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
>> >> >> >> >>> ---
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>> >> >> >> >>> 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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>> >> >> >> >> To view this discussion on the web visit 
>> >> >> >> >> https://groups.google.com/d/msgid/votca/CAHG27e4RwoWm-NDRSYAZPzycT%3DKAoOnK-HZ8JYVCC0Ej5X_%2BEA%40mail.gmail.com.
>> >> >> >> >
>> >> >> >> > --
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>> >> >> >> > ---
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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/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
>> >> >> >> ---
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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/CAHG27e7T7i1nF%3DJj_O4aPEJh6JmEomSn_mLn2kRXW9Q_N7fq%2Bg%40mail.gmail.com.
>> >> >> >
>> >> >> > --
>> >> >> > 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
>>
>> --
>> Join us on Slack: https://join.slack.com/t/votca/signup
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>
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