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When I run:

import shutil
import sys, os
from chemicalchecker.database import Molprop, Structure
from chemicalchecker.database import Molrepo
from chemicalchecker.util import HPC
from chemicalchecker.util import Config

molprops = ['chembl_target_predictions']

molrepo_ik_inchi = Molrepo.get_fields_by_molrepo_name("chembl",["inchikey","inchi"])

for mol in molprops:
    
    job_path = "/aloy/scratch/mduran/jobs_molprop_chembl_" + mol
    if os.path.isdir(job_path):
        shutil.rmtree(job_path)
    os.mkdir(job_path)

    molprop = Molprop(mol)

    # This method sends the job and waits for the job to finish
    cluster = molprop.molprop_hpc(job_path,molrepo_ik_inchi)

I get the following memory error:

---------------------------------------------------------------------------
MemoryError                               Traceback (most recent call last)
<ipython-input-2-6ed1f126b830> in <module>()
     20 
     21     # This method sends the job and waits for the job to finish
---> 22     cluster = molprop.molprop_hpc(job_path,molrepo_ik_inchi)

/aloy/home/mduran/myscripts/chemical_checker/package/chemicalchecker/database/molprop.pyc in molprop_hpc(job_path, inchikey_inchi, **kwargs)
    228             # submit jobs
    229             cluster = HPC(Config())
--> 230             cluster.submitMultiJob(command, **params)
    231             return cluster
    232 

/aloy/home/mduran/myscripts/chemical_checker/package/chemicalchecker/util/hpc/hpc.pyc in submitMultiJob(self, command, **kwargs)
     58 
     59         if self.job_id is None:
---> 60             self.job_id = self.hpc.submitMultiJob(command, **kwargs)
     61         else:
     62             raise Exception("HPC instance already in use")

/aloy/home/mduran/myscripts/chemical_checker/package/chemicalchecker/util/hpc/sge.pyc in submitMultiJob(self, command, **kwargs)
    165 
    166             input_dict = dict()
--> 167             for cid, chunk in enumerate(self._chunks(elements, num_jobs), 1):
    168                 input_dict[str(cid)] = chunk
    169             input_path = os.path.join(self.jobdir, str(uuid.uuid4()))

/aloy/home/mduran/myscripts/chemical_checker/package/chemicalchecker/util/hpc/sge.pyc in _chunks(self, l, n)
     81         """Yield successive n-sized chunks from l."""
     82         if isinstance(l, list):
---> 83             for i in np.array_split(l, n):
     84                 yield i
     85         elif isinstance(l, dict):

/opt/miniconda2/envs/py27/lib/python2.7/site-packages/numpy/lib/shape_base.pyc in array_split(ary, indices_or_sections, axis)
    760 
    761     sub_arys = []
--> 762     sary = _nx.swapaxes(ary, axis, 0)
    763     for i in range(Nsections):
    764         st = div_points[i]

/opt/miniconda2/envs/py27/lib/python2.7/site-packages/numpy/core/fromnumeric.pyc in swapaxes(a, axis1, axis2)
    583 
    584     """
--> 585     return _wrapfunc(a, 'swapaxes', axis1, axis2)
    586 
    587 

/opt/miniconda2/envs/py27/lib/python2.7/site-packages/numpy/core/fromnumeric.pyc in _wrapfunc(obj, method, *args, **kwds)
     64     # a downstream library like 'pandas'.
     65     except (AttributeError, TypeError):
---> 66         return _wrapit(obj, method, *args, **kwds)
     67 
     68 

/opt/miniconda2/envs/py27/lib/python2.7/site-packages/numpy/core/fromnumeric.pyc in _wrapit(obj, method, *args, **kwds)
     44     except AttributeError:
     45         wrap = None
---> 46     result = getattr(asarray(obj), method)(*args, **kwds)
     47     if wrap:
     48         if not isinstance(result, mu.ndarray):

/opt/miniconda2/envs/py27/lib/python2.7/site-packages/numpy/core/numeric.pyc in asarray(a, dtype, order)
    536 
    537     """
--> 538     return array(a, dtype, copy=False, order=order)
    539 
    540 

MemoryError: