Can you post the whole cmake output as well. Thibaut Wohrer schrieb am Mittwoch, 28. April 2021 um 09:02:46 UTC+2:
> Hello Jens, > > I tried a fresh install on Ubuntu using cmake/3.16.2. As this is located > on a cluster I loaded the following modules before attempting a fresh > install: > module load gromacs cmake eigen/3.3.7-gcc7 fftw sqlite libxc > hdf5/1.10.6-gcc7 gsl doxygen txt2tags orca > > > Thibaut > > On Wed, 28 Apr 2021 at 14:42, Jens Wehner <[email protected]> wrote: > >> Hi Thibaut, >> >> good question. Can you try a fresh install? Which system are you on? >> Which compiler? >> >> Thibaut Wohrer schrieb am Mittwoch, 28. April 2021 um 07:13:48 UTC+2: >> >>> 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 a topic in the >> Google Groups "votca" group. >> To unsubscribe from this topic, visit >> 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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/b410605b-e5b4-4513-8227-1736ef21705an%40googlegroups.com.
