cannot run on gordon

[haoyuanchen]

Died in the preparation step, before generating running CUs.

repex version: 0.2-feature-tuu-opt5-d2eb6bc- rp version: 0.35 fresh env, fresh install agent.err:

intel/2013.1.117(49):ERROR:105: Unable to locate a modulefile for 'mkl' % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed ^M 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0^M 32 1957k 32 639k 0 0 1498k 0 0:00:01 --:--:-- 0:00:01 3401k^M100 1957k 100 1957k 0 0 4104k 0 --:--:-- --:--:-- --:--:-- 8224k no previously-included directories found matching 'libcloud/test/secrets.py' Python 2.7.9 Traceback (most recent call last): File "", line 1, in File "/home/chen1990/.local/lib/python2.6/site-packages/saga_python-0.14-py2.6.egg/saga/init.py", line 47, in short_version, long_version, branch = ru.get_version ([root, pwd]) ValueError: too many values to unpack

end of agent.out:

(/home/chen1990/radical.pilot.sandbox/ve_gordon/bin/python) PYTHONPATH: /home/chen1990/radical.pilot.sandbox/rp.session.prot-55-247.rutgers.edu.haoyuan.016693.0002-pilot.0000/rp_install/lib/python2.7/site-packages:::/home/chen1990/.local/lib/python2.6/site-packages utils : 0.35 /home/chen1990/radical.pilot.sandbox/rp.session.prot-55-247.rutgers.edu.haoyuan.016693.0002-pilot.0000/rp_install/lib/python2.7/site-packages/radical/utils/init.pyc saga : install failed! ESC[HESC[J

[andre-merzky]

can you please make sure that you also use 0.35 for saga-python and radical.utils? Please let us know if the problem persists!

[haoyuanchen]

Hi Andre,

"sagapython-version" returns "0.35". For radical.utils I didn't see the version command but I think it should be 0.35 too because I uninstalled everything before I re-installed them and tried to run RepEx.

Thanks!

[andre-merzky]

Sorry, I should have seen this before, but it says right in your log:

/home/chen1990/.local/lib/python2.6/site-packages/saga_python-0.14-py2.6.egg/saga/init.py

If saga reports 0.35, then there must be a mixup at runtime, because that looks like 0.14. Maybe there is an old version lingering?

[haoyuanchen]

I just did "locate saga" and yes, there're lots of old versions existing, including 0.13, 0.14, 0.18...So how can I make sure that everything that uses saga will use the newest version? I can physically remove all the old ones but I guess it's gonna fail to find saga and crash. I'll try anyway.

[andre-merzky]

We usually recommend to start with a fresh virtualenv, like this:

virtualenv $HOME/ve
source $HOME/ve/bin/activate
pip install --upgrade radical.pilot

That basically creates a local python installation in $HOME/ve and installs the modules in there. The source line activates that environment -- which python should show that it is being used. If you want to uninstall the modules, you can run:

source $HOME/ve/bin/activate
pip uninstall -y radical.pilot
pip uninstall -y saga-python
pip uninstall -y radical.utils
pip install --upgrade radical.pilot

updating to a new release would be:

source $HOME/ve/bin/activate
pip install --upgrade radical.pilot

and at any time you can just remove the virtualenv and recreate it from scratch

As for your current installation: you probably will want to remove all versions for radical.utils, radical.pilot and saga-python, and then do a fresh install of radical.pilot, which will pull the right versions from pypi.

HtH, Andre.

[haoyuanchen]

I finally got it to work by also removing all the old saga-python and RP files on Gordon, besides doing what you suggested on my laptop. It seems that even if everything on my laptop is up-to-date, those old files on Gordon will still cause problems. Also, the default python on Gordon seems to be 2.6 and also caused some problems, I aliased it to 2.7 and it works then.

Thanks for your help Andre!

[andre-merzky]

Glad you got it working -- and sorry for the trouble...

Best, Andre.