took Artemis to give up the ghost and die, suggests that large amounts of memory were being swapped to disk as Ifeffit was trying to start and then trying to fail because memory had been exhausted. Do you think you are in one of those situations? Do you observe this behavior on another computer? (I suspect not, because your project file runs just fine on my computer here at my beamline.) Do you observe this behavior if you manually halt all the other things running on your computer? Or right after rebooting (when, presumably, lots of other stuff isn't running)? B PS: Among the many advantages to Matt's Larch project, which will eventually replace Ifeffit in my software and elsewhere, is that it is written in a way that does dynamic memory allocation. ________________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Matthias Filez [Matthias.Filez@ugent.be] Sent: Wednesday, January 16, 2013 5:32 AM To: 'XAFS Analysis using Ifeffit' Subject: Re: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding Hello, I looked inside the dartemis.log file before, but nothing was inside. Sorry for not mentioning that! Now, I waited for 20 minutes during the startup of (D)Artemis and the software seemed to work. I opened a project file (see attachment), but then Artemis gets stuck again. This time, a bug report could be obtained (see attachment). Matthias _____________________ Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Ravel, Bruce Sent: dinsdag 15 januari 2013 18:03 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding As I have said many, many times before, there's not much I can do without a proper bug report. http://bruceravel.github.com/demeter/pods/bugs.pod.html#Capturing_error_mess ages_from_Demete B ________________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Matthias Filez [Matthias.Filez@ugent.be] Sent: Tuesday, January 15, 2013 11:52 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] (D)Artemis and (D)Athena crash - perl not responding Dear all, Several days ago, I was using (D)Artemis of the Demeter with Strawberry Perl package version 0.9.13.1 on a Windows 7 64-bit Operating System. Suddenly, the software crashed when opening (D)Artemis. Ever since, (D)Artemis and (D)Athena do not respond anymore when I open them. The windows pop up, but the buttons inside the window do not appear anymore and the software gets stuck. When trying to check for a solution, "perl.exe does not respond" is given as a comment. (D)Hephaestos works fine. (D)Atoms functions until I load an .inp file, then it gets stuck too. I already tried to reinstall and to update to the newest version (9.14), but nothing helps. I tried to install Strawberry Perl's newest version, but since the necessary modules are included in the Demeter software this is probably useless. Does someone know what to do? Thanks a lot, Matthias Filez _____________________ Ir. Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering, Ghent University Krijgslaan 281 S5, B-9000 Ghent, Belgium Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php<http://helpdesk.ugent.be/e-mai ldisclaimer.php> _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
On Thursday, January 24, 2013 09:58:49 AM Matthias Filez wrote:
However, I encounter another crash of the software when I load an artemis project file (1 specific, other projects function perfectly). The log file is included in attachment. Could someone please have a look and give any suggestion about what goes wrong and what can be done to resolve this problem?
Feff failed to run correctly. Could you send me the atoms.inp, CIF file, or feff.inp file that you started with? B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
participants (3)
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Bruce Ravel -
Matthias Filez -
Ravel, Bruce