Hi Åke, Thanks, that worked perfectly.
Cheers, Loris Åke Sandgren <[email protected]> writes: > See https://github.com/easybuilders/easybuild-easyconfigs/pull/7973 for > a working PR for RDKit. > > On 4/1/19 3:05 PM, Loris Bennett wrote: >> 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]
