DYLD not loading when running root within python script

[icaro]

Hi
When I try to run a python shell script, like:

subprocess.call('./DumpWCDataCluster_pr ' + pr_files[i] + ' T_charge_cluster > pr_cluster.txt', shell= True)

I get the following error:

dyld: Library not loaded: @rpath/libCore.so
  Referenced from: /Users/ivan/Work/Cosmic_discriminator/./DumpWCDataCluster_pr
  Reason: image not found
/bin/sh: line 1: 13182 Abort trap: 6           ./DumpWCDataCluster_pr pr_files/pr_8556_8_438.root T_charge_cluster > pr_cluster.txt

Within my script I call upon the apparently missing library by doing,

os.getenv('$DYLD_LIBRARY_PATH')

I am running macOS High Sierra 10.13.3 with Root version 6.12/04.

I’ve also tried what was suggested in this post without any results.

Regards,
Ivan

[Danilo]

Hi,

it’s not clear to me what you mean by “calling upon the apparently missing library”.
Is the environment set correctly before invoking python or are you trying to set it for the invocation of your executable only from within the Python script?

D

[amadio]

If which python points to /usr/bin/python, then there is a “feature” of Mac OS that strips DYLD_LIBRARY_PATH for you. See https://stackoverflow.com/a/35570229/1034717 for more details. You may have to set the variable from within your script for it to work, as suggested in the link.

[icaro]

Hi,
What I mean is that outside of the python shell (before running my script), the enviromental variable is defined. I can verify this by doing,

$  echo $DYLD_LIBRARY_PATH 
/Applications/root_v6.12.04/lib

It does not load $DYLD_LIBRARY_PATH when running my root program within python shell script.

[suhl]

But the environment variable is not defined in python, you could try

$ python
>>> import os
>>> print os.getenv("DYLD_LIBRARY_PATH")
None

So any subprocess of python will not know about this variable.

You could try to add the required rpath during the linking stage of DumpWCDataCluster_pr with -Wl,-rpath,${ROOTSYS}/lib (or similar).

[amadio]

Inside Python the variable is not defined because Mac OS strips its value when running things from /usr.

[ksmith]

If you compile the outside process with the correct rpath, then DYLD_LIBRARY_PATH is not necessary. For example these flags to the gcc compiler:

-Wl,-rpath,$ROOTLIBDIR