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Error building NLopt-2.6.1-GCCcore-8.3.0.eb #9801

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verdurin opened this issue Jan 30, 2020 · 5 comments
Open

Error building NLopt-2.6.1-GCCcore-8.3.0.eb #9801

verdurin opened this issue Jan 30, 2020 · 5 comments
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@verdurin
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-- Found PythonInterp: /bin/python (found version "2.7.5")
-- Found PythonLibs: //lib64/libpython2.7.so (found version "2.7.5")
-- Found NumPy: version "1.7.1" /usr/lib64/python2.7/site-packages/numpy/core/include
-- Could NOT find Guile (missing: GUILE_EXECUTABLE GUILE_ROOT_DIR GUILE_INCLUDE_DIRS GUILE_LIBRARIES)
-- Found SWIG: /bin/swig (found version "2.0.10")
-- Performing Test UNDEFINED_SYMBOLS_ALLOWED - Success
-- Found Octave: /usr/bin/octave (found version "3.8.2")
-- Could NOT find Matlab (missing: Matlab_INCLUDE_DIRS Matlab_MEX_LIBRARY Matlab_MEX_EXTENSION Matlab_ROOT_DIR Matlab_MX_LIBRARY MX_LIBRARY) (found version "NOTFOUND")
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
OCTAVE_INCLUDE_DIR (ADVANCED)
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave
   used as include directory in directory /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/src/octave

-- Configuring incomplete, errors occurred!
See also "/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeOutput.log".
See also "/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeError.log".
 (at easybuild/tools/run.py:529 in parse_cmd_output)

This is a CentOS 7.6 node with EB 4.1.1. I'm trying to build R-3.6.2.

@verdurin
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CMakeErrorLog:

Performing C SOURCE FILE Test HAVE_THREAD_LOCAL_STORAGE failed with the following output:
Change Dir: /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp

Run Build Command(s):/bin/gmake cmTC_accda/fast && /bin/gmake -f CMakeFiles/cmTC_accda.dir/build.make CMakeFiles/cmTC_accda.dir/build
gmake[1]: Entering directory `/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_accda.dir/src.c.o
/apps/eb/skylake/software/GCCcore/8.3.0/bin/gcc   -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -DHAVE_THREAD_LOCAL_STORAGE   -o CMakeFiles/cmTC_accda.dir/src.c.o   -c /dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp/src.c
/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp/src.c:2:5: warning: return type defaults to 'int' [-Wimplicit-int]
     __declspec(thread) int tls;
     ^~~~~~~~~~
/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp/src.c: In function '__declspec':
/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp/src.c:4:20: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token
     int main(void) {
                    ^
/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp/src.c:2:5: warning: type of 'thread' defaults to 'int' [-Wimplicit-int]
     __declspec(thread) int tls;
     ^~~~~~~~~~
/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp/src.c:2:28: error: declaration for parameter 'tls' but no such parameter
     __declspec(thread) int tls;
                            ^~~
/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp/src.c:6: error: expected '{' at end of input
     }

gmake[1]: *** [CMakeFiles/cmTC_accda.dir/src.c.o] Error 1
gmake[1]: Leaving directory `/dev/shm/NLopt/2.6.1/GCCcore-8.3.0/nlopt-2.6.1/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_accda/fast] Error 2


Source file was:

    __declspec(thread) int tls;

    int main(void) {
        return 0;
    }

@verdurin
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octave-3.8.2-20.el7.x86_64 is installed on the build node.

@verdurin
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Build succeeds on a VM without octave.

@Flamefire
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Bug is caused by a broken FindOctave script: stevengj/nlopt#314

@Flamefire
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Fixed by them for their next release. Still: Probably best to create an EasyBlock to set ALL of https://github.com/stevengj/nlopt/blob/master/CMakeLists.txt#L43-L47 depending on whether they are actual dependencies

@boegel boegel added this to the 4.x milestone Feb 5, 2020
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