Hi Cormac, Sorry for not answering this earlier...
I'll try and reproduce this behavior to see what the problem is. It seems that Lmod is being called from a non-existing directory, which it doesn't like... Shouldn't be too hard to fix, I expect (if I can track down where this is happening exactly). Which Lmod version are you using here? The latest Lmod v5.2? regards, Kenneth On 23 Dec 2013, at 17:31, Garvey, Cormac T wrote: > 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 >
