Merge pull request #326 from openworm/dev_0.9.3_owm

Test with owmeta

Author: pgleeson

Dockerfile

@@ -64,39 +64,19 @@ RUN  sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
 
 RUN pip3 install neuron==8.0.1
 
-################################################################################
-########     Install pyNeuroML for handling NeuroML network model
-
-# Pin version of pymongo required for py3.6... TODO remove...
-RUN sudo pip install pymongo==4.1.1
-
-RUN git clone https://github.com/NeuroML/pyNeuroML.git && \
-  cd pyNeuroML && \
-  git checkout master  && \
-  sudo python3 setup.py install
-
-# TODO remove this line after we have better dependency management.  The
-# current version of gitpython requires python >= 3.7, which is newer than the
-# python included in the base image. Therefore, we manually install an older
-# gitpython to be used with OpenWormData.
-# See https://github.com/openworm/OpenWorm/pull/316
-RUN sudo pip install 'gitpython==2.1.15' markupsafe
-
-RUN git clone https://github.com/openworm/PyOpenWorm.git && \
-  cd PyOpenWorm && \
-  git checkout ow-0.9 && \
-  sudo apt-get install -y python3-cffi && \
-  sudo python3 setup.py install && \
-  pow clone https://github.com/openworm/OpenWormData.git
-
 
 ################################################################################
 ########     Install c302 for building neuronal network models
 
 RUN git clone https://github.com/openworm/c302.git && \
   cd c302 && \
-  git checkout ow-0.9.1 && \
-  sudo python3 setup.py install
+  git checkout ow-0.9.3 && \
+  sudo pip install .
+
+# Note: pyNeuroML installed with the above library
+
+RUN pip3 install owmeta-core==0.13.5
+RUN owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'
 
 
 ################################################################################
@@ -120,7 +100,6 @@ ENV SIBERNETIC_HOME=$HOME/sibernetic
 ENV PYTHONPATH=$PYTHONPATH:$HOME/c302:$SIBERNETIC_HOME
 
 
-
 ################################################################################
 ########     Install Intel OpenCL libraries needed for Sibernetic
 
@@ -149,20 +128,9 @@ RUN cd sibernetic && \
     sed -i -e "s/n2.7/n3.10/g" makefile && \
     make clean && make all  # Use python 3 libs
 
-# intel i5, hd 5500, linux 4.15.0-39-generic
-# ./Release/Sibernetic -f worm -no_g device=CPU    190ms
-# ./Release/Sibernetic -f worm -no_g device=GPU    150ms (initialization takes some time)
-
-# Intel(R) Xeon(R) CPU E5-1650 v4 @ 3.60GHz, linux 4.4.0-139-generic
-# ./Release/Sibernetic -f worm -no_g device=CPU    60ms
-#
-# after installing the nvidia driver used in host:
-## wget http://us.download.nvidia.com/tesla/390.30/nvidia-diag-driver-local-repo-ubuntu1604-390.30_1.0-1_amd64.deb
-## sudo dpkg -i nvidia-diag-driver-local-repo-ubuntu1604-390.30_1.0-1_amd64.deb
-## sudo apt-key add /var/nvidia-diag-driver-local-repo-390.30/7fa2af80.pub
-## sudo apt-get update
-## sudo apt-get install -y cuda-drivers
-# ./Release/Sibernetic -f worm -no_g device=GPU    37ms
+
+################################################################################
+########     Copy master python script
 
 # Not working with --chown=$USER:$USER
 COPY ./master_openworm.py $HOME/master_openworm.py

master_openworm.py

@@ -137,7 +137,7 @@ def execute_with_realtime_output(command, directory, env=None):
             'reference': 'FW',
             'c302params': 'C2',
             'verbose': False,
-            'device': 'GPU',
+            'device': 'CPU',
             'configuration': 'worm_crawl_half_resolution',
             'noc302': noc302,
             'datareader': 'UpdatedSpreadsheetDataReader2',