Hi Cormac, On 23 Dec 2013, at 18:37, Garvey, Cormac T wrote:
> Hi Kenneth > No problem, sorry for pulling you away from other tasks. > > Yes, I am using lmod 5.2 I've tried to reproduce your problem on my end, but no luck, the build is working fine for me even if I use Lmod. I'm using EasyBuild v1.9.0 and Lmod v5.2 as well. Can you please provide a full debug log of the failing Python + numpy build (just gzip the raw log file, and include it as attachment in reply, should be small enough)? I'm missing some context to figure out what's going on, a full debug log should help a lot. The first log message you showed (see below) tells me more is going on before the part you pasted, i.e. the real problem is happening earlier... > == 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) regards, Kenneth > > Merry Christmas, > Cormac. > > > On Mon, Dec 23, 2013 at 10:33 AM, Kenneth Hoste <[email protected]> > wrote: > 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 > > > > > > > -- > Cormac Garvey > HPC Software Consultant > Scientific Computing > Idaho National Laboratory > Ph: 208-526-6294 >
