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
>> >> >>>> > ---
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>> >> >>>> > Groups "votca" group.
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>> >> >>>> > 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
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>> >> >>>> https://groups.google.com/d/msgid/votca/CAHG27e5T9%2BYxURMfUrr8nVyERKqD1yMGGRMONw09eNeUggHNew%40mail.gmail.com.
>> >> >>>
>> >> >>> --
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>> >> >>
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>> >> >
>> >> > --
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>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >>
>> >> --
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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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>
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--
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Web: http://www.compphys.de
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