Hi, I am trying to write an easyconfig for RDKit (http://rdkit.org/) using the easyblock CMakePythonPackage:
###################################################################### easyblock = 'CMakePythonPackage' name = 'RDKit' version = '2018.09.3' homepage = 'http://rdkit.org' description = "Open-Source Cheminformatics Software" toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://www.github.com/rdkit/rdkit/archive/'] sources = ['Release_%s.zip' % (version.replace('.','_'))] builddependencies = [ ('CMake', '3.12.1'), ('Boost', '1.67.0'), ] dependencies = [ ('Python', '3.6.6'), ] sanity_check_paths = { } modextravars = {'RDKit': '%(installdir)s', 'RDBASE': '%(installdir)s/share/RDKit', 'LD_LIBRARY_PATH': '%(installdir)s/lib', 'PYTHONPATH': '%(installdir)/lib64/python2.6/site-packages', } moduleclass = 'chem' ###################################################################### The configure step seems to find pthread_create: -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE but the build step fails because 'pthread_create' isn't found: /trinity/shared/easybuild/software/CMake/3.12.1-GCCcore-7.3.0/bin/cmake -E cmake_link_script CMakeFiles/cmTC_4be86.dir/link.txt --verbose=1 /trinity/shared/easybuild/software/GCCcore/7.3.0/bin/gcc -O2 -ftree-vectorize -march=native -fno-math-errno -L/trinity/shared/easybuild/software/GCCcore/7.3.0/lib64 -L/trinity/shared/easybuild/software/GCCcore/7.3.0/lib -L/trinity/shared/easybuild/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib -L/trinity/shared/easybuild/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib -L/trinity/shared/easybuild/software/FFTW/3.3.8-gompi-2018b/lib -L/trinity/shared/easybuild/software/Python/3.6.6-foss-2018b/lib -L/trinity/shared/easybuild/software/Boost/1.67.0-foss-2018b/lib -rdynamic CMakeFiles/cmTC_4be86.dir/CheckSymbolExists.c.o -o cmTC_4be86 CMakeFiles/cmTC_4be86.dir/CheckSymbolExists.c.o:CheckSymbolExists.c:function main: error: undefined reference to 'pthread_create' collect2: error: ld returned 1 exit status Any ideas? Cheers, Loris PS: Is CMakePythonPackage the right easyblock? There don't seem to be any easyconfigs which use it. -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email [email protected]
