Re: [scipion-users] scipion installed, now what?

[Kyle D. <kyl...@ep...>]

Hi Patrick,

(I'm not a Scipion dev but have some suggestions.)


On 04/24/2018 11:21 PM, Patrick Goetz wrote:
>
>
> 2.
> I tried running one of the small tests (scipion tests 
> em.workflows.test_workflow_spiderMDA), but this failed with a couple 
> of python runtime errors.  These look like internal errors, but could 
> this have something to do with the fact that I'm trying to run the 
> test from a (non-graphical) terminal as root (because of the install 
> location)?
>
>
>   File "/root/scipion/software/lib/python2.7/subprocess.py", line 186, 
> in check_call
>     raise CalledProcessError(retcode, cmd)
> CalledProcessError: Command 
> '/root/scipion/software/em/spider-21.13/spider/bin/spider_linux_mp_intel64 
>  stk @cp_endian' returned non-zero exit status 127
> ('Creating project at: ', 
> '/root/ScipionUserData/projects/TestSpiderWorkflow/project.sqlite')
> >>>> python /root/scipion/scipion testdata --download hemoglobin_mda
>
>

Actually it looks like that error is coming from a call to a system 
command and is not directly caused by anything in Python. Exit status 
127 is returned when either 1) the file does not exist or 2) the file 
does not have execute permission for your user or group. Could you 
verify that spider_linux_mp_intel64 exists and has execute permissions 
set? You can use the command

ls -l /root/scipion/software/em/spider-21.13/spider/bin/ | grep 
spider_linux_mp_intel64

and check that an 'x' exists for the user/group? (I assume it's the root 
user.)

I would also think that you should give everyone read/write access to 
the ScipionUserData folder since you want multiple users to have access 
to it; this may not be true in your case since it is buried inside a 
folder belonging to root.

Finally, there are log files for stdout and stderr that are written to 
the ScipionUserData folder when you run a workflow or test. In my 
experience you can get more information about any errors from these files.

Hope this helps,
Kyle

-- 
Kyle M. Douglass, PhD
Post-doctoral researcher
The Laboratory of Experimental Biophysics
EPFL, Lausanne, Switzerland
http://kmdouglass.github.io
http://leb.epfl.ch