>>>> [Errno 2] No such file or directory: '/home/d04/d04/s0676011/.python26_compiled' <<<<< >>>> [Errno 2] No such file or directory: '/home/d04/d04/s0676011' <<<<< >>>> [Errno 2] No such file or directory: '/home/d04/d04' <<<<< >>>> [Errno 17] File exists: '/home/d04' <<<<< Traceback (most recent call last): File "/var/spool/alps/1009053/topographica_mpi", line 15, in <module> process_argv(argv[1:]) File "/esfs2/d04/d04/s0676011/topographica/topo/misc/commandline.py", line 474, in process_argv execfile(filename,__main__.__dict__) File "examples/matchmodel.ty", line 23, in <module> from topo import transferfn,pattern,projection,responsefn,learningfn,sheet,numbergen File "/esfs2/d04/d04/s0676011/topographica/topo/transferfn/__init__.py", line 25, in <module> from basic import a1.out bin but c_activity.out ChangeLog.txt compare_arrays.py contrib COPYING.txt cp.pbs cp.pbs~ cp.pbs.o321605 create_topographica_script.py c_timings.xml c_vs_python.sh debian demo doc draw_graph.py etc examples experiment.py external filename hostfile images include info ld_preload lib Makefile #Makefile# man matplotlib-bug.o mpi_experiments mpitest.py param parsetime.py README.txt results.pickle setup_app.py setup_exe.py setup_ez.py _setup.py setup.py share test_scripts timed_topographica.sh topo topographica topographica_mpi useful_info File "/esfs2/d04/d04/s0676011/topographica/topo/transferfn/basic.py", line 31, in <module> from topo.base.patterngenerator import PatternGenerator,Constant File "/esfs2/d04/d04/s0676011/topographica/topo/base/patterngenerator.py", line 238, in <module> from topo.misc.inlinec import inline,c_header File "/esfs2/d04/d04/s0676011/topographica/topo/misc/inlinec.py", line 59, in <module> import weave File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/__init__.py", line 9, in <module> from blitz_tools import blitz File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/blitz_tools.py", line 11, in <module> import inline_tools File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/inline_tools.py", line 15, in <module> function_catalog = catalog.catalog() File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/catalog.py", line 351, in __init__ sys.path.append(default_dir()) File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/catalog.py", line 202, in default_dir create_dir(path) File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/catalog.py", line 128, in create_dir create_dir(base) File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/catalog.py", line 128, in create_dir create_dir(base) File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/catalog.py", line 128, in create_dir create_dir(base) File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/catalog.py", line 131, in create_dir os.mkdir(p) OSError: [Errno 17] File exists: '/home/d04'
Thursday, 4 August 2011
the full error output
messages between these ">>>>>" "<<<<<" are printed exceptions that break execution, I added the print statements into weave/catalog.py:
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I think that you may be able to fix this stuff by building topographica in /work rather than /home to start with. If you do your full build of topographica in /work/d04/d04/s0676011/ then it should get round the problem as /work is completely visible from the backend of HECToR.
ReplyDeleteYou will probably need to do:
export HOME=/work/d04/d04/s0676011
before you build topographica too to ensure that it doesn't create stuff in /home still.
adrianj
i'll definitely try it, but I'm starting to have doubts that it's because of access rights.
ReplyDeleteIt's not access rights that are the problem on /home it's the fact that the whole /home file system is not visible from the backend (i.e. anything in your submissions scripts that is run using aprun). Only /work is mounted on the backend, they are two separate file systems.
ReplyDeleteactually, this way it totally makes sense that my C app creates the xml file without a problem: it creates it in the current directory, i.e. without specifying the absolute path, while python's libraries do use absolute paths. I've just submitted a job from the /work/d04/... topographica directory, waiting for results...
ReplyDeleteok, it runs, although it takes a bit long to complete for the parameters I've set...
ReplyDeleteit worked, thanks for the advice!
ReplyDelete