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MIC-DKFZ / BraTS2017

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error in running pre-processing step #1

Closed poornasandur closed 6 years ago

poornasandur commented 6 years ago

$ python run_preprocessing.py -m train

Traceback (most recent call last): File "run_preprocessing.py", line 17, in from dataset import run_preprocessing_BraTS2017_trainSet, run_preprocessing_BraTS2017_valOrTestSet File "/home/poornachandra/Downloads/brats_github/BraTS2017-master/dataset.py", line 22, in from utils import reshape_by_padding_upper_coords File "/home/poornachandra/Downloads/brats_github/BraTS2017-master/utils.py", line 16, in import theano.tensor as T File "/home/poornachandra/anaconda2/lib/python2.7/site-packages/theano/init.py", line 124, in from theano.scan_module import (scan, map, reduce, foldl, foldr, clone, File "/home/poornachandra/anaconda2/lib/python2.7/site-packages/theano/scan_module/init.py", line 41, in from theano.scan_module import scan_opt File "/home/poornachandra/anaconda2/lib/python2.7/site-packages/theano/scan_module/scan_opt.py", line 60, in from theano import tensor, scalar File "/home/poornachandra/anaconda2/lib/python2.7/site-packages/theano/tensor/init.py", line 17, in from theano.tensor import blas File "/home/poornachandra/anaconda2/lib/python2.7/site-packages/theano/tensor/blas.py", line 155, in from theano.tensor.blas_headers import blas_header_text File "/home/poornachandra/anaconda2/lib/python2.7/site-packages/theano/tensor/blas_headers.py", line 987, in if not config.blas.ldflags: File "/home/poornachandra/anaconda2/lib/python2.7/site-packages/theano/configparser.py", line 332, in get val_str = self.default() File "/home/poornachandra/anaconda2/lib/python2.7/site-packages/theano/configdefaults.py", line 1408, in default_blas_ldflags check_mkl_openmp() File "/home/poornachandra/anaconda2/lib/python2.7/site-packages/theano/configdefaults.py", line 1252, in check_mkl_openmp raise RuntimeError('To use MKL 2018 with Theano you MUST set "MKL_THREADING_LAYER=GNU" in your environement.') RuntimeError: To use MKL 2018 with Theano you MUST set "MKL_THREADING_LAYER=GNU" in your environement.

FabianIsensee commented 6 years ago

Hi there, it seems like your theano installation does not work. If that is the case then this is not an issue related to our project. Try running the following command from your shell: python -c "import theano" Regards, Fabian PS: The error message you got gives you a hint what to do.

To use MKL 2018 with Theano you MUST set "MKL_THREADING_LAYER=GNU" in your environement.

poornasandur commented 6 years ago

Thanks for the input Sir...

On Mon, Feb 12, 2018 at 1:41 PM, Fabian Isensee notifications@github.com wrote:

Hi there, it seems like your theano installation does not work. If that is the case then this is not an issue related to our project. Try running the following command from your shell: python -c "import theano" Regards, Fabian PS: The error message you got gives you a hint what to do.

To use MKL 2018 with Theano you MUST set "MKL_THREADING_LAYER=GNU" in your environement.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MIC-DKFZ/BraTS2017/issues/1#issuecomment-364852155, or mute the thread https://github.com/notifications/unsubscribe-auth/AXsXKCXMAT__PR8oExqxPPIHi_yCZtZEks5tT_JMgaJpZM4SA5PB .

-- warm regards, Poornachandra S +91-9901913049