Theano and MLK error on server

[soilmicrobiome]

Hi there,

I have used this tool locally works great! But for larger/more samples i tried to install it onto a server (where conda is not permitted) as follows:

$module load python/3.6 $virtualenv /home/USER/deepvirfinder_env $source /home/USER/deepvirfinder_env/bin/activate $cd bin $pip install numpy theano keras scikit-learn $pip install biopython $git clone https://github.com/jessieren/DeepVirFinder

But now i get the following error

_Using Theano backend. Traceback (most recent call last): File "/cvmfs/soft.server.com/easybuild/software/2017/Core/python/3.6.3/lib/python3.6/configparser.py", line 1138, in _unify_values sectiondict = self._sections[section] KeyError: 'blas'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 168, in fetch_val_for_key return theano_cfg.get(section, option) File "/cvmfs/soft.server.com/easybuild/software/2017/Core/python/3.6.3/lib/python3.6/configparser.py", line 781, in get d = self._unify_values(section, vars) File "/cvmfs/soft.server.com/easybuild/software/2017/Core/python/3.6.3/lib/python3.6/configparser.py", line 1141, in _unify_values raise NoSectionError(section) configparser.NoSectionError: No section: 'blas'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 328, in get delete_key=delete_key) File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 172, in fetch_val_for_key raise KeyError(key) KeyError: 'blas.ldflags'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/configdefaults.py", line 1250, in check_mkl_openmp import mkl ModuleNotFoundError: No module named 'mkl'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/deepvirfinder_env/bin/DeepVirFinder/dvf.py", line 53, in import keras File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/keras/init.py", line 3, in from . import utils File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/keras/utils/init.py", line 6, in from . import conv_utils File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in from .. import backend as K File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/keras/backend/init.py", line 1, in from .load_backend import epsilon File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/keras/backend/load_backend.py", line 87, in from .theano_backend import * File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/keras/backend/theano_backend.py", line 7, in import theano File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/init.py", line 124, in from theano.scan_module import (scan, map, reduce, foldl, foldr, clone, File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/scan_module/init.py", line 41, in from theano.scan_module import scan_opt File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/scan_module/scan_opt.py", line 60, in from theano import tensor, scalar File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/tensor/init.py", line 17, in from theano.tensor import blas File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/tensor/blas.py", line 155, in from theano.tensor.blas_headers import blas_header_text File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/tensor/blas_headers.py", line 987, in if not config.blas.ldflags: File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 332, in get val_str = self.default() File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/configdefaults.py", line 1430, in default_blas_ldflags check_mkl_openmp() File "/home/user/deepvirfinder_env/lib/python3.6/site-packages/theano/configdefaults.py", line 1262, in check_mkl_openmp """) RuntimeError: Could not import 'mkl'. Either install mkl-service with conda or set MKL_THREADING_LAYER=GNU in your environment for MKL 2018.

If you have MKL 2017 install and are not in a conda environment you can set the Theano flag blas.check_openmp to False. Be warned that if you set this flag and don't set the appropriate environment or make sure you have the right version you will get wrong results._

Any thoughts?