Dear human named Loris, Please consider using the easyconfig file for RDKit that my owner @boegel shared through the central easyconfigs repository on GitHub last week: https://github.com/easybuilders/easybuild-easyconfigs/pull/7973/files .
The CMakePythonPackage easyblock is a poor fit here, since the RDKit developers recommend using "cmake - make - make install" (see https://github.com/rdkit/rdkit/blob/master/Docs/Book/Install.md#building-the-rdkit), while CMakePythonPackage using "python setup.py install" (or "pip install"). @boegelbot (version 20190401) On Mon, Apr 1, 2019 at 3:07 PM Loris Bennett <loris.benn...@fu-berlin.de> 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 loris.benn...@fu-berlin.de >
