cmake eror in votca installation

[Pragati Sharma]

Dear Votca users/developers, 

I am trying to build votca on my machine using cmake and following the instructions provided in the README.md file. 

Briefly, I get into the master branch directory and create a build directory and enter it (mkdir build && cd build).

I then run the cmake command as follows:

cmake -DBUILD_CSGAPPS=ON  -DFFTW3_INCLUDE_DIR=/apps/FFTW/fftw-3.3.8/include -DFFTW3_LIBRARY=/apps/FFTW/fftw-3.3.8/lib -DGROMACS_INCLUDE_DIR=/apps/GROMACS/gromacs-2019.0_tmpi/include -DGROMACS_LIBRARY=/apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so  -DCMAKE_INSTALL_PREFIX=/apps/VOTCA/votca-wdgromacs/ ..

however I get the following errors which I can't understnd.

Am I missing anything? 

Could you please help me to solve the problem? 

This is the output of cmake:

-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- 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/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS-Wall
-- Performing Test COMPILER_SUPPORTS-Wall - Success
-- Performing Test COMPILER_SUPPORTS-Wextra
-- Performing Test COMPILER_SUPPORTS-Wextra - Success
-- Performing Test COMPILER_SUPPORTS-Wpedantic
-- Performing Test COMPILER_SUPPORTS-Wpedantic - Success
-- Performing Test COMPILER_SUPPORTS-Wshadow
-- Performing Test COMPILER_SUPPORTS-Wshadow - Success
-- Performing Test COMPILER_SUPPORTS-Wconversion
-- Performing Test COMPILER_SUPPORTS-Wconversion - Success
-- Found Git: /usr/bin/git (found version "2.7.4")
-- Check size of int
-- Check size of int - done
-- Found MKL: /opt/intel/mkl/include 
-- 'Intel OpenMP' used for MKL parallelisation
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE 
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   program_options
--   filesystem
--   system
-- Found Eigen3: /usr/local/share/eigen3/cmake
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Checking for module 'fftw3'
--   No package 'fftw3' found
-- Found FFTW3: /apps/FFTW/fftw-3.3.8/lib 
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stack
-- Looking for C++ include stack - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Found EXPAT: /usr/lib/x86_64-linux-gnu/libexpat.so (found version "2.1.0")
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE)
-- txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE
-- Found UnixCommands: /bin/bash 
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   program_options
--   filesystem
--   system
-- Found Eigen3: /usr/local/share/eigen3/cmake
-- Found VOTCA_TOOLS:
-- Checking for module 'libgromacs_d'
--   No package 'libgromacs_d' found
-- Checking for module 'libgromacs'
--   Found libgromacs, version 2019
-- Looking for c++ gmx_version in /apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so
-- Looking for c++ gmx_version in /apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so - found
-- Looking for c++ gmx_is_single_precision in /apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so
-- Looking for c++ gmx_is_single_precision in /apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so - found
-- Looking for c++ gmx_is_double_precision in /apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so
-- Looking for c++ gmx_is_double_precision in /apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so - not found
-- Found GROMACS: /apps/GROMACS/gromacs-2019.0_tmpi/lib/libgromacs.so (found suitable version "2019.0", minimum required is "2019")
-- Could NOT find GMX (missing: GMX_EXECUTABLE)
-- Looking for C++ include algorithm
-- Looking for C++ include algorithm - found
-- Looking for C++ include iomanip
-- Looking for C++ include iomanip - found
-- Looking for C++ include numeric
-- Looking for C++ include numeric - found
-- Looking for C++ include cstdlib
-- Looking for C++ include cstdlib - found
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.8.16") found components:  C
-- Could NOT find LMP (missing: LMP_EXECUTABLE)
-- Found VOTCA_CSG:
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.11") found components:  doxygen missing components:  dot
-- Could NOT find SPHINX (missing: SPHINX_EXECUTABLE)
CMake Error at /usr/share/llvm-3.8/cmake/LLVMConfig.cmake:178 (include):
  include could not find load file:

    /usr/share/llvm/cmake/LLVMExports.cmake
Call Stack (most recent call first):
  CMakeLists.txt:106 (_find_package)
  share/format/CMakeLists.txt:1 (find_package)


CMake Error at /usr/share/llvm-3.8/cmake/LLVMConfig.cmake:181 (include):
  include could not find load file:

    /usr/share/llvm/cmake/LLVM-Config.cmake
Call Stack (most recent call first):
  CMakeLists.txt:106 (_find_package)
  share/format/CMakeLists.txt:1 (find_package)


-- The following features have been enabled:

 * BUILD_CSGAPPS, Build extra app using csg
 * BUILD_MANPAGES, Build manpages (disable for cross-compile)
 * INSTALL_RC_FILES, Install votca rc files (VOTCARC.bash etc.)

-- The following OPTIONAL packages have been found:

 * Git
   Generated version for development version
 * MKL
   Enables accelerated performance with MKL
 * UnixCommands
   Used to build manpages
 * Doxygen
   Needed to build API documentation
 * LLVM
   Needed for automatic code formatting with clang-format

-- The following RECOMMENDED packages have been found:

 * FFTW3
   Enables FFT functionality
 * PkgConfig
   Used to detect fftw package
   Used to detect gromacs package
 * GROMACS (required version >= 2019)
   Used to read/write gromacs data files
 * HDF5
   Used to read h5md data files

-- The following REQUIRED packages have been found:

 * EXPAT
   Used for XML parsing
 * Boost (required version >= 1.53.0)
   Extended C++ libraries
 * Eigen3 (required version >= 3.3.0)
   C++ vector data structures
 * Threads
   Used for thread parallelization

-- The following features have been disabled:

 * BUILD_XTP, Build xtp module
 * BUILD_CSG_MANUAL, Build csg-manual
 * ENABLE_TESTING, Enable unit tests
 * ENABLE_RPATH_INJECT, Inject rpath into executables
 * BUILD_OWN_GROMACS, Build an internal version of gromacs
 * ENABLE_REGRESSION_TESTING, Enable regression tests

-- The following OPTIONAL packages have not been found:

 * TXT2TAGS
   Used to build manpages
 * Clang
   Needed for automatic code formatting with clang-format

-- Configuring incomplete, errors occurred!

I have attached a cmakeError.log file also

Thank you in advance for your time.

Pragati

[Christoph Junghans]

Something seems to be wrong with your LLVM installation. try to add
-DCMAKE_DISABLE_FIND_PACKAGE_LLVM=ON.

Christoph

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

[Pragati Sharma]

Thanks Christoph, Adding -DCMAKE_DISABLE_FIND_PACKAGE_LLVM=ON. to cmake worked. but then a new error came in next "make" step.

make -j8

Screen output:

/usr/bin/ld: cannot find -lmkl_core
/usr/bin/ld: cannot find /apps/FFTW/fftw-3.3.8/lib: File format not recognized
collect2: error: ld returned 1 exit status
tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:618: recipe for target 'tools/src/libtools/libvotca_tools.so.7' failed
make[2]: *** [tools/src/libtools/libvotca_tools.so.7] Error 1
CMakeFiles/Makefile2:214: recipe for target 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed
make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

Thank you in advance for your time.

Pragati

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e794hKbeTaw49-0KZMjWyrvRN6foKSNs4730wV-QRBvrw%40mail.gmail.com.

[Christoph Junghans]

On Wed, May 20, 2020, 23:42 Pragati Sharma <praga...@gmail.com> wrote:

Thanks Christoph, Adding -DCMAKE_DISABLE_FIND_PACKAGE_LLVM=ON. to cmake worked. but then a new error came in next "make" step.

make -j8

Screen output:

/usr/bin/ld: cannot find -lmkl_core

Seems something is wrong with your mkl installation, just disable the usage with -DCMAKE_DISABLE_FIND_PACKAGE_MKL=on

/usr/bin/ld: cannot find /apps/FFTW/fftw-3.3.8/lib: File format not recognized

The problem is the value of FFTW3_LIBRARY you specified is wrong, it needs to be the location of the library itself.

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAMpF9Q0cBC2U7-rhu0fRHP-Xy4qdBN%3Dj133NqEgLfnY7%3DO27OA%40mail.gmail.com.