Hi All, When I build Python + numpy with lmod disabled, it builds correctly. It looks like a problem building python (with extensions) with lmod enabled.
Thanks, Cormac. On Wed, Dec 18, 2013 at 5:17 PM, Garvey, Cormac T <[email protected]>wrote: > > Also, note when I build numpy as a separate module, it builds correctly. > > numpy easyconfig > > > name = 'numpy' > version = '1.7.1' > python = 'Python' > pyver = '2.7.5' > versionsuffix = '-%s-%s' % (python, pyver) > > homepage = 'http://www.numpy.org' > description = """NumPy is the fundamental package for scientific computing > with Python. It contains among other things: > a powerful N-dimensional array object, sophisticated (broadcasting) > functions, tools for integrating C/C++ and Fortran > code, useful linear algebra, Fourier transform, and random number > capabilities. Besides its obvious scientific uses, > NumPy can also be used as an efficient multi-dimensional container of > generic data. Arbitrary data-types can be > defined. This allows NumPy to seamlessly and speedily integrate with a > wide variety of databases.""" > > > toolchain = {'name': 'gnupack', 'version': '1.1.1'} > > source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % > version, 'download')] > sources = ['%s-%s.tar.gz' % (name, version)] > > nose = 'nose' > nosever = '1.3.0' > > builddependencies = [ > (nose,nosever,'-%s-%s' % (python,pyver)), > ] > > dependencies = [ > (python, pyver), > ] > > moduleclass = 'math' > > > > Thanks, > Cormac. > > > > On Wed, Dec 18, 2013 at 4:17 PM, Garvey, Cormac T > <[email protected]>wrote: > >> >> Hi All, >> I am having some difficult build python 2.7.5 with Easybuild 1.9.0 + lmod >> >> My easyconfig file looks like >> >> name = 'Python' >> version = '2.7.5' >> >> homepage = 'http://python.org/' >> description = "Python is a programming language that lets you work more >> quickly and integrate your systems more effectively." >> >> toolchain = {'name': 'gnupack', 'version': '1.1.1'} >> toolchainopts = {'pic': True, 'opt': True, 'optarch': True} >> >> numpyversion = '1.7.1' >> >> source_urls = ['http://www.python.org/ftp/%s/%s/' % (name.lower(), >> version)] >> sources = ['%s-%s.tgz' % (name, version)] >> >> patches = ['python-%(version)s_libffi_int128_icc.patch'] >> >> exts_list = [ >> ('nose', '1.3.0', { >> 'source_urls': ['http://pypi.python.org/packages/source/n/nose/' >> ], >> }), >> ('numpy', numpyversion, { >> 'source_urls': [(' >> http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, >> 'download')], >> 'patches': [ >> 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, >> 'numpy-iqacml.patch', >> ], >> }), >> ] >> >> moduleclass = 'lang' >> >> >> >> With debugging turned on (EASYBUILD_DEBUG=1), I get an error building the >> module numpy. >> >> == 2013-12-18 14:39:49,745 main.filetools WARNING Found 5 errors in >> command output (output: collect2: error: ld returned 1 exit status, >> collect2: error: ld returned 1 exit status, collect2: error: ld returned 1 >> exit status, collect2: error: ld returned 1 exit status, collect2: error: >> ld returned 1 exit status) >> == 2013-12-18 14:39:49,745 main.environment INFO Environment variable >> PYTHONPATH set to >> /hpc-common/software/easybuild/inl-easyconfigs:/hpc-common/software/easybuild/1.9.0/gcc/opt/lib/python2.7/site-packages >> == 2013-12-18 14:39:50,759 main.filetools INFO Path >> /apps/local/easybuild/build/Python/2.7.5/gnupack-1.1.1/numpy successfully >> removed. >> == 2013-12-18 14:39:50,761 main.Lmod INFO $MODULEPATH set based on list >> of module paths: >> /tmp/tmpT3IMq2/all:/apps/local/easybuild/modules/all:/apps/local/modules/modulefiles:/apps/projects/modules/modulefiles:/apps/local/modules/modulefiles/Linux:/apps/local/modules/modulefiles/Core >> == 2013-12-18 14:39:50,762 main.filetools INFO Command lmod found at >> /apps/projects/lmod/5.2/gcc-4.5.1/opt/lmod/lmod/libexec/lmod >> == 2013-12-18 14:39:50,762 main.Lmod INFO Full path for module command is >> /apps/projects/lmod/5.2/gcc-4.5.1/opt/lmod/lmod/libexec/lmod, so using it >> == 2013-12-18 14:39:50,763 main.Lmod ERROR EasyBuild crashed with an >> error (at >> easybuild/1.9.0/gcc/opt/lib/python2.7/site-packages/easybuild/tools/modules.py:625 >> in __init__): Failed to check Lmod version: [Errno 2] No such file or >> directory >> >> The exception is occurring at the line below (file modules.py, function >> run_module), when it tries to execute os.getcwd()? >> >> self.log.debug("Running module command '%s' from %s" % (' '.join(cmdlist >> + args), os.getcwd())) >> >> >> When I turn debugging-off >> >> I get the following error >> >> == 2013-12-18 16:13:28,127 main.filetools WARNING Found 5 errors in >> command output (output: collect2: error: ld returned 1 exit status, >> collect2: error: ld returned 1 exit status, collect2: error: ld returned 1 >> exit status, collect2: error: ld returned 1 exit status, collect2: error: >> ld returned 1 exit status) >> == 2013-12-18 16:13:28,128 main.environment INFO Environment variable >> PYTHONPATH set to >> /hpc-common/software/easybuild/inl-easyconfigs:/hpc-common/software/easybuild/1.9.0/gcc/opt/lib/python2.7/site-packages >> == 2013-12-18 16:13:29,178 main.filetools INFO Path >> /apps/local/easybuild/build/Python/2.7.5/gnupack-1.1.1/numpy successfully >> removed. >> == 2013-12-18 16:13:29,181 main.Lmod INFO $MODULEPATH set based on list >> of module paths: >> /tmp/tmpv_sTqF/all:/apps/local/easybuild/modules/all:/apps/local/modules/modulefiles:/apps/projects/modules/modulefiles:/apps/local/modules/modulefiles/Linux:/apps/local/modules/modulefiles/Core >> == 2013-12-18 16:13:29,182 main.filetools INFO Command lmod found at >> /apps/projects/lmod/5.2/gcc-4.5.1/opt/lmod/lmod/libexec/lmod >> == 2013-12-18 16:13:29,182 main.Lmod INFO Full path for module command is >> /apps/projects/lmod/5.2/gcc-4.5.1/opt/lmod/lmod/libexec/lmod, so using it >> == 2013-12-18 16:13:29,182 main.Lmod INFO Before module update >> == 2013-12-18 16:13:29,269 main.Lmod INFO After module update >> == 2013-12-18 16:13:29,270 main.Lmod INFO After tempfile >> == 2013-12-18 16:13:29,270 main.Lmod INFO Before open >> == 2013-12-18 16:13:29,270 main.Lmod INFO After open >> == 2013-12-18 16:13:29,355 main.Lmod INFO After subprocess >> == 2013-12-18 16:13:29,356 main.Lmod INFO After open >> == 2013-12-18 16:13:29,356 main.Lmod INFO After read >> == 2013-12-18 16:13:29,356 main.Lmod INFO lmod help output: >> /apps/projects/lua/5.1.4.5/gcc-4.5.1/opt/bin/lua: >> ...gcc-4.5.1/opt/lmod/lmod/libexec/../tools/fileOps.lua:295: bad argument >> #1 to 'chdir' (string expected, got nil) >> stack traceback: >> [C]: in function 'chdir' >> ...gcc-4.5.1/opt/lmod/lmod/libexec/../tools/fileOps.lua:295: in >> function 'abspath' >> ...s/lmod/5.2/gcc-4.5.1/opt/lmod/lmod/libexec/utils.lua:427: in >> function 'readRC' >> ...ojects/lmod/5.2/gcc-4.5.1/opt/lmod/lmod/libexec/lmod:472: in >> function 'main' >> ...ojects/lmod/5.2/gcc-4.5.1/opt/lmod/lmod/libexec/lmod:618: in >> main chunk >> [C]: ? >> >> >> Any suggestions? >> >> Thanks, >> Cormac. >> > > > > -- > Cormac Garvey > HPC Software Consultant > Scientific Computing > Idaho National Laboratory > Ph: 208-526-6294 > > -- Cormac Garvey HPC Software Consultant Scientific Computing Idaho National Laboratory Ph: 208-526-6294
