The complete output is: -- The CXX compiler identification is Intel 18.0.5.20180823 -- Check for working CXX compiler: /apps/intel/psxe_2018u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/icpc -- Check for working CXX compiler: /apps/intel/psxe_2018u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/icpc -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test COMPILER_SUPPORTS-Wall -- Performing Test COMPILER_SUPPORTS-Wall - Success -- Performing Test COMPILER_SUPPORTS-Wextra -- Performing Test COMPILER_SUPPORTS-Wextra - Success -- Performing Test COMPILER_SUPPORTS-Wpedantic -- Performing Test COMPILER_SUPPORTS-Wpedantic - Failed -- Performing Test COMPILER_SUPPORTS-Wshadow -- Performing Test COMPILER_SUPPORTS-Wshadow - Success -- Performing Test COMPILER_SUPPORTS-Wconversion -- Performing Test COMPILER_SUPPORTS-Wconversion - Success -- Found Git: /usr/bin/git (found version "1.8.3.1") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found Boost: /apps/boost/1.71.0/intelcc-2018.5/lib/cmake/Boost-1.71.0/BoostConfig.cmake (found suitable version "1.71.0", minimum required is "1.53.0") found components: program_options filesystem system -- Found Python: /usr/bin/python3.6 (found suitable version "3.6.8", minimum required is "3") found components: Interpreter -- Found Eigen3: /apps/eigen/3.3.7/gcc-7.4.0/share/eigen3/cmake -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") -- Checking for module 'fftw3' -- Found fftw3, version 3.3.8 -- Found FFTW3: /apps/fftw3/3.3.8/intel-v18/lib/libfftw3.so -- Looking for C++ include cassert -- Looking for C++ include cassert - found -- Looking for C++ include cmath -- Looking for C++ include cmath - found -- Looking for C++ include fstream -- Looking for C++ include fstream - not found CMake Error at tools/CMakeLists.txt:109 (message): Could not find needed header - fstream
-- Configuring incomplete, errors occurred! See also "/home/users/astar/ihpc/stuthiba/scratch/ASTAR/votca-xtp-install2/builddir/CMakeFiles/CMakeOutput.log". See also "/home/users/astar/ihpc/stuthiba/scratch/ASTAR/votca-xtp-install2/builddir/CMakeFiles/CMakeError.log". On Wed, 28 Apr 2021 at 19:14, Jens Wehner <[email protected]> wrote: > 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 >>> 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/0d85da9d-4ea6-4c07-8fd2-c68f9e050bbcn%40googlegroups.com >>> <https://groups.google.com/d/msgid/votca/0d85da9d-4ea6-4c07-8fd2-c68f9e050bbcn%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 > 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/b410605b-e5b4-4513-8227-1736ef21705an%40googlegroups.com > <https://groups.google.com/d/msgid/votca/b410605b-e5b4-4513-8227-1736ef21705an%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/CALKNByFWvyJ4gHkU90OggA8q7GyorAb%3DmCk5HRz0aCxA1LoZfA%40mail.gmail.com.
