Can you try without the intel compiler and see if it works? Otherwise I do not have a good idea. fstream is a systems header, so that is not really votca territory.
Thibaut Wohrer schrieb am Mittwoch, 28. April 2021 um 14:44:18 UTC+2: > 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: 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