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. 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/514a18ae-7d88-466c-a299-34459bc44643n%40googlegroups.com.
