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.
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
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
> >> >> >> >> ---
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> 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
> >> >> >> > ---
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> >> >> >> > 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
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> 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
> >> >> > ---
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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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> .
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
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>
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