I have attached the printed output from cmake command herewith
On Sat, Apr 25, 2020 at 1:41 PM Christoph Junghans <[email protected]>
wrote:
>
>
> On Sat, Apr 25, 2020 at 11:25 Salman Bin Kashif <[email protected]>
> wrote:
>
>> Thank you. That works too. Next error was encountered in make -j5 command.
>>
>
>> /home/sbinkas/software/include/eigen3/unsupported/Eigen/FFT:75:21: fatal
>> error: fftw3.h: No such file or directory
>>
> it seems the fftw3 dev package is missing!
>
> Can you post the output of your CMake execution, what fftw3 found?
>
> Christoph
>
>>
>>
>> I didn't find fftw.h in the entire eigen folder though. I am not sure
>> which path should I provide then.
>>
>> On Sat, Apr 25, 2020 at 1:03 PM Christoph Junghans <[email protected]>
>> wrote:
>>
>>> On Sat, Apr 25, 2020 at 10:52 AM Salman Bin Kashif <[email protected]>
>>> wrote:
>>> >
>>> > Thank you. This suggestion works. The cmake command did not throw any
>>> fatal error this time.
>>> >
>>> > However, I would like to discuss some caveats:
>>> >
>>> > 1. Would TXT2TAGS not being found be an issue in later steps? Like
>>> when running the simulation? It does suggest optional. But I assume it may
>>> be used for generating xml files during run.
>>> txt2tags is only used to build the manpage (documentation), so no issue
>>> here.
>>> >
>>> > 2. Warning with run time library:
>>> >
>>> > Cannot generate a safe runtime search path for target votca_tools
>>> because
>>> > files in some directories may conflict with libraries in implicit
>>> > directories:
>>> >
>>> > runtime library [libexpat.so.1] in /usr/lib64 may be hidden by
>>> files in:
>>> > /home/sbinkas/software/lib
>>> This error basically means there are two libexpat in your
>>> LD_LIBRARY_PATH.
>>> You tell CMake to explicitly use the one from
>>> /home/sbinkas/software/lib by add
>>> -DCMAKE_PREFIX_PATH=/home/sbinkas/software.
>>>
>>> Christoph
>>> >
>>> > I kind of get where is it coming from. This /home/sbinkas/software/lib
>>> got added while installing one of the dependencies. I don't remember which
>>> one to be exact, but possibly it was from eigen3. So a conflict may have
>>> arisen. Should I worry about it?
>>> >
>>> > Again, I very much appreciate your help.
>>> >
>>> > -Salman
>>> >
>>> >
>>> > Output:
>>> >
>>> >
>>> > - The following OPTIONAL packages have been found:
>>> >
>>> > * Git
>>> > * FFTW3
>>> > * UnixCommands
>>> > * PkgConfig
>>> > * HDF5
>>> > * Doxygen
>>> >
>>> > -- The following REQUIRED packages have been found:
>>> >
>>> > * EXPAT
>>> > * Threads
>>> > * Boost (required version >= 1.53.0)
>>> > * Eigen3 (required version >= 3.3.0)
>>> > * GROMACS (required version >= 2016)
>>> >
>>> > -- The following OPTIONAL packages have not been found:
>>> >
>>> > * MKL
>>> > * TXT2TAGS
>>> > * CLANG_FORMAT (required version >= 7.0.1)
>>> >
>>> > -- Configuring done
>>> > CMake Warning at tools/src/libtools/CMakeLists.txt:5 (add_library):
>>> > Cannot generate a safe runtime search path for target votca_tools
>>> because
>>> > files in some directories may conflict with libraries in implicit
>>> > directories:
>>> >
>>> > runtime library [libexpat.so.1] in /usr/lib64 may be hidden by
>>> files in:
>>> > /home/sbinkas/software/lib
>>> >
>>> > Some of these libraries may not be found correctly.
>>> >
>>> >
>>> > -- Generating done
>>> > -- Build files have been written to: /home/sbinkas/software/votca/build
>>> >
>>> > On Sat, Apr 25, 2020 at 12:31 PM Christoph Junghans <
>>> [email protected]> wrote:
>>> >>
>>> >> On Sat, Apr 25, 2020 at 10:26 AM Salman Bin Kashif <
>>> [email protected]> wrote:
>>> >> >
>>> >> > This is the error associated with libgromacs:
>>> >> >
>>> >> > gmake[1]: *** No rule to make target
>>> `/home/sbinkas/gromacs/lib/libgromacs.so', needed by `cmTC_b3327 '.
>>> Stop.
>>> >> > 101 gmake[1]: Leaving directory
>>> `/home/sbinkas/software/votca/build/CMakeFiles/CMakeTmp'
>>> >> > 102 gmake: *** [cmTC_b3327/fast] Error 2
>>> >> In the CMake output it says, it is using
>>> >> /home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so, but now it
>>> >> is looking for
>>> >> `/home/sbinkas/gromacs/lib/libgromacs.so, you might want to help CMake
>>> >> by setting
>>> -DGROMACS_LIBRARY=/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so.
>>> >>
>>> >> Christoph
>>> >> >
>>> >> > On Sat, Apr 25, 2020 at 12:12 PM Christoph Junghans <
>>> [email protected]> wrote:
>>> >> >>
>>> >> >> On Sat, Apr 25, 2020 at 8:53 AM Salman Bin Kashif <
>>> [email protected]> wrote:
>>> >> >> >
>>> >> >> > Thanks very much for being patient with me.
>>> >> >> >
>>> >> >> > I had installed eigen3 easier which incidentally happen to be
>>> from the same source you pointed out. Eigen is being read properly I assume.
>>> >> >> >
>>> >> >> > -- Found Eigen3:
>>> /home/sbinkas/software/eigen-eigen-67e894c6cd8f/build_dir
>>> >> >> >
>>> >> >> > However, there are two more issues:
>>> >> >> >
>>> >> >> > -- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE)
>>> >> >> > txt2tags not found, help cmake to find it by setting
>>> TXT2TAGS_EXECUTABLE
>>> >> >> >
>>> >> >> >
>>> >> >> > I have provided the path to executable txt2tags file in
>>> /home/software/txt2tags-2.6/txt2tags but it still is not fould. However,
>>> the error was not fatal due to it.
>>> >> >> Don't worry this one is optional.
>>> >> >>
>>> >> >> >
>>> >> >> > The error was fatal due to not having been able to read c++
>>> version in gromacs library. It is reaching to the libgromacs.so file though.
>>> >> >> >
>>> >> >> > The error message is as follows:
>>> >> >> >
>>> >> >> > -- Looking for c++ gmx_version in
>>> /home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so
>>> >> >> > -- Looking for c++ gmx_version in
>>> /home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so - not found
>>> >> >> > CMake Error at csg/CMakeModules/FindGROMACS.cmake:57 (message):
>>> >> >> > Could not find a suitable gromacs library. gmx_version is not
>>> defined in
>>> >> >> > the gromacs library, that is very very strange, take a look at
>>> the error
>>> >> >> > message in
>>> /home/sbinkas/software/votca/build/CMakeFiles/CMakeError.log to
>>> >> >> > find out what was going wrong. This most likely means that
>>> your gromacs
>>> >> >> > version is too old, we need at least gromacs 2016!
>>> >> >> >
>>> >> >> > My version is 2018.3
>>> >> >> >
>>> >> >> > I have used this command for cmake:
>>> >> >> >
>>> >> >> > cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix}
>>> -DWITH_GMX=ON ..
>>> >> >> >
>>> >> >> > Providing the path to include directory and library also makes
>>> no difference.
>>> >> >> >
>>> >> >> > However, I would note a caveat. The gromacs version I installed
>>> manually on cluster was installed with -DGMX_MPI=OFF.
>>> >> >> >
>>> >> >> > But, the dependencies requirement suggests gromacs-openmpi. Can
>>> that be a reason?
>>> >> >> Votca needs a non-mpi version, so that should be fine. You only
>>> need
>>> >> >> gromacs with mpi at runtime to do parallel simulations.
>>> >> >> Have a look at the end of
>>> >> >> /home/sbinkas/software/votca/build/CMakeFiles/CMakeError.log to see
>>> >> >> what is wrong with your libgromacs.
>>> >> >>
>>> >> >>
>>> >> >> > PS: I am talking about installation on cluster now. On local
>>> machine Votca package got installed using apt-get but as expected, the
>>> simulations were super slow.
>>> >> >> Usually you can speed up the gromacs simulation part by running on
>>> all cores.
>>> >> >>
>>> >> >> Christoph
>>> >> >> >
>>> >> >> > Thanks for all your help again.
>>> >> >> >
>>> >> >> > On Sat, Apr 25, 2020 at 9:41 AM Christoph Junghans <
>>> [email protected]> wrote:
>>> >> >> >>
>>> >> >> >> On Sat, Apr 25, 2020 at 7:15 AM Salman Bin Kashif <
>>> [email protected]> wrote:
>>> >> >> >> >
>>> >> >> >> > Okay. I will install a newer version manually and apt-get
>>> consider the 3.3-beta1 version to be the latest.
>>> >> >> >> That might help:
>>> >> >> >>
>>> https://askubuntu.com/questions/1068232/how-to-update-libeigen3-to-version-3-3-on-16-04-xenial
>>> >> >> >>
>>> >> >> >> >
>>> >> >> >> > My linux version is:
>>> >> >> >> >
>>> >> >> >> > Ubuntu 16.04.4 LTS
>>> >> >> >> Hmm, as the name suggests that Ubuntu is from 2016 and we will
>>> only
>>> >> >> >> support the latest LTS version, which currently is 18.04 (until
>>> later
>>> >> >> >> this month when 20.04 LTS is released). We just don't have the
>>> >> >> >> manpower to support anything but the latest versions of most
>>> Linux
>>> >> >> >> distributions.
>>> >> >> >>
>>> >> >> >> Plus, the gromacs version in 16.04 might be also too old to be
>>> used
>>> >> >> >> with VOTCA-1.6.
>>> >> >> >>
>>> >> >> >> Christoph
>>> >> >> >> >
>>> >> >> >> > On Sat, Apr 25, 2020 at 9:10 AM Christoph Junghans <
>>> [email protected]> wrote:
>>> >> >> >> >>
>>> >> >> >> >> On Fri, Apr 24, 2020 at 10:07 PM Salman Bin Kashif <
>>> [email protected]> wrote:
>>> >> >> >> >> >
>>> >> >> >> >> > Thanks again for answering my questions.
>>> >> >> >> >> >
>>> >> >> >> >> > "What version do you have installed?"
>>> >> >> >> >> >
>>> >> >> >> >> > For eigen3, I have installed the version libeigen3-dev
>>> which is mentioned in the dependencies section. The version information for
>>> eigen3 is as follows:
>>> >> >> >> >> >
>>> >> >> >> >> > libeigen3-dev is already the newest version (3.3~beta1-2)
>>> >> >> >> >> Yes, and 3.3-beta1 is older than 3.3.0, so you need a newer
>>> version of eigen3.
>>> >> >> >> >>
>>> >> >> >> >> What Linux distribution are you using?
>>> >> >> >> >>
>>> >> >> >> >> Christoph
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> > -Salman
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> > On Sat, Apr 25, 2020 at 12:00 AM Christoph Junghans <
>>> [email protected]> wrote:
>>> >> >> >> >> >>
>>> >> >> >> >> >>
>>> >> >> >> >> >>
>>> >> >> >> >> >> On Fri, Apr 24, 2020, 21:00 Salman Bin Kashif <
>>> [email protected]> wrote:
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> Thank you, Christoph. I now tried installing v 1.6. I am
>>> trying on local machine for now since it is easier to install all the
>>> dependencies.
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> Initially, my cmake version was old which was 3.5.1 and
>>> on installing votca it was throwing an error that minimum 3.10 version is
>>> required for cmake. Hence I manually installed cmake version 3.16.5
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> I verified cmake installation by checking the cmake
>>> --version
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> However, on installing the votca back I got the
>>> following error:
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> Could not find a configuration file for package "Eigen3"
>>> that is compatible
>>> >> >> >> >> >>> with requested version "3.3.0".
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> The following configuration files were considered but
>>> not accepted:
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> /usr/lib/cmake/eigen3/Eigen3Config.cmake, version:
>>> unknown
>>> >> >> >> >> >>
>>> >> >> >> >> >> This error means the Eigen3 you have installed is too
>>> old. Eigen-3.3.0 got released back in Nov. 2016, so that isn't very new
>>> either.
>>> >> >> >> >> >>
>>> >> >> >> >> >> What version do you have installed?
>>> >> >> >> >> >>
>>> >> >> >> >> >> Christoph
>>> >> >> >> >> >>
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> Would I have to install specific cmake version?
>>> >> >> >> >> >>>
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> On Fri, Apr 24, 2020 at 9:10 PM Christoph Junghans <
>>> [email protected]> wrote:
>>> >> >> >> >> >>>>
>>> >> >> >> >> >>>> Votca-1.4.1 was released back in Sept. 2017 and we
>>> don't really
>>> >> >> >> >> >>>> support such old versions anymore.
>>> >> >> >> >> >>>> If you don't have a strong reason to use v1.4.1 try to
>>> use Votca-1.6.
>>> >> >> >> >> >>>> see
>>> https://github.com/votca/votca/blob/master/README.md
>>> >> >> >> >> >>>>
>>> >> >> >> >> >>>>
>>> >> >> >> >> >>>> On Fri, Apr 24, 2020 at 6:59 PM Salman Bin Kashif <
>>> [email protected]> wrote:
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > I am trying to Install Votca on cluster. In have
>>> loaded the required modules there. However, I am getting an error in terms
>>> of finding the package.I used the following command:
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > cmake -DCMAKE_INSTALL_PREFIX=${prefix}
>>> -DWITH_FFTW=OFF -DWITH_SQLITE3=OFF ..
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > The error message I get is:
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > -- Boost version: 1.53.0
>>> >> >> >> >> >>>> > -- Found the following Boost libraries:
>>> >> >> >> >> >>>> > -- program_options
>>> >> >> >> >> >>>> > -- filesystem
>>> >> >> >> >> >>>> > -- system
>>> >> >> >> >> >>>> > -- checking for module 'gsl'
>>> >> >> >> >> >>>> > -- package 'gsl' not found
>>> >> >> >> >> >>>> > -- Could NOT find GSL (missing: GSL_LIBRARY
>>> GSL_INCLUDE_DIR)
>>> >> >> >> >> >>>> > -- Intel(R) MKL could not be found.
>>> >> >> >> >> >>>> > --
>>> >> >> >> >> >>>> > -- The following OPTIONAL packages have been found:
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > * PkgConfig
>>> >> >> >> >> >>>> > * EXPAT
>>> >> >> >> >> >>>> > * Doxygen
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > -- The following REQUIRED packages have been found:
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > * Threads
>>> >> >> >> >> >>>> > * Boost (required version >= 1.39.0)
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > -- The following OPTIONAL packages have not been
>>> found:
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > * GSL
>>> >> >> >> >> >>>> > * MKL
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > -- Could NOT find TXT2TAGS (missing:
>>> TXT2TAGS_EXECUTABLE)
>>> >> >> >> >> >>>> > txt2tags not found, help cmake to find it by setting
>>> TXT2TAGS_EXECUTABLE
>>> >> >> >> >> >>>> > -- Boost version: 1.53.0
>>> >> >> >> >> >>>> > -- Found the following Boost libraries:
>>> >> >> >> >> >>>> > -- program_options
>>> >> >> >> >> >>>> > -- filesystem
>>> >> >> >> >> >>>> > -- system
>>> >> >> >> >> >>>> > -- checking for module 'libvotca_tools'
>>> >> >> >> >> >>>> > -- package 'libvotca_tools' not found
>>> >> >> >> >> >>>> > CMake Error at
>>> /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:108 (message):
>>> >> >> >> >> >>>> > Could NOT find SQLITE3 (missing:
>>> SQLITE3_INCLUDE_DIR)
>>> >> >> >> >> >>>> > Call Stack (most recent call first):
>>> >> >> >> >> >>>> >
>>> /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:315
>>> (_FPHSA_FAILURE_MESSAGE)
>>> >> >> >> >> >>>> > csg/CMakeModules/FindSQLITE3.cmake:34
>>> (find_package_handle_standard_args)
>>> >> >> >> >> >>>> > csg/CMakeModules/FindVOTCA_TOOLS.cmake:32
>>> (find_package)
>>> >> >> >> >> >>>> > csg/CMakeLists.txt:83 (find_package)
>>> >> >> >> >> >>>> Usually WITH_SQLITE3=OFF should disable the search for
>>> sqlite3,
>>> >> >> >> >> >>>> something funky is going on here as L32 in v1.4.1 isn't
>>> actually
>>> >> >> >> >> >>>> checking for sqlite3:
>>> >> >> >> >> >>>>
>>> https://github.com/votca/csg/blob/v1.4.1/CMakeModules/FindVOTCA_CSG.cmake
>>> >> >> >> >> >>>> Please check you are using the correct version of csg.
>>> >> >> >> >> >>>>
>>> >> >> >> >> >>>> Christoph
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > -- Configuring incomplete, errors occurred!
>>> >> >> >> >> >>>> > See also
>>> "/home/sbinkas/votca/build/CMakeFiles/CMakeOutput.log".
>>> >> >> >> >> >>>> > See also
>>> "/home/sbinkas/votca/build/CMakeFiles/CMakeError.log".
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> >
>>> >> >> >> >> >>>> > --
>>> >> >> >> >> >>>> > 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/187cdc4c-6526-4716-8532-d60341aec7a1%40googlegroups.com
>>> .
>>> >> >> >> >> >>>>
>>> >> >> >> >> >>>>
>>> >> >> >> >> >>>>
>>> >> >> >> >> >>>> --
>>> >> >> >> >> >>>> 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/CAHG27e5T9%2BYxURMfUrr8nVyERKqD1yMGGRMONw09eNeUggHNew%40mail.gmail.com
>>> .
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> --
>>> >> >> >> >> >>> 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/CAFwyQHy-N%3DpNKX4tQ-KXSU6Aghh23Af%2Bg_M1pJiAB8KsQAi-UQ%40mail.gmail.com
>>> .
>>> >> >> >> >> >>
>>> >> >> >> >> >> --
>>> >> >> >> >> >> 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/CAHG27e4RwoWm-NDRSYAZPzycT%3DKAoOnK-HZ8JYVCC0Ej5X_%2BEA%40mail.gmail.com
>>> .
>>> >> >> >> >> >
>>> >> >> >> >> > --
>>> >> >> >> >> > 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/CAFwyQHwpcxE%3D%3DZK%3D2Udw9fSFpn3d2rkCk1COVSpY5MaDQ_TpCw%40mail.gmail.com
>>> .
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >> --
>>> >> >> >> >> 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/CAHG27e7T7i1nF%3DJj_O4aPEJh6JmEomSn_mLn2kRXW9Q_N7fq%2Bg%40mail.gmail.com
>>> .
>>> >> >> >> >
>>> >> >> >> > --
>>> >> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>>> >> >> >> > ---
>>> >> >> >> > You received this message because you are subscribed to the
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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
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>>> .
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> --
>>> >> >> >> 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
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>>> .
>>> >> >> >
>>> >> >> > --
>>> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>>> >> >> > ---
>>> >> >> > You received this message because you are subscribed to the
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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
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>>> .
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> --
>>> >> >> 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
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>>> .
>>> >> >
>>> >> > --
>>> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>>> >> > ---
>>> >> > You received this message because you are subscribed to the Google
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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
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>>> .
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> 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].
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>>> .
>>> >
>>> > --
>>> > Join us on Slack: https://join.slack.com/t/votca/signup
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>>> an email to [email protected].
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>>> .
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>>> --
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>>>
>>> --
>>> Join us on Slack: https://join.slack.com/t/votca/signup
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> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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[sbinkas@node0170 build]$ cmake -DBUILD_CSGAPPS=ON
-DCMAKE_INSTALL_PREFIX=${prefix} -DWITH_GMX=ON
-DGROMACS_INCLUDE_DIR=/home/sbinkas/software/gromacs-2018.3/include
-DGROMACS_LIBRARY=/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so
-DCMAKE_PREFIX_PATH=/home/sbinkas/software ..
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /software/gcc/5.4.0/bin/gcc
-- Check for working C compiler: /software/gcc/5.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /software/gcc/5.4.0/bin/g++
-- Check for working CXX compiler: /software/gcc/5.4.0/bin/g++ -- 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 - Success
-- Performing Test COMPILER_SUPPORTS-Wshadow
-- Performing Test COMPILER_SUPPORTS-Wshadow - Success
-- Performing Test COMPILER_SUPPORTS-Wconversion
-- Performing Test COMPILER_SUPPORTS-Wconversion - Success
-- Found Git: /bin/git (found version "1.8.3.1")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- 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
-- Boost version: 1.53.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Check size of int
-- Check size of int - done
-- Could NOT find MKL (missing: MKL_INCLUDE_DIR MKL_Core_LINK_LIBRARY)
-- Found Eigen3: /home/sbinkas/software/share/eigen3/cmake
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1")
-- Checking for module 'fftw3'
-- Found fftw3, version 3.3.8
-- Found FFTW3: /home/sbinkas/software/lib/libfftw3.so
-- Looking for fftw_plan_r2r_1d in /home/sbinkas/software/lib/libfftw3.so;
-- Looking for fftw_plan_r2r_1d in /home/sbinkas/software/lib/libfftw3.so; -
found
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stack
-- Looking for C++ include stack - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Found EXPAT: /home/sbinkas/software/lib/libexpat.so (found version "2.2.9")
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE)
txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE
-- Found UnixCommands: /bin/bash
-- Boost version: 1.53.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Found Eigen3: /home/sbinkas/software/share/eigen3/cmake
-- Found VOTCA_TOOLS:
-- Checking for module 'libgromacs_d'
-- No package 'libgromacs_d' found
-- Checking for module 'libgromacs'
-- No package 'libgromacs' found
-- Looking for c++ gmx_version in
/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so
-- Looking for c++ gmx_version in
/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so - found
-- Looking for c++ gmx_is_single_precision in
/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so
-- Looking for c++ gmx_is_single_precision in
/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so - found
-- Looking for c++ gmx_is_double_precision in
/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so
-- Looking for c++ gmx_is_double_precision in
/home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so - not found
-- Found GROMACS: /home/sbinkas/software/gromacs-2018.3/lib64/libgromacs.so
(found suitable version "2018.3", minimum required is "2016")
-- Could NOT find GMX (missing: GMX_EXECUTABLE)
-- Looking for C++ include algorithm
-- Looking for C++ include algorithm - found
-- Looking for C++ include iomanip
-- Looking for C++ include iomanip - found
-- Looking for C++ include numeric
-- Looking for C++ include numeric - found
-- Looking for C++ include cstdlib
-- Looking for C++ include cstdlib - found
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5:
/home/sbinkas/software/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so
(found version "1.10.0.1") found components: C
-- Could NOT find LMP (missing: LMP_EXECUTABLE)
-- Found VOTCA_CSG:
-- Found Doxygen: /bin/doxygen (found version "1.8.5") found components:
doxygen dot
-- Could NOT find CLANG_FORMAT: Found unsuitable version "0.0", but required is
at least "7.0.1" (found CLANG_FORMAT_EXECUTABLE-NOTFOUND)
-- The following OPTIONAL packages have been found:
* Git
* FFTW3
* UnixCommands
* PkgConfig
* HDF5
* Doxygen
-- The following REQUIRED packages have been found:
* EXPAT
* Threads
* Boost (required version >= 1.53.0)
* Eigen3 (required version >= 3.3.0)
* GROMACS (required version >= 2016)
-- The following OPTIONAL packages have not been found:
* MKL
* TXT2TAGS
* CLANG_FORMAT (required version >= 7.0.1)
-- Configuring done
-- Generating done
-- Build files have been written to: /home/sbinkas/software/votca/build
