You where right, I unset the LD_LIBRARY_PATH variable and the error went away. libsvml.so is indeed in the same location as libmodeller.so.4 However, it took me back to the initial problem:
echo "Running model-fast.py" Running model-fast.py modpy.sh python model-fast.py > model-fast.log 'import site' failed; use -v for traceback
echo "Running model-parallel.py" Running model-parallel.py modpy.sh python model-parallel.py > model-parallel.log 'import site' failed; use -v for traceback Traceback (most recent call last):
File "model-parallel.py", line 4, in ? from modeller.parallel import * File "/****/modeller9v5/modlib/modeller/parallel/__init__.py", line 1, in ? from job import job File "/****/modeller9v5/modlib/modeller/parallel/job.py", line 1, in ?
import socket, random, os, select ImportError: No module named socket
On Thu, Dec 4, 2008 at 5:23 PM, Modeller Caretaker <">> wrote:
Mauricio Carrillo Tripp wrote:
> This must be a dumb error from my part, but I followed directions to run
> the scripts and now I'm getting a different error on all scripts. Here's
> the output:
Interesting - that symbol is part of the Intel runtime (libsvml.so).
There should be a copy of that library in the same directory as
libmodeller.so.4. Do you perhaps have the LD_LIBRARY_PATH variable set?
If so, perhaps there is another libsvml.so library in that path (that
will take precedence over the copy bundled with Modeller). Maybe you
have the Intel C or Fortran compilers installed on your computer? If so,
you should either unset the LD_LIBRARY_PATH variable when running
Modeller with Python, or take the paths containing libsvml.so out of
that variable and put them in /etc/ld.so.conf instead.
-- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | "> 0 | http://www.scripps.edu/~trippm