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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