Re: [ESPResSo-users] make does not find gsl headers

[Konrad Breitsprecher]

Glad it did work! Looking at the code, GSL is currently used solely in the calculation of the fractal dimension of a particle cluster.

I have no idea for the issue with the FFTW path though.

Best,

Konrad

Am Mi., 17. Juli 2019 um 12:50 Uhr schrieb hecke <address@hidden>:

Hi Konrad,

thanks, that did work.
Only to make sure: This does not compromise the functionality of
espresso, but only the performance in a very few routines?

thanks
        Hecke

On 7/17/19 9:55 AM, Konrad Breitsprecher wrote:
> Hi Hecke,
> you might get away with just turning off GSL (cmake -DWITH_GSL=OFF),
> it's just needed for a specific cluster analysis method.
> Cheers,
> Konrad
>
> Am Di., 16. Juli 2019 um 18:46 Uhr schrieb hecke <address@hidden
> <mailto:address@hidden>>:
>
>     Dear Espresso-people,
>
>     I am trying to compile espresso on a cluster here at MPIDS in
>     Goettingen. We have lots of  custom compiled libraries in non-standard
>     directories, so linking is always a bit tricky.
>
>     Now, after some serious work, I got cmake to run through smoothly, but
>     when running make I more or less immediately run into the problem that
>     the gsl headers are not found. Although cmake lists the correct path to
>     the right gsl.
>
>     Any hint on what I might be doing wrong here?
>     To me it looks as if custom paths are not correctly put into the
>     Makefiles by cmake.
>
>     (btw, in order to get -DFFTW3_ROOT to work, I needed to set
>     cmake_policy(SET CMP0074 NEW) in the root CMakeLists.txt, otherwise,
>     cmake would not configure the FFTW paths correctly, but tell me that
>     WARNING: Target "EspressoCore" requests linking to directory
>     "/usr/lmp/fftw-3.3.8-mvapich2-2.3-gcc-8.2.0/lib".  Targets may link
>     only
>     to libraries.  CMake is dropping the item.
>     while I set -DFFTW3_LIBRARIES and -DFFTW3_INCLUDE_DIR
>     Is this intended behavior?)
>
>     cheers
>              Hecke
>
>
>     -------------------------------------------------------------------------
>
>     # cmake -DWITH_CUDA=off
>     -DFFTW3_ROOT=/usr/lmp/fftw-3.3.8-mvapich2-2.3-gcc-8.2.0/
>     -DFFTW3_INCLUDE_DIR=/usr/lmp/fftw-3.3.8-mvapich2-2.3-gcc-8.2.0/include
>     -DGSL_INCLUDE_DIR=/usr/lmp/gsl-2.5-gcc-8.2.0/include
>     -DGSL_LIBRARY=/usr/lmp/gsl-2.5-gcc-8.2.0/lib
>     -DGSL_CBLAS_LIBRARY=/usr/lmp/gsl-2.5-gcc-8.2.0/lib/libgslcblas.so
>     -DCMAKE_C_COMPILER=/usr/lmp/mvapich2-2.3-gcc-8.2.0/bin/mpicc
>     -DCMAKE_CXX_COMPILER=/usr/lmp/mvapich2-2.3-gcc-8.2.0/bin/mpicxx
>     -DCMAKE_FORTRAN_COMPILER=/usr/lmp/mvapich2-2.3-gcc-8.2.0/bin/mpif90
>     -DBOOST_LIBRARIES=/usr/lmp/boost-1.69.0-mvapich2-2.3-gcc-8.2.0/lib
>     -DBOOST_ROOT=/usr/lmp/boost-1.69.0-mvapich2-2.3-gcc-8.2.0/ ..
>     -- The C compiler identification is GNU 8.2.0
>     -- The CXX compiler identification is GNU 8.2.0
>     -- Check for working C compiler:
>     /usr/lmp/mvapich2-2.3-gcc-8.2.0/bin/mpicc
>     -- Check for working C compiler:
>     /usr/lmp/mvapich2-2.3-gcc-8.2.0/bin/mpicc -- 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:
>     /usr/lmp/mvapich2-2.3-gcc-8.2.0/bin/mpicxx
>     -- Check for working CXX compiler:
>     /usr/lmp/mvapich2-2.3-gcc-8.2.0/bin/mpicxx -- works
>     -- Detecting CXX compiler ABI info
>     -- Detecting CXX compiler ABI info - done
>     -- Detecting CXX compile features
>     -- Detecting CXX compile features - done
>     -- Config file:
>     /usr/lmp/SOURCES.ORIGINAL/espresso-4.0.2/src/core/myconfig-default.hpp
>     -- Performing Test result__PRETTY_FUNCTION__
>     -- Performing Test result__PRETTY_FUNCTION__ - Success
>     -- Found PythonInterp: /usr/lmp/anaconda3/bin/python (found version
>     "3.7.1")
>     -- Found Cython version 0.29.2
>     -- Found Cython: /usr/lmp/anaconda3/bin/cython (Required is at least
>     version "0.23")
>     -- Found NumPy:
>     /usr/lmp/anaconda3/lib/python3.7/site-packages/numpy/core/include
>     (found
>     version "1.15.4")
>     -- NumPy ver. 1.15.4 found (include:
>     /usr/lmp/anaconda3/lib/python3.7/site-packages/numpy/core/include)
>     -- HDF5: Using hdf5 compiler wrapper to determine C configuration
>     -- Found HDF5:
>     /usr/lmp/anaconda3-2018.12/lib/libhdf5.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so;/usr/lmp/anaconda3-2018.12/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so
>
>     (found suitable version "1.10.2", minimum required is "1.8") found
>     components:  C
>     -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1")
>     -- Found GSL: /usr/lmp/gsl-2.5-gcc-8.2.0/include (found version "2.4")
>     -- Found MPI_C: /usr/lmp/mvapich2-2.3-gcc-8.2.0/bin/mpicc (found
>     version
>     "3.1")
>     -- Found MPI_CXX: /usr/lmp/mvapich2-2.3-gcc-8.2.0/bin/mpicxx (found
>     version "3.1")
>     -- Found MPI: TRUE (found version "3.1")
>     -- Boost version: 1.69.0
>     -- Found the following Boost libraries:
>     --   mpi
>     --   serialization
>     --   filesystem
>     --   system
>     --   unit_test_framework
>     -- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found
>     components:  doxygen missing components:  dot
>     -- Found Sphinx: /usr/lmp/anaconda3/bin/sphinx-build (found suitable
>     version "1.8.2", minimum required is "1.6.6")
>     -- writing
>     /usr/lmp/SOURCES.ORIGINAL/espresso-4.0.2/build/myconfig-sample.hpp
>     -- The following OPTIONAL packages have been found:
>
>        * FFTW3
>        * HDF5 (required version >= 1.8)
>        * PkgConfig
>        * GSL
>        * Doxygen
>        * Sphinx (required version >= 1.6.6)
>
>     -- The following REQUIRED packages have been found:
>
>        * PythonInterp
>        * Cython (required version >= 0.23)
>        * NumPy
>        * MPI
>        * Boost (required version >= 1.53.0)
>
>     -- Configuring done
>     -- Generating done
>     CMake Warning:
>         Manually-specified variables were not used by the project:
>
>           BOOST_LIBRARIES
>           CMAKE_FORTRAN_COMPILER
>
>
>     -- Build files have been written to:
>     /usr/lmp/SOURCES.ORIGINAL/espresso-4.0.2/build
>
>     --------------------------------------------------------------------------------
>
>
>
>     # make
>     [  0%] Built target myconfig
>     [  0%] Built target check_myconfig
>     [  1%] Built target EspressoConfig
>     [  2%] Building CXX object
>     src/core/cluster_analysis/CMakeFiles/cluster_analysis.dir/Cluster.cpp.o
>     /usr/lmp/SOURCES.ORIGINAL/espresso-4.0.2/src/core/cluster_analysis/Cluster.cpp:23:10:
>
>     fatal error: gsl/gsl_fit.h: No such file or directory
>        #include "gsl/gsl_fit.h"
>                 ^~~~~~~~~~~~~~~
>     compilation terminated.
>
>
>
>