So apart from KMC tutorials the rest should work in master now. Sorry for the errors.
Cheers Jens Jens Wehner schrieb am Dienstag, 27. April 2021 um 13:53:15 UTC+2: > Hi Thibaut, > > you were right, there were several bugs in there. I made some PRs to fix > these. > > https://github.com/votca/xtp-tutorials/pull/73 > > If you want to test already checkout the tutorial_fix branch in xtp and > xtp-tutorials. > > So far I have only fixed the GROMACS tutorial, I have not checked LAMMPS, > will do that tomorrow. > > Jens Wehner schrieb am Montag, 26. April 2021 um 14:27:48 UTC+2: > >> Hi Thibaut, >> >> I will dig into it today. I am currently working on making all the >> options nice and workable, because we had some trouble in the past. >> >> Cheers Jens >> >> Thibaut Wohrer schrieb am Montag, 26. April 2021 um 08:51:11 UTC+2: >> >>> Hello and apologies for digging up this thread, >>> >>> I have upgraded Votca to the newest version and have attempted to run >>> the complete tutorial. After updating the Optionfiles I have once again >>> encountered an issue during the last section with this time an error >>> occurring at the line >>> xtp_parallel -e qmmm -o OPTIONFILES/qmmm.xml -f state.hdf5 -j "write" >>> producing >>> >>> property not found: .regions >>> This was done using the default qmmm.xml file provided and the manual >>> does not state any .regions options. >>> In addition to this I have noticed that several examples in the tutorial >>> display error messages in the text box: >>> >>> !xtp_parallel -e iqm -o OPTIONFILES/iqm.xml -f state.hdf5 -p 2 -s 0 -j run >>> -c 1 >>> >>> ================================================== >>> ======== VOTCA (http://www.votca.org) ======== >>> ================================================== >>> >>> please submit bugs to https://github.com/votca/xtp/issues >>> >>> xtp_parallel, version 2022-dev gitid: 59a5962 (compiled Apr 24 2021, >>> 21:06:33) >>> votca_csg, version 2022-dev gitid: 59a5962 (compiled Apr 24 2021, 20:53:18) >>> votca_tools, version 2022-dev gitid: 59a5962 (compiled Apr 24 2021, >>> 20:51:00) >>> >>> Initializing calculator >>> ... iqm >>> ... ... Initialized with 1 threads. >>> >>> ... ... Using 2 openmp threads for 1x2=2 total threads. >>> 1 frames in statefile, Ids are: 0 >>> Starting at frame 0 >>> Evaluating frame 0 >>> Import MD Topology (i.e. frame 0) from state.hdf5 >>> .... >>> ... iqm >>> MST ERR Job file = 'iqm.jobs', cache size = 1 >>> MST ERR Initialize jobs from iqm.jobsan error occurred:iqm.jobs: Parse >>> error at line 2 >>> no element found: iostream error >>> >>> Is this due to a display error or is it normal? >>> >>> Sincerely, >>> >>> Thibaut Wohrer >>> >>> >>> On Tue, 13 Apr 2021 at 21:45, Christoph Junghans <[email protected]> >>> wrote: >>> >>>> >>>> >>>> On Tue, Apr 13, 2021 at 07:17 Thibaut Wohrer <[email protected]> wrote: >>>> >>>>> Hello, >>>>> >>>>> I have attempted to reinstall Votca as its latest version but using >>>>> the same steps I obtain this error >>>>> -- Checking for module 'libint2>=2.6' >>>>> -- No package 'libint2' found >>>>> >>>> This above line means libint-2.6 or higher could not be found, this is >>>> a new dependency in version 2021. >>>> >>>> Christoph >>>> >>>>> >>>>> CMake Error at >>>>> /gpfs2/apps/spack-software/environments/default/packages/linux-rhel7-avx2_512/gcc-4.8.5/cmake-3.16.2-s6lhty27ap52usu6qkfnioit7xpbc47z/share/cmake-3.16/Modules/FindPkgConfig.cmake:463 >>>>> >>>>> (message): >>>>> A required package was not found >>>>> Call Stack (most recent call first): >>>>> >>>>> /gpfs2/apps/spack-software/environments/default/packages/linux-rhel7-avx2_512/gcc-4.8.5/cmake-3.16.2-s6lhty27ap52usu6qkfnioit7xpbc47z/share/cmake-3.16/Modules/FindPkgConfig.cmake:643 >>>>> >>>>> (_pkg_check_modules_internal) >>>>> xtp/CMakeLists.txt:51 (pkg_check_modules) >>>>> >>>>> when using the Cmake command. As the procedure worked before I am not >>>>> sure why it no longer seems to work. >>>>> >>>>> Sincerely, >>>>> Thibaut Wohrer >>>>> >>>>> >>>>> >>>>> On Mon, 12 Apr 2021 at 20:11, Christoph Junghans <[email protected]> >>>>> wrote: >>>>> >>>>>> >>>>>> >>>>>> On Mon, Apr 12, 2021 at 03:42 Thibaut Wohrer <[email protected]> >>>>>> wrote: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I installed Votca version 1.6.2 through the installation guide >>>>>>> using the general installation instructions. >>>>>>> >>>>>> I would try the most recent version, 2021, first! >>>>>> >>>>>> Christoph >>>>>> >>>>>> >>>>>>> Sincerely, >>>>>>> >>>>>>> Thibaut Wohrer >>>>>>> >>>>>>> On Sun, 11 Apr 2021 at 20:07, Jens Wehner <[email protected]> >>>>>>> wrote: >>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> thanks for asking. As I developed this part I probably screwed it >>>>>>>> up. I will investigate a bit and come back to it. >>>>>>>> I think you are basically missing a default option. >>>>>>>> >>>>>>>> How did you install votca / which version are you using? >>>>>>>> >>>>>>>> Cheers Jens >>>>>>>> >>>>>>>> >>>>>>>> Thibaut Wohrer schrieb am Freitag, 9. April 2021 um 16:56:34 UTC+2: >>>>>>>> >>>>>>>>> Hello, >>>>>>>>> >>>>>>>>> I have been experiencing issues when running the tutorial for QMMM >>>>>>>>> calculation the XTP module as described here >>>>>>>>> https://www.votca.org/xtp-tutorials/QMMM_GROMACS.html >>>>>>>>> Specifically upon reaching the final section of the actual QMMM >>>>>>>>> calculations, when inputting the line >>>>>>>>> xtp_parallel -e qmmm -o OPTIONFILES/qmmm.xml -p 2 -f state.hdf5 -j >>>>>>>>> run >>>>>>>>> The first calculation runs normally for job ID 0 but moving to job >>>>>>>>> ID 1 leads to the following error. >>>>>>>>> ERROR: Job file incomplete. >>>>>>>>> Job with id 1 is not finished. Check your job file for FAIL, >>>>>>>>> AVAILABLE, or ASSIGNED. Exiting >>>>>>>>> >>>>>>>>> terminate called after throwing an instance of 'std::runtime_error' >>>>>>>>> what(): Error: filters is not found >>>>>>>>> >>>>>>>>> This error occurs on a normal machine and for a PBS submitted >>>>>>>>> script. This error also occurs regardless of using >>>>>>>>> sed -i '0,/COMPLETE/s/COMPLETE/AVAILABLE/' qmmm_jobs.xml >>>>>>>>> and this type of error does not occur in any of the previous >>>>>>>>> calculations of the tutorial. >>>>>>>>> >>>>>>>>> Any help on this issue would be much appreciated! >>>>>>>>> >>>>>>>> -- >>>>>>>> Join us on Slack: https://join.slack.com/t/votca/signup >>>>>>>> --- >>>>>>>> You received this message because you are subscribed to a topic in >>>>>>>> the Google Groups "votca" group. >>>>>>>> To unsubscribe from this topic, visit >>>>>>>> https://groups.google.com/d/topic/votca/4bgodqD7vxs/unsubscribe. >>>>>>>> To unsubscribe from this group and all its topics, send an email to >>>>>>>> [email protected]. >>>>>>>> To view this discussion on the web visit >>>>>>>> https://groups.google.com/d/msgid/votca/c6bee565-d2b1-4a7f-a898-154cc1ffbfa9n%40googlegroups.com >>>>>>>> >>>>>>>> <https://groups.google.com/d/msgid/votca/c6bee565-d2b1-4a7f-a898-154cc1ffbfa9n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>>> . >>>>>>>> >>>>>>> -- >>>>>>> Join us on Slack: https://join.slack.com/t/votca/signup >>>>>>> --- >>>>>>> You received this message because you are subscribed to the Google >>>>>>> Groups "votca" group. >>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>> send an email to [email protected]. >>>>>>> To view this discussion on the web visit >>>>>>> https://groups.google.com/d/msgid/votca/CALKNByGC0qkHz2xbsp%2B9WO8WA4wdjxwGw4Yd7o3-Hx%2BwUkkgOA%40mail.gmail.com >>>>>>> >>>>>>> <https://groups.google.com/d/msgid/votca/CALKNByGC0qkHz2xbsp%2B9WO8WA4wdjxwGw4Yd7o3-Hx%2BwUkkgOA%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>>> . >>>>>>> >>>>>> -- >>>>>> Christoph Junghans >>>>>> Web: http://www.compphys.de >>>>>> >>>>>> -- >>>>>> Join us on Slack: https://join.slack.com/t/votca/signup >>>>>> --- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "votca" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to [email protected]. >>>>>> >>>>> To view this discussion on the web visit >>>>>> https://groups.google.com/d/msgid/votca/CAHG27e4HcvnHS94DC%3DnSty4xb4pShtBvw%3DWRGr5DyxbRGbr3Xg%40mail.gmail.com >>>>>> >>>>>> <https://groups.google.com/d/msgid/votca/CAHG27e4HcvnHS94DC%3DnSty4xb4pShtBvw%3DWRGr5DyxbRGbr3Xg%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>> . >>>>>> >>>>> -- >>>>> Join us on Slack: https://join.slack.com/t/votca/signup >>>>> --- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "votca" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to [email protected]. >>>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/votca/CALKNByHyjeyEyAn_dni-T94eqXFumNv-eFOqJDN7Q6MJn6o7mg%40mail.gmail.com >>>>> >>>>> <https://groups.google.com/d/msgid/votca/CALKNByHyjeyEyAn_dni-T94eqXFumNv-eFOqJDN7Q6MJn6o7mg%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> -- >>>> Christoph Junghans >>>> Web: http://www.compphys.de >>>> >>>> -- >>>> Join us on Slack: https://join.slack.com/t/votca/signup >>>> --- >>>> You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> >>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/votca/CAHG27e7v%3D93joXWjkQMWUZXiA%3D6nfU88mMnnCYe_6L8dkA3mdQ%40mail.gmail.com >>>> >>>> <https://groups.google.com/d/msgid/votca/CAHG27e7v%3D93joXWjkQMWUZXiA%3D6nfU88mMnnCYe_6L8dkA3mdQ%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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