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Re: [moose-devel] Compile problem
|
From: Saeed S. <sa...@gn...> - 2014-05-01 19:16:49
|
Hi
It's very interesting! I did not know about Travis-CI.
Thank yoy.
BTW, Cmake in the 5338 works perfectly.
Saeed
On 05/01/2014 04:04 PM, Dilawar Singh wrote:
> Hi Saeed,
>
> Removed this error also.
>
> Also, I just made an mirror of async13 branch on github and Travis-CI for
> checking the build.
>
> http://github.com/dilawar/moose
>
> The latest commit is passing the build on Travis-CI. If a commit gets
> successfully compiled, one can see a "build/passing" image on project
> README file on github. This will help you find the stable commit on the
> branch.
>
> Commit r5340 is current stable revision.
>
> Thanks again for testing the cmake based build.
>
> Dilawar
>
> On Thu, May 01, 2014 at 03:25:18PM -0300, Saeed Shariati wrote:
>> Cmake in revision 6339 produces error which is attach.
>> My system is Ubuntu 12.04
>>
>> On 05/01/2014 03:02 PM, Dilawar Singh wrote:
>>> Thanks a lot Saeed,
>>>
>>> Libxml2 turns out to be unnecessary. It has been removed now from cmake.
>>>
>>> Removed some of the compiler flags specific to gcc-4.8. This should compile
>>> now. Moose also compiles with clang++.
>>>
>>> A couple to tests might fail on default tests enabled in cmake.
>>>
>>> Dilawar
>>>
>>> On Thu, May 01, 2014 at 11:36:56AM -0300, Saeed Shariati wrote:
>>>> Thank you Dilawar.
>>>>
>>>> The CMake build system needs also libxml2-dev package to be installed
>>>> and after executing, produce the outputs which is attached to this
>>>> email.
>>>>
>>>> On 05/01/2014 01:35 AM, Dilawar Singh wrote:
>>>>> Hi Saeed,
>>>>>
>>>>> Fixed. Added missing files.
>>>>>
>>>>> Also there is a cmake based build system. I'd be happy if you can test it on
>>>>> your system and let me know how it went. You need to install cmake and do the
>>>>> following in async branch.
>>>>>
>>>>> $ cd buildMooseUsingCmake
>>>>> $ ./build_me.sh
>>>>>
>>>>> Dilawar
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>>>> unparalleled scalability from the best Selenium testing platform available.
>>>>> Simple to use. Nothing to install. Get started now for free."
>>>>> http://p.sf.net/sfu/SauceLabs
>>>>> _______________________________________________
>>>>> moose-devel mailing list
>>>>> moo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>>>>
>>>>>
>>>> Removing any accidentally created cmake files.
>>>> -- The C compiler identification is GNU
>>>> -- The CXX compiler identification is GNU
>>>> -- Check for working C compiler: /usr/bin/gcc
>>>> -- Check for working C compiler: /usr/bin/gcc -- works
>>>> -- Detecting C compiler ABI info
>>>> -- Detecting C compiler ABI info - 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
>>>> /usr
>>>> -- Using GSL from /usr
>>>> ++ Unit testing enabled.
>>>> ++ Verbosity of output is 1
>>>> -- Found: /usr/lib/libhdf5.so
>>>> -- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
>>>> --
>>>> -- Could NOT find LIBSBML (missing: LIBSBML_LIBRARY LIBSBML_INCLUDE_DIR)
>>>> -- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so
>>>> -- Could NOT find Readline (missing: Readline_INCLUDE_DIR)
>>>> -- Found LibXML2: /usr/lib/x86_64-linux-gnu/libxml2.so
>>>> -- Found PythonInterp: /usr/bin/python (found version "2.7.3")
>>>> -- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
>>>> -- Found PythonLibs: optimized;/usr/lib/libpython2.7.so.1;debug;/usr/lib/libpython2.7.so.1 (found version "2.7")
>>>> ++ PYTHONPATH is set to /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/python
>>>> -- Configuring done
>>>> -- Generating done
>>>> -- Build files have been written to: /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/buildMooseUsingCmake
>>>> Scanning dependencies of target utility
>>>> [ 1%] Building CXX object utility/CMakeFiles/utility.dir/strutil.cpp.o
>>>> [ 1%] Building CXX object utility/CMakeFiles/utility.dir/types.cpp.o
>>>> [ 2%] Building CXX object utility/CMakeFiles/utility.dir/setupenv.cpp.o
>>>> [ 2%] Building CXX object utility/CMakeFiles/utility.dir/numutil.cpp.o
>>>> [ 3%] Building CXX object utility/CMakeFiles/utility.dir/Annotator.cpp.o
>>>> [ 4%] Building CXX object utility/CMakeFiles/utility.dir/Vec.cpp.o
>>>> Linking CXX static library libutility.a
>>>> [ 4%] Built target utility
>>>> Scanning dependencies of target debug_print
>>>> [ 4%] Building CXX object external/debug/CMakeFiles/debug_print.dir/print_function.cc.o
>>>> Linking CXX static library libdebug_print.a
>>>> [ 4%] Built target debug_print
>>>> Scanning dependencies of target biophysics
>>>> [ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeRingBuffer.cpp.o
>>>> [ 5%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynHandler.cpp.o
>>>> [ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IntFire.cpp.o
>>>> [ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Synapse.cpp.o
>>>> [ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeGen.cpp.o
>>>> [ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Compartment.cpp.o
>>>> [ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SymCompartment.cpp.o
>>>> [ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ChanBase.cpp.o
>>>> [ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannel.cpp.o
>>>> [ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate.cpp.o
>>>> [ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConc.cpp.o
>>>> [ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Neuron.cpp.o
>>>> [ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadCell.cpp.o
>>>> [ 12%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChanBase.cpp.o
>>>> [ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChan.cpp.o
>>>> [ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/testBiophysics.cpp.o
>>>> [ 14%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IzhikevichNrn.cpp.o
>>>> Linking CXX static library libbiophysics.a
>>>> [ 14%] Built target biophysics
>>>> Scanning dependencies of target basecode
>>>> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/consts.cpp.o
>>>> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/Element.cpp.o
>>>> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/DataElement.cpp.o
>>>> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/GlobalDataElement.cpp.o
>>>> [ 17%] Building CXX object basecode/CMakeFiles/basecode.dir/LocalDataElement.cpp.o
>>>> [ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Eref.cpp.o
>>>> [ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Finfo.cpp.o
>>>> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/DestFinfo.cpp.o
>>>> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o
>>>> In file included from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/header.h:17:0,
>>>> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:10:
>>>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h: In function ???std::string mapToString(const std::map<A, B>&, bool) [with A = std::basic_string<char>, B = Cinfo*, std::string = std::basic_string<char>]???:
>>>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:208:55: instantiated from here
>>>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:110:18: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare]
>>>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:112:9: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare]
>>>> At global scope:
>>>> cc1plus: error: unrecognized command line option "-Wno-unused-private-field" [-Werror]
>>>> cc1plus: error: unrecognized command line option "-Wno-return-type-c-linkage" [-Werror]
>>>> cc1plus: all warnings being treated as errors
>>>> make[2]: *** [basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o] Error 1
>>>> make[1]: *** [basecode/CMakeFiles/basecode.dir/all] Error 2
>>>> make: *** [all] Error 2
>>>> ------------------------------------------------------------------------------
>>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>>> unparalleled scalability from the best Selenium testing platform available.
>>>> Simple to use. Nothing to install. Get started now for free."
>>>> http://p.sf.net/sfu/SauceLabs
>>>> _______________________________________________
>>>> moose-devel mailing list
>>>> moo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>> ------------------------------------------------------------------------------
>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>> unparalleled scalability from the best Selenium testing platform available.
>>> Simple to use. Nothing to install. Get started now for free."
>>> http://p.sf.net/sfu/SauceLabs
>>> _______________________________________________
>>> moose-devel mailing list
>>> moo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>>
>>>
>> Removing any accidentally created cmake files.
>> -- The C compiler identification is GNU
>> -- The CXX compiler identification is GNU
>> -- Check for working C compiler: /usr/bin/gcc
>> -- Check for working C compiler: /usr/bin/gcc -- works
>> -- Detecting C compiler ABI info
>> -- Detecting C compiler ABI info - 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
>> /usr
>> -- Using GSL from /usr
>> ++ Unit testing enabled.
>> ++ Verbosity of output is 1
>> -- Found: /usr/lib/libhdf5.so
>> -- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
>> --
>> -- Could NOT find LIBSBML (missing: LIBSBML_LIBRARY LIBSBML_INCLUDE_DIR)
>> -- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so
>> -- Could NOT find Readline (missing: Readline_INCLUDE_DIR)
>> -- Found PythonInterp: /usr/bin/python (found version "2.7.3")
>> -- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
>> -- Found PythonLibs: optimized;/usr/lib/libpython2.7.so.1;debug;/usr/lib/libpython2.7.so.1 (found version "2.7")
>> ++ PYTHONPATH is set to /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/python
>> -- Configuring done
>> -- Generating done
>> -- Build files have been written to: /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/buildMooseUsingCmake
>> Scanning dependencies of target debug_print
>> [ 0%] Building CXX object external/debug/CMakeFiles/debug_print.dir/print_function.cc.o
>> Linking CXX static library libdebug_print.a
>> [ 0%] Built target debug_print
>> Scanning dependencies of target biophysics
>> [ 0%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeRingBuffer.cpp.o
>> [ 1%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynHandler.cpp.o
>> [ 2%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IntFire.cpp.o
>> [ 2%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Synapse.cpp.o
>> [ 3%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeGen.cpp.o
>> [ 3%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Compartment.cpp.o
>> [ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SymCompartment.cpp.o
>> [ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ChanBase.cpp.o
>> [ 5%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannel.cpp.o
>> [ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate.cpp.o
>> [ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConc.cpp.o
>> [ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Neuron.cpp.o
>> [ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadCell.cpp.o
>> [ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChanBase.cpp.o
>> [ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChan.cpp.o
>> [ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/testBiophysics.cpp.o
>> [ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IzhikevichNrn.cpp.o
>> Linking CXX static library libbiophysics.a
>> [ 10%] Built target biophysics
>> Scanning dependencies of target basecode
>> [ 11%] Building CXX object basecode/CMakeFiles/basecode.dir/consts.cpp.o
>> [ 11%] Building CXX object basecode/CMakeFiles/basecode.dir/Element.cpp.o
>> [ 12%] Building CXX object basecode/CMakeFiles/basecode.dir/DataElement.cpp.o
>> [ 12%] Building CXX object basecode/CMakeFiles/basecode.dir/GlobalDataElement.cpp.o
>> [ 13%] Building CXX object basecode/CMakeFiles/basecode.dir/LocalDataElement.cpp.o
>> [ 14%] Building CXX object basecode/CMakeFiles/basecode.dir/Eref.cpp.o
>> [ 14%] Building CXX object basecode/CMakeFiles/basecode.dir/Finfo.cpp.o
>> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/DestFinfo.cpp.o
>> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o
>> In file included from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/header.h:17:0,
>> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:10:
>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h: In function ???std::string mapToString(const std::map<A, B>&, bool) [with A = std::basic_string<char>, B = Cinfo*, std::string = std::basic_string<char>]???:
>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:208:55: instantiated from here
>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:110:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:112:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
>> At global scope:
>> cc1plus: warning: unrecognized command line option "-Wno-unused-private-field" [enabled by default]
>> cc1plus: warning: unrecognized command line option "-Wno-return-type-c-linkage" [enabled by default]
>> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/SrcFinfo.cpp.o
>> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/ValueFinfo.cpp.o
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>> [ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/FieldElement.cpp.o
>> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/Id.cpp.o
>> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/PrepackedBuffer.cpp.o
>> [ 20%] Building CXX object basecode/CMakeFiles/basecode.dir/ObjId.cpp.o
>> [ 21%] Building CXX object basecode/CMakeFiles/basecode.dir/global.cpp.o
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>> [ 24%] Building CXX object basecode/CMakeFiles/basecode.dir/doubleEq.cpp.o
>> [ 25%] Building CXX object basecode/CMakeFiles/basecode.dir/testAsync.cpp.o
>> Linking CXX static library libbasecode.a
>> [ 25%] Built target basecode
>> Scanning dependencies of target kinetics
>> [ 26%] Building CXX object kinetics/CMakeFiles/kinetics.dir/PoolBase.cpp.o
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>> [ 31%] Building CXX object kinetics/CMakeFiles/kinetics.dir/MMenz.cpp.o
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>> [ 37%] Building CXX object kinetics/CMakeFiles/kinetics.dir/lookupVolumeFromMesh.cpp.o
>> [ 37%] Building CXX object kinetics/CMakeFiles/kinetics.dir/testKinetics.cpp.o
>> Linking CXX static library libkinetics.a
>> [ 37%] Built target kinetics
>> Scanning dependencies of target randnum
>> [ 38%] Building CXX object randnum/CMakeFiles/randnum.dir/mt19937ar.cpp.o
>> Linking CXX static library librandnum.a
>> [ 38%] Built target randnum
>> Scanning dependencies of target msg
>> [ 39%] Building CXX object msg/CMakeFiles/msg.dir/Msg.cpp.o
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>> Linking CXX static library libutility.a
>> [ 47%] Built target utility
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>> [ 48%] Building CXX object pymoose/CMakeFiles/moosepython.dir/vec.cpp.o
>> [ 48%] Building CXX object pymoose/CMakeFiles/moosepython.dir/mfield.cpp.o
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>> [ 50%] Building CXX object pymoose/CMakeFiles/moosepython.dir/test_moosemodule.cpp.o
>> In file included from /usr/include/python2.7/Python.h:8:0,
>> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/pymoose/test_moosemodule.cpp:49:
>> /usr/include/python2.7/pyconfig.h:1161:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
>> /usr/include/features.h:164:0: note: this is the location of the previous definition
>> /usr/include/python2.7/pyconfig.h:1183:0: warning: "_XOPEN_SOURCE" redefined [enabled by default]
>> /usr/include/features.h:166:0: note: this is the location of the previous definition
>> cc1plus: warning: unrecognized command line option "-Wno-unused-private-field" [enabled by default]
>> cc1plus: warning: unrecognized command line option "-Wno-return-type-c-linkage" [enabled by default]
>> Linking CXX static library libmoosepython.a
>> [ 50%] Built target moosepython
>> Scanning dependencies of target shell
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>> Linking CXX static library libshell.a
>> [ 54%] Built target shell
>> Scanning dependencies of target scheduling
>> [ 54%] Building CXX object scheduling/CMakeFiles/scheduling.dir/testScheduling.cpp.o
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>> Linking CXX static library libscheduling.a
>> [ 55%] Built target scheduling
>> Scanning dependencies of target moose_builtins
>> [ 55%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Arith.cpp.o
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>> Linking CXX static library libmoose_builtins.a
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>> pymoose/libmoosepython.a(vec.cpp.o): could not read symbols: Bad value
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>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> moose-devel mailing list
>> moo...@li...
>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos. Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> moose-devel mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-devel
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