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:
export -p LD_LIBRARY_PATH= export -p PYTHONHOME=/usr/lib64/python2.3/ export MODINSTALL9v5=/****/modeller9v5 export EXECUTABLE_TYPE9v5=x86_64-intel8 export -p LIBS_LIB9v5=${MODINSTALL9v5}/modlib/libs.lib export KEY_MODELLER9v5=**** export -p PATH=${PATH}:${MODINSTALL9v5}/bin ## limit stacksize unlimited
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 < modeller-care@salilab.org> 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: > ... > > ImportError: > > /usr/people/trippm/bin/modeller9v5/lib/x86_64-intel8/libmodeller.so.4: > > undefined symbol: __svml_cosf4 > > 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. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >