HPX fails to build with enabled hdf5 examples

[arturas-venskus-flf]

Hi,

HPX fails to build when flag -DHPX_WITH_EXAMPLES_HDF5=On is passed to cmake.
HDF5 library is present in system and reported by cmake as found.

Best,
Arturas

[hkaiser]

@arturas-venskus-flf: Would you mind posting your cmake output and build logs, please?

[arturas-venskus-flf]

Error occurred during linking stage. From CMakeError.log: /usr/bin/ld cannot find -lpthreads
System contains libpthread.so but not libpthreads.so. Maybe somewhere is misspelled library name as stated for example here https://stackoverflow.com/questions/37967086/usr-bin-ld-cannot-find-lpthreads.

Sorry cannot post output and logs due to company's policy
Arturas

[hkaiser]

@arturas-venskus-flf: We do not add -lthreads to our build scripts anywhere. The only thing we do is to add -pthread to the compiler command line, if appropriate.

What version of cmake do you use. We've had issues with certain cmake versions before...

Also, what target failed to link for you?

[arturas-venskus-flf]

@hkaiser: CMake version is 3.5.1. Failures in CMakeError:

1. Determining if the pthread_create exist failed ... CheckSymbolsExists.c undefined reference to 'pthread_create'

2. Determining if the function pthread_create exist in the pthread failed ... CheckFunctionExists.c ... /usr/bin/ld cannot find -lpthreads

[hkaiser]

@arturas-venskus-flf from what I can see, this error message you're seeing is produced by one of the feature tests automatically generated by cmake. This should have no impact on building HPX at all as this test is invoked to figure out what library is exporting the pthread symbols on the current platform (some platforms have libthread.so, some libthreads.so).

Is this error in the cmake log the only 'indication' that something is 'wrong'?

[arturas-venskus-flf]

@hkaiser I was able to reproduce issue in my laptop. Please find error, output and cout dump files attached:
CMakeError.txt
CMakeOutput.txt
install_hpx.txt
In install_hpx.txt also other cmake errors are captured.

[hkaiser]

@arturas-venskus-flf Thanks.

Could you please provide the following additional information:

• cmake version
• gcc version
• HPX version
• cmake command line

Also, from what I can see from those logs, the -lpthreads problem you listed above is a non-issue. Something else is wrong. I also think that this issue is unrelated to enabling the HDF5 examples.

[hkaiser]

Ok, I saw now, that you're using gcc 6.2. Are those logs still generated by cmake 3.5.1?

[arturas-venskus-flf]

gcc 6.2
cmake 3.5.1 (with 3.8.2 the same issue)
HPX version 1.0.0
command: cmake -DCMAKE_CXX_FLAGS=-std=c++14 -DCMAKE_INSTALL_PREFIX=/opt/hpx_1.0.0 -DHWLOC_ROOT=/usr -DHPX_WITH_MALLOC=system -DHPX_WITH_EXAMPLES_HDF5=On /home/USER/Libs/hpx_1.0.0 | tee install_hpx.log

CMakeError.txt list problem related to lpthreads

I've succeeded to compile hpx core, tests, examples, examples with tbb, openmp. Only the problem appears when -DHPX_WITH_EXAMPLES_HDF5=On is passed to cmake, otherwise compilation is ok.

[hkaiser]

@arturas-venskus-flf Ok, thanks for this information. I think we can close this issue at this point as the HDF5 examples are massively broken in V1.0.0 anyways (I just fixed them here: #2749, if you really need them, the fixed examples should compile fine against V1.0.0 - although I have not tried it).

I'd suggest you don't use -DHPX_WITH_EXAMPLES_HDF5 with this version of HPX.

Thanks for reporting this issue! I have started start a list of known issues with V1.0.0 for others to avoid running into those problems: https://github.com/STEllAR-GROUP/hpx/wiki/Known-issues-in-HPX-V1.0.0.

Please feel free to reopen this issue if needed.