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

[Konrad Breitsprecher]

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>:

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.