[votca] Error when installing VOTCA in Ubuntu 18.04

[Kim Foo]

Dear Christoph,

I am currently in the midst of installing VOTCA on my Ubuntu 18.04 system 
which I have already installed GROMACS 2019 on but I encountered an error 
when running the following command:

cmake -B builddir -S votca -DBUILD_XTP=ON 
-DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.so 
 -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include

The error shown in the terminal states that I do not have any 
*gromacs_version* when I have already defined the path for it in the 
command and checked that the libgromacs.so file does exist in the specified 
path. The output in the terminal:

-- Found Boost: 
/home/kimfoo/miniconda3/lib/cmake/Boost-1.74.0/BoostConfig.cmake (found 
suitable version "1.74.0", minimum required is "1.71.0") found components: 
program_options filesystem system
-- Found Python: /home/kimfoo/miniconda3/bin/python3.9 (found suitable 
version "3.9.13", minimum required is "3") found components: Interpreter
-- MKL: Thread Layer(GNU OpenMP) Interface(4-byte Integer)
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Could NOT find MKL: Source the compilervars.sh or mklvars.sh scripts 
included with your installation of MKL. This script searches for the 
libraries in MKLROOT, LIBRARY_PATHS(Linux), and LIB(Windows) environment 
variables (missing: MKL_INCLUDE_DIR)
-- Could NOT find MKL: Source the compilervars.sh or mklvars.sh scripts 
included with your installation of MKL. This script searches for the 
libraries in MKLROOT, LIBRARY_PATHS(Linux), and LIB(Windows) environment 
variables (missing: MKL_INCLUDE_DIR MKL_Core_STATIC_LINK_LIBRARY 
MKL_Interface_STATIC_LINK_LIBRARY MKL_ThreadLayer_STATIC_LINK_LIBRARY)
-- Found OpenMP_CXX: -fopenmp (found suitable version "4.5", minimum 
required is "4.5")
-- Found OpenMP: TRUE (found suitable version "4.5", minimum required is 
"4.5")
-- Found Eigen3: /home/kimfoo/miniconda3/share/eigen3/cmake
-- Checking for module 'fftw3'
--   /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or 
directory
No package 'fftw3' found
-- Found Python: /home/kimfoo/miniconda3/bin/python3.9 (found suitable 
version "3.9.13", minimum required is "3.5") found components: Interpreter
-- Found Boost: 
/home/kimfoo/miniconda3/lib/cmake/Boost-1.74.0/BoostConfig.cmake (found 
suitable version "1.74.0", minimum required is "1.71.0") found components: 
program_options filesystem system regex
-- Found Eigen3: /home/kimfoo/miniconda3/share/eigen3/cmake
-- Found VOTCA_TOOLS:
-- Checking for module 'libgromacs_d'
--   /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or 
directory
No package 'libgromacs_d' found
CMake Error at csg/CMakeModules/FindGROMACS.cmake:58 (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/kimfoo/builddir/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!
Call Stack (most recent call first):
  CMakeLists.txt:132 (_find_package)
  csg/CMakeLists.txt:80 (find_package)


-- Configuring incomplete, errors occurred!
See also "/home/kimfoo/builddir/CMakeFiles/CMakeOutput.log".
See also "/home/kimfoo/builddir/CMakeFiles/CMakeError.log".

I have attached the CMakeError.log file for reference. I checked the error 
and there are a two warnings:

/home/kimfoo/miniconda3/bin/ld: warning: libhwloc.so.15, needed by 
/usr/local/gromacs/lib/libgromacs.so, not found (try using -rpath or 
-rpath-link)
/home/kimfoo/miniconda3/bin/ld: warning: libgomp.so.1, needed by 
/usr/local/gromacs/lib/libgromacs.so, not found (try using -rpath or 
-rpath-link)

I am not sure if these are the reasons for the failure in cmake command. I 
am fairly new to cmake so any advice that you have will be greatly 
appreciated. Would you suggest that I use -DBUILD_OWN_GROMACS=ON ? However, 
the version I would like to install is the 2019 version because I find that 
the csg-tutorials can run with the 2019 version but not newer.

Thank you very much for your time.

Best regards,
Kimberly

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    arg [/lib64/ld-linux-x86-64.so.2] ==> ignore
    arg [-pie] ==> ignore
    arg [-znow] ==> ignore
    arg [-zrelro] ==> ignore
    arg [-o] ==> ignore
    arg [cmTC_45a99] ==> ignore
    arg [-L/usr/lib/gcc/x86_64-linux-gnu/7] ==> dir 
[/usr/lib/gcc/x86_64-linux-gnu/7]
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[/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu]
    arg [-L/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib] ==> dir 
[/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib]
    arg [-L/lib/x86_64-linux-gnu] ==> dir [/lib/x86_64-linux-gnu]
    arg [-L/lib/../lib] ==> dir [/lib/../lib]
    arg [-L/usr/lib/x86_64-linux-gnu] ==> dir [/usr/lib/x86_64-linux-gnu]
    arg [-L/usr/lib/../lib] ==> dir [/usr/lib/../lib]
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[/usr/lib/x86_64-linux-gnu]
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[/usr/lib]
  collapse library dir [/lib/x86_64-linux-gnu] ==> [/lib/x86_64-linux-gnu]
  collapse library dir [/lib/../lib] ==> [/lib]
  collapse library dir [/usr/lib/x86_64-linux-gnu] ==> 
[/usr/lib/x86_64-linux-gnu]
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Determining size of int passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_a5365/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_a5365.dir/build.make CMakeFiles/cmTC_a5365.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_a5365.dir/INT_SIZE.cpp.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_a5365.dir/INT_SIZE.cpp.o -c 
/home/kimfoo/builddir/CMakeFiles/CheckTypeSize/INT_SIZE.cpp
Linking CXX executable cmTC_a5365
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_a5365.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_a5365.dir/INT_SIZE.cpp.o -o cmTC_a5365 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file cassert exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_e692f/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_e692f.dir/build.make CMakeFiles/cmTC_e692f.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_e692f.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_e692f.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_e692f
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_e692f.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_e692f.dir/CheckIncludeFile.cxx.o -o cmTC_e692f 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file cmath exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_12ec0/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_12ec0.dir/build.make CMakeFiles/cmTC_12ec0.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_12ec0.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_12ec0.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_12ec0
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_12ec0.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_12ec0.dir/CheckIncludeFile.cxx.o -o cmTC_12ec0 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file fstream exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_315d7/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_315d7.dir/build.make CMakeFiles/cmTC_315d7.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_315d7.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_315d7.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_315d7
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_315d7.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_315d7.dir/CheckIncludeFile.cxx.o -o cmTC_315d7 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file functional exists passed with the following 
output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_b3236/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_b3236.dir/build.make CMakeFiles/cmTC_b3236.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_b3236.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_b3236.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_b3236
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_b3236.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_b3236.dir/CheckIncludeFile.cxx.o -o cmTC_b3236 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file iostream exists passed with the following 
output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_e0128/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_e0128.dir/build.make CMakeFiles/cmTC_e0128.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_e0128.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_e0128.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_e0128
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_e0128.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_e0128.dir/CheckIncludeFile.cxx.o -o cmTC_e0128 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file limits exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_8c34b/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_8c34b.dir/build.make CMakeFiles/cmTC_8c34b.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_8c34b.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_8c34b.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_8c34b
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_8c34b.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_8c34b.dir/CheckIncludeFile.cxx.o -o cmTC_8c34b 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file list exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_a3c91/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_a3c91.dir/build.make CMakeFiles/cmTC_a3c91.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_a3c91.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_a3c91.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_a3c91
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_a3c91.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_a3c91.dir/CheckIncludeFile.cxx.o -o cmTC_a3c91 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file map exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_9f6f2/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_9f6f2.dir/build.make CMakeFiles/cmTC_9f6f2.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_9f6f2.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_9f6f2.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_9f6f2
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_9f6f2.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_9f6f2.dir/CheckIncludeFile.cxx.o -o cmTC_9f6f2 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file ostream exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_47c0c/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_47c0c.dir/build.make CMakeFiles/cmTC_47c0c.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_47c0c.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_47c0c.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_47c0c
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_47c0c.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_47c0c.dir/CheckIncludeFile.cxx.o -o cmTC_47c0c 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file sstream exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_e1ed6/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_e1ed6.dir/build.make CMakeFiles/cmTC_e1ed6.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_e1ed6.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_e1ed6.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_e1ed6
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_e1ed6.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_e1ed6.dir/CheckIncludeFile.cxx.o -o cmTC_e1ed6 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file stack exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_cb2c6/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_cb2c6.dir/build.make CMakeFiles/cmTC_cb2c6.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_cb2c6.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_cb2c6.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_cb2c6
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_cb2c6.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_cb2c6.dir/CheckIncludeFile.cxx.o -o cmTC_cb2c6 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file stdexcept exists passed with the following 
output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_3166a/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_3166a.dir/build.make CMakeFiles/cmTC_3166a.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_3166a.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_3166a.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_3166a
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_3166a.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_3166a.dir/CheckIncludeFile.cxx.o -o cmTC_3166a 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file string exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_d96c3/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_d96c3.dir/build.make CMakeFiles/cmTC_d96c3.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_d96c3.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_d96c3.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_d96c3
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_d96c3.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_d96c3.dir/CheckIncludeFile.cxx.o -o cmTC_d96c3 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'



Determining if the include file vector exists passed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_2919d/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_2919d.dir/build.make CMakeFiles/cmTC_2919d.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_2919d.dir/CheckIncludeFile.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
-std=c++1z -o CMakeFiles/cmTC_2919d.dir/CheckIncludeFile.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
Linking CXX executable cmTC_2919d
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_2919d.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_2919d.dir/CheckIncludeFile.cxx.o -o cmTC_2919d 
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'




Performing C++ SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the 
following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_ebe29/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_ebe29.dir/build.make CMakeFiles/cmTC_ebe29.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_ebe29.dir/src.cxx.o
/usr/bin/c++ -DCMAKE_HAVE_LIBC_PTHREAD  -Wall -Wextra -Wpedantic -Wshadow 
-Wconversion -march=native  -std=c++1z -o CMakeFiles/cmTC_ebe29.dir/src.cxx.o 
-c /home/kimfoo/builddir/CMakeFiles/CMakeTmp/src.cxx
Linking CXX executable cmTC_ebe29
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_ebe29.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native  
CMakeFiles/cmTC_ebe29.dir/src.cxx.o -o cmTC_ebe29 
/home/kimfoo/miniconda3/bin/ld: CMakeFiles/cmTC_ebe29.dir/src.cxx.o: in 
function `main':
src.cxx:(.text+0x3e): undefined reference to `pthread_create'
/home/kimfoo/miniconda3/bin/ld: src.cxx:(.text+0x4a): undefined reference to 
`pthread_detach'
/home/kimfoo/miniconda3/bin/ld: src.cxx:(.text+0x56): undefined reference to 
`pthread_cancel'
/home/kimfoo/miniconda3/bin/ld: src.cxx:(.text+0x67): undefined reference to 
`pthread_join'
/home/kimfoo/miniconda3/bin/ld: src.cxx:(.text+0x7b): undefined reference to 
`pthread_atfork'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_ebe29.dir/build.make:98: recipe for target 'cmTC_ebe29' failed
make[1]: *** [cmTC_ebe29] Error 1
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Makefile:127: recipe for target 'cmTC_ebe29/fast' failed
make: *** [cmTC_ebe29/fast] Error 2


Source file was:
#include <pthread.h>

static void* test_func(void* data)
{
  return data;
}

int main(void)
{
  pthread_t thread;
  pthread_create(&thread, NULL, test_func, NULL);
  pthread_detach(thread);
  pthread_cancel(thread);
  pthread_join(thread, NULL);
  pthread_atfork(NULL, NULL, NULL);
  pthread_exit(NULL);

  return 0;
}

Determining if the function pthread_create exists in the pthreads failed with 
the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_95d44/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_95d44.dir/build.make CMakeFiles/cmTC_95d44.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_95d44.dir/CheckFunctionExists.cxx.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native 
-DCHECK_FUNCTION_EXISTS=pthread_create -std=c++1z -o 
CMakeFiles/cmTC_95d44.dir/CheckFunctionExists.cxx.o -c 
/home/kimfoo/builddir/CMakeFiles/CheckLibraryExists/CheckFunctionExists.cxx
Linking CXX executable cmTC_95d44
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_95d44.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native 
-DCHECK_FUNCTION_EXISTS=pthread_create 
CMakeFiles/cmTC_95d44.dir/CheckFunctionExists.cxx.o -o cmTC_95d44  -lpthreads 
/home/kimfoo/miniconda3/bin/ld: cannot find -lpthreads: No such file or 
directory
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_95d44.dir/build.make:98: recipe for target 'cmTC_95d44' failed
make[1]: *** [cmTC_95d44] Error 1
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Makefile:127: recipe for target 'cmTC_95d44/fast' failed
make: *** [cmTC_95d44/fast] Error 2



Determining if the function gmx_version exists in the 
/usr/local/gromacs/lib/libgromacs.so failed with the following output:
Change Dir: /home/kimfoo/builddir/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_312f3/fast && /usr/bin/make 
 -f CMakeFiles/cmTC_312f3.dir/build.make CMakeFiles/cmTC_312f3.dir/build
make[1]: Entering directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_312f3.dir/CheckFunctionExists.cpp.o
/usr/bin/c++   -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native 
-DCHECK_FUNCTION_EXISTS=gmx_version -std=c++1z -o 
CMakeFiles/cmTC_312f3.dir/CheckFunctionExists.cpp.o -c 
/home/kimfoo/votca/csg/CMakeModules/CheckFunctionExists.cpp
Linking CXX executable cmTC_312f3
/home/kimfoo/miniconda3/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_312f3.dir/link.txt --verbose=1
/usr/bin/c++  -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native 
-DCHECK_FUNCTION_EXISTS=gmx_version 
CMakeFiles/cmTC_312f3.dir/CheckFunctionExists.cpp.o -o cmTC_312f3  
-Wl,-rpath,/usr/local/gromacs/lib /usr/local/gromacs/lib/libgromacs.so 
/home/kimfoo/miniconda3/bin/ld: warning: libhwloc.so.15, needed by 
/usr/local/gromacs/lib/libgromacs.so, not found (try using -rpath or 
-rpath-link)
/home/kimfoo/miniconda3/bin/ld: warning: libgomp.so.1, needed by 
/usr/local/gromacs/lib/libgromacs.so, not found (try using -rpath or 
-rpath-link)
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_distances_get'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_critical_start@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_atomic_start@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_obj_type_is_dcache'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_barrier@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_parallel@GOMP_4.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_topology_load'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `omp_set_num_threads@OMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_loop_dynamic_next@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_ordered_end@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_get_nbobjs_by_depth'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_atomic_end@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_loop_end_nowait@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `omp_get_thread_num@OMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_topology_destroy'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_critical_end@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_ordered_start@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_topology_set_io_types_filter'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_loop_end@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: 
/home/kimfoo/miniconda3/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0:
 undefined reference to `h_errno@GLIBC_PRIVATE'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_get_type_depth'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_loop_dynamic_start@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_single_start@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_loop_ordered_static_next@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_distances_release'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `GOMP_loop_ordered_static_start@GOMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_get_obj_by_depth'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_topology_init'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `omp_get_num_procs@OMP_1.0'
/home/kimfoo/miniconda3/bin/ld: 
/home/kimfoo/miniconda3/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0:
 undefined reference to `__libc_dl_error_tsd@GLIBC_PRIVATE'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `omp_get_num_threads@OMP_1.0'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `hwloc_topology_is_thissystem'
/home/kimfoo/miniconda3/bin/ld: 
/home/kimfoo/miniconda3/bin/../x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0:
 undefined reference to `__vdso_clock_gettime@GLIBC_PRIVATE'
/home/kimfoo/miniconda3/bin/ld: /usr/local/gromacs/lib/libgromacs.so: undefined 
reference to `omp_get_max_threads@OMP_1.0'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_312f3.dir/build.make:99: recipe for target 'cmTC_312f3' failed
make[1]: *** [cmTC_312f3] Error 1
make[1]: Leaving directory '/home/kimfoo/builddir/CMakeFiles/CMakeTmp'
Makefile:127: recipe for target 'cmTC_312f3/fast' failed
make: *** [cmTC_312f3/fast] Error 2