Re: [Wien] Xcrygen compilation
Well in the meanwhile I finished my compilation (the binaries may be a slightly more user and time-friendly route). My conclusions: It seems that Tcl/Tk 8.6 they removed the result method from 'Tcl_Interp' which gets accessed quite a lot and makes it fail. The readme says it supports tcl = 8.4 so practically this means you have to use 8.4 or 8.5 . Also, I think when our HPC team installed it they disabled Bwidget, I currently didn't and see that the text sometimes seems a bit (vertically) misaligned. Gavin Abo schreef op 17/07/2014 0:09: Correction: xcConfigure.sh should be in the scripts folder not the bin folder. On 7/16/2014 4:04 PM, Gavin Abo wrote: Can you tell us what kind of systems this happens on and what the errors are? The information might be helpful to others. I had xcrysden-1.5.53-linux_x86_64-semishared.tar.gz installed on a ubuntu 64 bit 14.04 LTS system. I just downloaded xcrysden-1.5.60-linux_x86_64-semishared.tar.gz from the xcrysden website, extracted it with tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz, removed the xcrysden block in .bashrc for 1.5.53, ran xcConfigure.sh in the bin folder of the xcrysden installation to create a new xcrysden block for 1.5.60 in .bashrc, reloaded the new .bashrc settings (by closing terminal and opening a new one), and finally I ran xcrysden. It opens fine without any errors, but maybe I have to do other things to encounter the problems that you refer to. Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrygen compilation
Actually, you can use Tcl/Tk 8.6, but have to include a CFLAG: -DUSE_INTERP_RESULT See this: http://www.democritos.it/pipermail/xcrysden/2013-November/001510.html Sincerely, Oliver Albertini On Thu, Jul 17, 2014 at 10:08 AM, Michael Sluydts michael.sluy...@ugent.be wrote: Well in the meanwhile I finished my compilation (the binaries may be a slightly more user and time-friendly route). My conclusions: It seems that Tcl/Tk 8.6 they removed the result method from 'Tcl_Interp' which gets accessed quite a lot and makes it fail. The readme says it supports tcl = 8.4 so practically this means you have to use 8.4 or 8.5 . Also, I think when our HPC team installed it they disabled Bwidget, I currently didn't and see that the text sometimes seems a bit (vertically) misaligned. Gavin Abo schreef op 17/07/2014 0:09: Correction: xcConfigure.sh should be in the scripts folder not the bin folder. On 7/16/2014 4:04 PM, Gavin Abo wrote: Can you tell us what kind of systems this happens on and what the errors are? The information might be helpful to others. I had xcrysden-1.5.53-linux_x86_64-semishared.tar.gz installed on a ubuntu 64 bit 14.04 LTS system. I just downloaded xcrysden-1.5.60-linux_x86_64-semishared.tar.gz from the xcrysden website, extracted it with tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz, removed the xcrysden block in .bashrc for 1.5.53, ran xcConfigure.sh in the bin folder of the xcrysden installation to create a new xcrysden block for 1.5.60 in .bashrc, reloaded the new .bashrc settings (by closing terminal and opening a new one), and finally I ran xcrysden. It opens fine without any errors, but maybe I have to do other things to encounter the problems that you refer to. Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Xcrygen compilation
Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrygen compilation
Our local HPC team has been developing a framework called easybuild to quickly recompile various software. They save the configuration in python files called easyblocks. There is one for xcrysden. I'm however not sure if there were any remaining issues (and testing it again/making a new compile has been on my to do list). The easyblock can be found here: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/x/xcrysden.py Laurence Marks schreef op 16/07/2014 19:41: Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrygen compilation
While I can probably fight my way around installing easyblocks, it would be useful for the general user if a bit more information was provided (by you or your local HPC team). For instance, I suspect it is something like: * Download the easyblocks module from http://hpcugent.github.com/easybuild (what else is needed ?) * cd to the directory (unzip ?) and do python setup.py install'' (is root access needed ?) * Download the script xcrysden (to xcrysden directory ?) * do python xcrysden.py N.B., I am probably missing some steps such as setting CC and other environmental variables.including destination. On Wed, Jul 16, 2014 at 12:48 PM, Michael Sluydts michael.sluy...@ugent.be wrote: Our local HPC team has been developing a framework called easybuild to quickly recompile various software. They save the configuration in python files called easyblocks. There is one for xcrysden. I'm however not sure if there were any remaining issues (and testing it again/making a new compile has been on my to do list). The easyblock can be found here: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/x/xcrysden.py Laurence Marks schreef op 16/07/2014 19:41: Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing listw...@zeus.theochem.tuwien.ac.athttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrygen compilation
Yeah, it takes some getting used to (and may take too much time if only used for xcrysden). I've only used it a few times myself, it does work nicely for wien2k (with some tweaks of the public easyblock for 13). Practically you first need to install easybuild itself, which has an eb command that builds the software into a specific path (and organizes it by software, version, toolchain). It takes an 'easyconfig' file as input which contains more info on toolchains and patches used for the compilation, while the easyblock defines the more detailed instructions (like input for siteconfig for wien). It then builds the software (and makes a module file i think). The source it finds in some standard directory but there are command-line options to change all the source and destination folders etc. They have a reference site here: http://hpcugent.github.io/easybuild/, the slides there link to other pages in their wiki. Like I said this may be time-inefficient though and I'm not sure if the xcrysden install worked fully. The version they tried it on was 1.5.53, I myself always continued to used an old version in my account (1.5.21) (for which I don't think I did anything special). The combination of easyblock/easyconfig and the patch in the easyconfig folder may give some hints about what exactly they did. Since I need to build it again myself, maybe I'll give it a try tomorrow. The easyconfig and patch are here: https://github.com/hpcugent/easybuild-easyconfigs/tree/master/easybuild/easyconfigs/x/XCrySDen example for wien2k 12.1 install easyblock: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/w/wien2k.py easyconfig: https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-ictce-4.0.6.eb (when using easybuild itself these things get downloaded with it) Laurence Marks schreef op 16/07/2014 20:34: While I can probably fight my way around installing easyblocks, it would be useful for the general user if a bit more information was provided (by you or your local HPC team). For instance, I suspect it is something like: * Download the easyblocks module from http://hpcugent.github.com/easybuild (what else is needed ?) * cd to the directory (unzip ?) and do python setup.py install'' (is root access needed ?) * Download the script xcrysden (to xcrysden directory ?) * do python xcrysden.py N.B., I am probably missing some steps such as setting CC and other environmental variables.including destination. On Wed, Jul 16, 2014 at 12:48 PM, Michael Sluydts michael.sluy...@ugent.be mailto:michael.sluy...@ugent.be wrote: Our local HPC team has been developing a framework called easybuild to quickly recompile various software. They save the configuration in python files called easyblocks. There is one for xcrysden. I'm however not sure if there were any remaining issues (and testing it again/making a new compile has been on my to do list). The easyblock can be found here: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/x/xcrysden.py Laurence Marks schreef op 16/07/2014 19:41: Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at:http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrygen compilation
Can you tell us what kind of systems this happens on and what the errors are? The information might be helpful to others. I had xcrysden-1.5.53-linux_x86_64-semishared.tar.gz installed on a ubuntu 64 bit 14.04 LTS system. I just downloaded xcrysden-1.5.60-linux_x86_64-semishared.tar.gz from the xcrysden website, extracted it with tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz, removed the xcrysden block in .bashrc for 1.5.53, ran xcConfigure.sh in the bin folder of the xcrysden installation to create a new xcrysden block for 1.5.60 in .bashrc, reloaded the new .bashrc settings (by closing terminal and opening a new one), and finally I ran xcrysden. It opens fine without any errors, but maybe I have to do other things to encounter the problems that you refer to. Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrygen compilation
Correction: xcConfigure.sh should be in the scripts folder not the bin folder. On 7/16/2014 4:04 PM, Gavin Abo wrote: Can you tell us what kind of systems this happens on and what the errors are? The information might be helpful to others. I had xcrysden-1.5.53-linux_x86_64-semishared.tar.gz installed on a ubuntu 64 bit 14.04 LTS system. I just downloaded xcrysden-1.5.60-linux_x86_64-semishared.tar.gz from the xcrysden website, extracted it with tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz, removed the xcrysden block in .bashrc for 1.5.53, ran xcConfigure.sh in the bin folder of the xcrysden installation to create a new xcrysden block for 1.5.60 in .bashrc, reloaded the new .bashrc settings (by closing terminal and opening a new one), and finally I ran xcrysden. It opens fine without any errors, but maybe I have to do other things to encounter the problems that you refer to. Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
