Hello, When updating votca I now find the error when attempting the Cmake compilation command CMake Error at tools/CMakeLists.txt:109 (message): Could not find needed header - fstream
an error that has apparently been reported before: https://github.com/votca/csg/issues/200 I have attached the associated CmakeError.log file. Sincerely, Thibaut On Wed, 28 Apr 2021 at 03:23, Jens Wehner <[email protected]> wrote: > 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. > 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/d4571fd3-185d-4fac-8bdb-82afa4c8237cn%40googlegroups.com > <https://groups.google.com/d/msgid/votca/d4571fd3-185d-4fac-8bdb-82afa4c8237cn%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. 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CMakeError.log
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