I'm running on CentOS with Julia 0.3.7. I'm writing an executable Julia
script for other non-Julia, non-Python users to run as a batch job. The
script generates plots using the following setup:
using PyCall
pyimport("matplotlib")[:use]("Agg") # Doesn't require X connection
@pyimport matplotlib.pyplot as plt
Prior to this it first checks that Anaconda Python is set up in the user's
path. If not, it sets the appropriate values of environment variables as
follows
pypath = ""
stderrold = STDERR; (rd,wr) = redirect_stderr()
try
pypath = readall(`which python`)
end
redirect_stderr(stderrold)
if isempty(search(pypath, "anaconda"))
println("Adding Anaconda Python to environment variables")
PREFIX = "/projects/antenna_eng/tools/python/CentOS/anaconda"
ENV["PATH"] = "$(PREFIX)/bin:$(ENV["PATH"])"
ENV["LD_LIBRARY_PATH"] =
"""$(PREFIX)/lib:$(ENV["LD_LIBRARY_PATH"])"""
pyversion=readchomp(`python -c "import sys; print
sys.version.split()[0]"`)
ENV["PYTHONSRC"] = "$(PREFIX)/src/Python-$(pyversion)"
end
These valiues for the environment variables are taken from the file
python_envars.sh that is installed with Anaconda Python.
The pyimport and @pyimport commands work fine. However, when the Julia
script gets to the part where it actually generates plots, Python complains
that it can't find a file:
ERROR: PyError (:PyImport_ImportModule) <type 'exceptions.ImportError'>
ImportError('libjpeg.so.8: cannot open shared object file: No such file or
directory',)
This shared library is actually sitting in the directory in the Anaconda
installation that was added to the LD_LIBRARY_PATH environment variable.
If I set up the environment variables before launching the Julia script,
all is well.
Is this expected behavior? I thought that if I altered the environment
variables, they would be passed along to any programs launched by the Julia
script, including Python via the PyCall package. I guess I could write a
shell script that sets up the environment variables and then calls my Julia
script, but I would prefer to do this all with a single Julia script, if
possible. Any suggestions?
Thanks,
--Peter
