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.
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?
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.
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
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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
> 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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> >> >>>> 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
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> .
> >> >>
> >> >> --
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> .
> >> >
> >> > --
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> send an email to [email protected].
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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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> .
>
>
>
> --
> 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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