struggling to install demeter under ubuntu 16.04
Hi im trying to install demeter under ubuntu 16.04 following the protocol given by david hughes https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.ht... I have followed through all steps but I encountered a few errors when doing the /Build install and when i want to run the application by "dathena" i get the following: marquinhos@marquinhos-Lapi:~/demeter$ dathena No command 'dathena' found, did you mean: Command 'athena' from package 'horae' (multiverse) dathena: command not found I have attached the error file to this mail produced via "./Build test | tee ~/test_errors.txt" thanks in advance marcus
On 11/30/2016 08:53 AM, mfehse wrote:
I have followed through all steps but I encountered a few errors when doing the /Build install and when i want to run the application by "dathena" i get the following:
marquinhos@marquinhos-Lapi:~/demeter$ dathena No command 'dathena' found, did you mean: Command 'athena' from package 'horae' (multiverse) dathena: command not found
Hi Marcus, My best guess here is that you need to reset the shell to recognize the new executables in the PATH. Doing "hash -r", as explained here, should help: http://superuser.com/questions/490983/how-to-rehash-executables-in-path-with... Another possibility is that the place that "./Build install" is installing to is not in the path. You can check the path by doing "echo $PATH". "./Build install" should tell you where it is installing to. Do let me know if either of those is the issue. If so, I will add a note to the installation instructions about it.
I have attached the error file to this mail produced via "./Build test | tee ~/test_errors.txt"
Good job on the attachment. Thanks! I suspect this problem will be resolved when the first problem is resolved. If not, let me know. In that case, please do: ./Build test verbose=1 --test_files t/001_base.t | tee ~/test_errors.txt That will give the verbose output, but only run the first failing test. That will help me (I hope!) further track down the problem. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Hi In my struggle to install demeter under ubuntu 16.04 I'm slowly advancing. I think some of the packages that were supposed to be installed following the first line of the protocol were incomplete. I have redone this and have now managed to build the dathena and other files, but when I want to start it I get the following error message: "marquinhos@marquinhos-Lapi:~/demeter$ bin/dathena Could not find Larch Server -- falling back to Ifeffit Can't locate object method "new" via package "Graphics::GnuplotIF" at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter.pm line 239. Compilation failed in require at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm line 24. Compilation failed in require at bin/dathena line 27. BEGIN failed--compilation aborted at bin/dathena line 27. Can't exec "-p": No such file or directory at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Larch.pm line 270. " any ideas what might be the problem? many thanks On 30/11/2016 14:53, mfehse wrote:
Hi im trying to install demeter under ubuntu 16.04 following the protocol given by david hughes https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.ht...
I have followed through all steps but I encountered a few errors when doing the /Build install and when i want to run the application by "dathena" i get the following:
marquinhos@marquinhos-Lapi:~/demeter$ dathena No command 'dathena' found, did you mean: Command 'athena' from package 'horae' (multiverse) dathena: command not found
I have attached the error file to this mail produced via "./Build test | tee ~/test_errors.txt"
thanks in advance
marcus
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
On 12/01/2016 09:12 AM, mfehse wrote:
In my struggle to install demeter under ubuntu 16.04 I'm slowly advancing. I think some of the packages that were supposed to be installed following the first line of the protocol were incomplete. I have redone this and have now managed to build the dathena and other files, but when I want to start it I get the following error message:
"marquinhos@marquinhos-Lapi:~/demeter$ bin/dathena
Could not find Larch Server -- falling back to Ifeffit Can't locate object method "new" via package "Graphics::GnuplotIF" at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter.pm line 239. Compilation failed in require at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm line 24. Compilation failed in require at bin/dathena line 27. BEGIN failed--compilation aborted at bin/dathena line 27. Can't exec "-p": No such file or directory at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Larch.pm line 270. "
any ideas what might be the problem?
That seems to be saying that Graphics::GnuplotIF is not installed. It should have been installed when you did the "./Build installdeps" step. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Hi, I installed demeter recently under 16.04 lts. In response to Juan's issues, I described what I did here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-November/008888.html One additional deviation was that I had already installed gfortran and gunplot (sudo apt install) beforehand. Matt noted in the next message that a larch issue needs addressing when importing files http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-November/008889.html but the ifeffit backend works. I haven't tried everything, but reading and processing a file in Athena works fine. -R. On 12/1/2016 6:21 AM, Bruce Ravel wrote:
On 12/01/2016 09:12 AM, mfehse wrote:
In my struggle to install demeter under ubuntu 16.04 I'm slowly advancing. I think some of the packages that were supposed to be installed following the first line of the protocol were incomplete. I have redone this and have now managed to build the dathena and other files, but when I want to start it I get the following error message:
"marquinhos@marquinhos-Lapi:~/demeter$ bin/dathena
Could not find Larch Server -- falling back to Ifeffit Can't locate object method "new" via package "Graphics::GnuplotIF" at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter.pm
line 239. Compilation failed in require at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm
line 24. BEGIN failed--compilation aborted at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm
line 24. Compilation failed in require at bin/dathena line 27. BEGIN failed--compilation aborted at bin/dathena line 27. Can't exec "-p": No such file or directory at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Larch.pm
line 270. "
any ideas what might be the problem?
That seems to be saying that Graphics::GnuplotIF is not installed.
It should have been installed when you did the "./Build installdeps" step.
B
Hi to all,
Is there a switch in demeter to select the backend? Or in other words, to
go back to ifeffit, should I delete the larch binaries?
Juan
----------------------------------------------------------------------------
Juan de la Figuera
Instituto de Quimica-Fisica Rocasolano
c/ serrano, 119
Madrid, Spain 28006
Phone: +34 91 745 9517
http://surfmoss.iqfr.csic.es/juandelafiguera
http://surfmoss.iqfr.csic.es/surflab/people/juan-de-la-figuera
http://scholar.google.com/citations?user=GOiP624AAAAJ
-----------------------------------------------------------------------------
On Thu, Dec 1, 2016 at 5:52 PM, Robert Gordon
Hi,
I installed demeter recently under 16.04 lts. In response to Juan's issues, I described what I did here:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-Nove mber/008888.html
One additional deviation was that I had already installed gfortran and gunplot (sudo apt install) beforehand.
Matt noted in the next message that a larch issue needs addressing when importing files
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-Nove mber/008889.html
but the ifeffit backend works.
I haven't tried everything, but reading and processing a file in Athena works fine.
-R.
On 12/1/2016 6:21 AM, Bruce Ravel wrote:
On 12/01/2016 09:12 AM, mfehse wrote:
In my struggle to install demeter under ubuntu 16.04 I'm slowly advancing. I think some of the packages that were supposed to be installed following the first line of the protocol were incomplete. I have redone this and have now managed to build the dathena and other files, but when I want to start it I get the following error message:
"marquinhos@marquinhos-Lapi:~/demeter$ bin/dathena
Could not find Larch Server -- falling back to Ifeffit Can't locate object method "new" via package "Graphics::GnuplotIF" at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter.pm
line 239. Compilation failed in require at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm
line 24. BEGIN failed--compilation aborted at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm
line 24. Compilation failed in require at bin/dathena line 27. BEGIN failed--compilation aborted at bin/dathena line 27. Can't exec "-p": No such file or directory at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Larch.pm
line 270. "
any ideas what might be the problem?
That seems to be saying that Graphics::GnuplotIF is not installed.
It should have been installed when you did the "./Build installdeps" step.
B
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
On 12/01/2016 12:57 PM, Juan de la figuera wrote:
Is there a switch in demeter to select the backend? Or in other words, to go back to ifeffit, should I delete the larch binaries?
At the command line: export DEMETER_FORCE_IFEFFIT=1 dathena or put export DEMETER_FORCE_IFEFFIT=1 in your ~/.bashrc file B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Sorry. That wasn't quite right. At the command line: DEMETER_FORCE_IFEFFIT=1 dathena to force the use of Ifeffit in that instance of Athena. Or, export DEMETER_FORCE_IFEFFIT=1 later, dathena That forces the use of Ifeffit in that instance of the shell so that, later, when you fire up Athena, it uses Ifeffit. Or put the "export" line in your .bashrc to make it persist the next time you log in. B On 12/01/2016 01:18 PM, Bruce Ravel wrote:
On 12/01/2016 12:57 PM, Juan de la figuera wrote:
Is there a switch in demeter to select the backend? Or in other words, to go back to ifeffit, should I delete the larch binaries?
At the command line:
export DEMETER_FORCE_IFEFFIT=1 dathena
or put
export DEMETER_FORCE_IFEFFIT=1
in your ~/.bashrc file
B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
hi thanks for the hint, I installed the following gnuplot packages libgnuplot-iostream-dev libalien-gnuplot-perl libchart-gnuplot-perl libgraph-writer-dsm-perl libgraphics-gnuplotif-perl libpdl-graphics-gnuplot-perl and am now able to launch the athena and it seems to work, however i still get the error message: "Could not find Larch Server -- falling back to Ifeffit" is this something i should care about? many thanks On 01/12/2016 15:21, Bruce Ravel wrote:
On 12/01/2016 09:12 AM, mfehse wrote:
In my struggle to install demeter under ubuntu 16.04 I'm slowly advancing. I think some of the packages that were supposed to be installed following the first line of the protocol were incomplete. I have redone this and have now managed to build the dathena and other files, but when I want to start it I get the following error message:
"marquinhos@marquinhos-Lapi:~/demeter$ bin/dathena
Could not find Larch Server -- falling back to Ifeffit Can't locate object method "new" via package "Graphics::GnuplotIF" at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter.pm line 239. Compilation failed in require at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm line 24. Compilation failed in require at bin/dathena line 27. BEGIN failed--compilation aborted at bin/dathena line 27. Can't exec "-p": No such file or directory at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Larch.pm line 270. "
any ideas what might be the problem?
That seems to be saying that Graphics::GnuplotIF is not installed.
It should have been installed when you did the "./Build installdeps" step.
B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973
Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
On 12/01/2016 01:20 PM, mfehse wrote:
and am now able to launch the athena and it seems to work, however i still get the error message: "Could not find Larch Server -- falling back to Ifeffit" is this something i should care about?
Nope. It's a message that will eventually go away. Right now, Matt and I are working on migrating to Larch. This week we have been figuring out how to make Athena's interaction with Larch work reliably. That message is there so that I know what is going on while I am working on the code. In this case, it is Demeter telling you that it is gracefully recognizing that you do not have Larch installed. If you don't want to be looking at the head of the main branch, then you could download the zip file for the most recently tagged release: https://github.com/bruceravel/demeter/tree/0.9.25 B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Hi so i have created a little Artemis project to practice. Its tio2 data file with anatase cif file, i just included teh first path but havent done any fitting yet. When i close artemis and want to reopen it I get the following error: "You must define a method name at /usr/lib/i386-linux-gnu/perl5/5.22/Class/MOP/Mixin/HasMethods.pm line 96 Class::MOP::Mixin::HasMethods::has_method('Class::MOP::Class::Immutable::Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0xe06c454)', '') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 442 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', ' :') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 465 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', 'space = I 41/a m d :1') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 390 Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x106b5394)') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 200 Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x106b5394)', '/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp', '') called at accessor Demeter::Atoms::file (defined at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 204) line 10 Demeter::Atoms::file('Demeter::Atoms=HASH(0x106b5394)', '/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Atoms/Xtal.pm line 667 Demeter::UI::Atoms::Xtal::open_file('Demeter::UI::Atoms::Xtal=HASH(0x1312b8e0)', '/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm line 1388 Demeter::UI::Artemis::make_feff_frame('Wx::Frame=HASH(0x127f5b3c)', '/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp', 1010942) called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis/Project.pm line 351 Demeter::UI::Artemis::Project::read_project('HASH(0x102e8084)', '/home/marquinhos/Desktop/TIO2_tryout.fpj') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm line 1026 Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x127f5b3c)', 'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm line 440 Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x127f5b3c)', 'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at demeter/bin/dartemis line 31 eval {...} at demeter/bin/dartemis line 31 " i have attached the project so you can try if you can open it on your artemis many thanks marcus On 01/12/2016 19:26, Bruce Ravel wrote:
On 12/01/2016 01:20 PM, mfehse wrote:
and am now able to launch the athena and it seems to work, however i still get the error message: "Could not find Larch Server -- falling back to Ifeffit" is this something i should care about?
Nope.
It's a message that will eventually go away. Right now, Matt and I are working on migrating to Larch. This week we have been figuring out how to make Athena's interaction with Larch work reliably. That message is there so that I know what is going on while I am working on the code. In this case, it is Demeter telling you that it is gracefully recognizing that you do not have Larch installed.
If you don't want to be looking at the head of the main branch, then you could download the zip file for the most recently tagged release: https://github.com/bruceravel/demeter/tree/0.9.25
B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973
Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Marcus, Your cif file triggered a very specific bug in my software that has nothing to do with your recent difficulties. Had you picked almost any other cif file for any other material, you would have been fine. I am guessing you chose this one: http://www.crystallography.net/cod/cod/cif/7/20/60/7206075.cif or something very similar. Demeter makes a mistake parsing the space group symbol in that file. Try this: http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp It seems to work correctly without triggering the specific problem that the cif file triggers which, again, has to do with the specific symbol used and how Demeter parses it. Thanks for reporting this. I'll work on it. B On 12/02/2016 06:07 AM, mfehse wrote:
Hi
so i have created a little Artemis project to practice. Its tio2 data file with anatase cif file, i just included teh first path but havent done any fitting yet. When i close artemis and want to reopen it I get the following error:
"You must define a method name at /usr/lib/i386-linux-gnu/perl5/5.22/Class/MOP/Mixin/HasMethods.pm line 96 Class::MOP::Mixin::HasMethods::has_method('Class::MOP::Class::Immutable::Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0xe06c454)', '') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 442 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', ' :') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 465 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', 'space = I 41/a m d :1') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 390 Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x106b5394)') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 200 Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x106b5394)', '/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp', '') called at accessor Demeter::Atoms::file (defined at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm line 204) line 10 Demeter::Atoms::file('Demeter::Atoms=HASH(0x106b5394)', '/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Atoms/Xtal.pm line 667 Demeter::UI::Atoms::Xtal::open_file('Demeter::UI::Atoms::Xtal=HASH(0x1312b8e0)', '/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm line 1388 Demeter::UI::Artemis::make_feff_frame('Wx::Frame=HASH(0x127f5b3c)', '/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp', 1010942) called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis/Project.pm line 351 Demeter::UI::Artemis::Project::read_project('HASH(0x102e8084)', '/home/marquinhos/Desktop/TIO2_tryout.fpj') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm line 1026 Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x127f5b3c)', 'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm line 440 Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x127f5b3c)', 'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at demeter/bin/dartemis line 31 eval {...} at demeter/bin/dartemis line 31 "
i have attached the project so you can try if you can open it on your artemis
many thanks
marcus
On 01/12/2016 19:26, Bruce Ravel wrote:
On 12/01/2016 01:20 PM, mfehse wrote:
and am now able to launch the athena and it seems to work, however i still get the error message: "Could not find Larch Server -- falling back to Ifeffit" is this something i should care about?
Nope.
It's a message that will eventually go away. Right now, Matt and I are working on migrating to Larch. This week we have been figuring out how to make Athena's interaction with Larch work reliably. That message is there so that I know what is going on while I am working on the code. In this case, it is Demeter telling you that it is gracefully recognizing that you do not have Larch installed.
If you don't want to be looking at the head of the main branch, then you could download the zip file for the most recently tagged release: https://github.com/bruceravel/demeter/tree/0.9.25
B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973
Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
On 12/02/2016 09:01 AM, Bruce Ravel wrote:
Your cif file triggered a very specific bug in my software that has nothing to do with your recent difficulties.
Had you picked almost any other cif file for any other material, you would have been fine.
I am guessing you chose this one:
http://www.crystallography.net/cod/cod/cif/7/20/60/7206075.cif
or something very similar. Demeter makes a mistake parsing the space group symbol in that file.
Try this:
http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp
It seems to work correctly without triggering the specific problem that the cif file triggers which, again, has to do with the specific symbol used and how Demeter parses it.
Thanks for reporting this. I'll work on it.
I just pushed a fix for this to github. The project file you sent me is not fixable (well ... not easily). The best thing to do is to discard it and start again. Thanks again for uncovering a fairly obscure bug! B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
participants (4)
-
Bruce Ravel -
Juan de la figuera -
mfehse -
Robert Gordon