[Users] Update on compilation: Problem in linking with "pthread_atfork"

[Erik Schnetter]

You can change the configuration variable LIBS to include "pthread" (without the "-l"). This should make things work. The underlying problem is with thorn MPI; thorn MPI should include the pthread library automatically. Can you open a ticket, and post your configuration options there?

-erik

> On Feb 9, 2015, at 15:25 , Islam, Tanzima <islam3 at llnl.gov> wrote:
> 
> Hi All,
>  Slight update: Instead of using sim, I used gmake <config> name to build the executable. Seems like this time
> I configured my compilers correctly, so that everything built without a problem. However, the last task of
> linking everything to build the executable failed: because it could not link to libpthread, I am assuming.
> 
> I could not find the file where linking step is included. Could I specify -lpthread manually there?
> -----------------------------------------------------------------------------------------------------------
> Creating cactus_cab in /p/lscratche/islam3/Apps/Cactus/exe from ExternalLibraries/BLAS CactusBase/Boundary CactusBase/CartGrid3D CactusNumerical/Cartoon2D CactusBase/CoordBase CactusDoc/CoreDoc CactusExamples/DemoInterp CactusNumerical/Dissipation CactusElliptic/EllBase CactusElliptic/EllSOR ExternalLibraries/F5 ExternalLibraries/FFTW3 CactusExamples/FleshInfo CactusUtils/Formaline CactusBase/Fortran ExternalLibraries/GSL ExternalLibraries/HDF5 CactusConnect/HTTPD CactusConnect/HTTPDExtra CactusExamples/HelloWorld CactusWave/IDScalarWave  CactusWave/IDScalarWaveC CactusWave/IDScalarWaveCXX CactusWave/IDScalarWaveElliptic CactusExamples/IDWaveMoL CactusBase/IOASCII CactusBase/IOBasic CactusPUGHIO/IOHDF5 CactusPUGHIO/IOHDF5Util CactusIO/IOJpeg CactusBase/IOUtil CactusBase/InitBase CactusNumerical/InterpToArray ExternalLibraries/LAPACK CactusNumerical/LocalInterp CactusNumerical/LocalReduce ExternalLibraries/MPI CactusNumerical/MoL CactusUtils/NaNChecker CactusUtils/Nice CactusUtils/NoMPI CactusNumerical/Noise CactusNumerical/Norms ExternalLibraries/OpenSSL CactusPUGH/PUGH CactusPUGH/PUGHInterp CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusNumerical/Periodic CactusNumerical/ReflectionSymmetry CactusNumerical/RotatingSymmetry180 CactusNumerical/RotatingSymmetry90 CactusExamples/SampleBoundary CactusExamples/SampleIO CactusNumerical/Slab CactusNumerical/SlabTest CactusConnect/Socket CactusNumerical/SpaceMask CactusNumerical/SphericalSurface CactusBase/SymBase TAT/TATelliptic CactusUtils/TerminationTrigger CactusTest/TestArrays CactusTest/TestComplex CactusTest/TestCoordinates CactusTest/TestFortranCrayPointers CactusTest/TestFortranDependencies1 CactusTest/TestFortranDependencies2 CactusTest/TestFpointerNULL CactusTest/TestFreeF90 CactusTest/TestGlobalReduce CactusTest/TestInclude1 CactusTest/TestInclude2 CactusTest/TestLocalReduce CactusTest/TestLoop CactusTest/TestPar CactusTest/TestReduce CactusTest/TestSchedule CactusTest/TestStrings CactusTest/TestTable CactusTest/TestTimers CactusTest/TestTypes CactusBase/Time CactusExamples/TimerInfo CactusUtils/TimerReport CactusWave/WaveBinarySource CactusExamples/WaveMoL CactusExamples/WaveToy1DF77 CactusExamples/WaveToy2DF77 CactusWave/WaveToyC CactusWave/WaveToyCXX CactusWave/WaveToyExtra CactusWave/WaveToyF77 CactusWave/WaveToyF90 CactusWave/WaveToyFreeF90 ExternalLibraries/curl ExternalLibraries/flickcurl ExternalLibraries/git ExternalLibraries/hwloc ExternalLibraries/libjpeg ExternalLibraries/libpng ExternalLibraries/libxml2 ExternalLibraries/lua ExternalLibraries/zlib
> userApps/Cactus/configs/cab/scratch/external/MPI/lib/libmpi.a(ompi_mpi_init.o): In function `ompi_warn_fork':
> ompi_mpi_init.c:(.text+0xf4a): undefined reference to `pthread_atfork'
> collect2: ld returned 1 exit status
> gmake[1]: *** [/p/lscratche/islam3/Apps/Cactus/exe/cactus_cab] Error 1
> gmake: *** [cab] Error 2
> -----------------------------------------------------------------------------------------------------------
> 
> Thanks!
> --Tanzima
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--
Erik Schnetter <schnetter at cct.lsu.edu>
http://www.perimeterinstitute.ca/personal/eschnetter/

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