Merge branch 'master' of github.com:jonescompneurolab/hnn

installer/centos/build.sh → installer/centos/centos6-installer.sh

@@ -1,19 +1,19 @@
-# start with this since it gets input needed
-
-# HNN repo from bitbucket
-#git clone https://bitbucket.org/samnemo/hnn.git# old repo
+# this whole script probably needs to be run with root permissions to avoid sudo timeouts
 
+# start with this since it gets input needed
+sudo yum -y install git
 # HNN repo from github - moved to github on April 8, 2018
 git clone https://github.com/jonescompneurolab/hnn.git
 
-wget https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
-sudo rpm -i epel-release-latest-7.noarch.rpm
-sudo yum -y install python34-devel.x86_64
+sudo yum -y install epel-release
+sudo yum -y install python34-devel
+sudo yum -y install gcc-c++
 sudo yum -y install libX11-devel
-sudo yum -y group install "Development Tools"
+sudo yum -y groupinstall "Development tools"
 sudo yum -y install xorg-x11-fonts-100dpi 
-sudo yum -y install Cython
-sudo yum -y install python34-pip python-tools
+sudo yum -y install python34-Cython
+sudo yum -y install python34-setuptools
+sudo easy_install-3.4 pip
 sudo pip3 install matplotlib
 # make sure matplotlib version 2 is used -- is this strictly needed?
 sudo pip3 install --upgrade matplotlib
@@ -28,8 +28,8 @@ sudo PATH=$PATH:/usr/lib64/openmpi/bin pip3 install mpi4py
 startdir=$(pwd)
 echo $startdir
 
-git clone https://github.com/nrnhines/nrn
-git clone https://github.com/nrnhines/iv
+git clone https://github.com/neuronsimulator/nrn
+git clone https://github.com/neuronsimulator/iv
 cd iv
 git checkout d4bb059
 ./build.sh
@@ -39,7 +39,7 @@ sudo make install -j4
 cd ../nrn
 #git checkout be2997e
 ./build.sh
-./configure --with-nrnpython=python3 --with-paranrn --disable-rx3d
+./configure --with-nrnpython=python3 --with-paranrn
 make -j4
 sudo PATH=$PATH:/usr/lib64/openmpi/bin make install -j4
 cd src/nrnpython
@@ -48,6 +48,10 @@ sudo python3 setup.py install
 # move outside of nrn directories
 cd $startdir
 
+# cleanup the nrn and iv folders, since NEURON Has been installed
+sudo rm -rf iv
+sudo rm -rf nrn
+
 # setup HNN itself
 cd hnn
 # make compiles the mod files
@@ -56,14 +60,31 @@ export PATH=$PATH:/usr/local/nrn/$CPU/bin
 make
 cd ..
 
+# delete the installed hnn folder in the event that it already exists
+sudo rm -rf /usr/local/hnn
+
+# move the hnn folder to the programs directory
+sudo mv hnn /usr/local
+
+# make the program accessable via the terminal command 'hnn'
+sudo ln -fs /usr/local/hnn/hnn /usr/local/bin/hnn
+
+# create the global session variables, make available for all users
+echo '# these lines define global session variables for HNN' | sudo tee -a /etc/profile.d/hnn.sh
+echo 'export CPU=$(uname -m)' | sudo tee -a /etc/profile.d/hnn.sh
+echo 'export PATH=$PATH::/usr/lib64/openmpi/bin:/usr/local/nrn/$CPU/bin' | sudo tee -a /etc/profile.d/hnn.sh
+
 # qt, pyqt, and supporting packages - needed for GUI
+# SIP unforutnately not available as a wheel for Python 3.4, so have to compile
 wget https://sourceforge.net/projects/pyqt/files/sip/sip-4.19.2/sip-4.19.2.tar.gz
 tar -zxf sip-4.19.2.tar.gz
 cd sip-4.19.2
 sudo python3 configure.py
 make -j4
 sudo make install -j4
 cd ..
+sudo rm -rf sip-4.19.2
+rm -f sip-4.19.2.tar.gz
 
 sudo yum -y install qt-devel
 sudo yum -y install qt5-qtbase
@@ -76,18 +97,14 @@ python3 configure.py --qmake=/usr/lib64/qt5/bin/qmake --confirm-license
 make -j4
 sudo make install -j4
 cd ..
+rm -rf PyQt5_gpl-5.8.2
+rm -f PyQt5_gpl-5.8.2.tar.gz
 
 # used by pqtgraph - for visualization
 sudo pip3 install PyOpenGL PyOpenGL_accelerate
 
 # pyqtgraph - only used for visualization
-cd hnn
-git clone https://github.com/pyqtgraph/pyqtgraph.git
-cd pyqtgraph
-git checkout pyqt5
-git pull
-sudo python3 setup.py install
+sudo pip3 install pyqtgraph
 
 # needed for matplotlib
 sudo yum -y install python34-tkinter
-

installer/centos/centos7-installer.sh

@@ -0,0 +1,103 @@
+# start with this since it gets input needed
+sudo yum -y install git
+# HNN repo from github - moved to github on April 8, 2018
+git clone https://github.com/jonescompneurolab/hnn.git
+
+sudo yum -y install epel-release
+sudo yum -y install python34-devel.x86_64
+sudo yum -y install libX11-devel
+sudo yum -y group install "Development Tools"
+sudo yum -y install xorg-x11-fonts-100dpi 
+sudo yum -y install python34-Cython
+sudo yum -y install python34-pip
+# have to upgrade pip because the version provided by python34-pip
+# does not check the installed Python version and will attempt to
+# install modules that require newer versions of Python
+sudo pip3 install --upgrade pip
+sudo pip3 install matplotlib
+# make sure matplotlib version 2 is used -- is this strictly needed?
+sudo pip3 install --upgrade matplotlib
+sudo pip3 install scipy
+sudo yum -y install ncurses-devel
+sudo yum -y install openmpi openmpi-devel
+sudo yum -y install libXext libXext-devel
+export PATH=$PATH:/usr/lib64/openmpi/bin
+sudo PATH=$PATH:/usr/lib64/openmpi/bin pip3 install mpi4py
+
+# save dir installing hnn to
+startdir=$(pwd)
+echo $startdir
+
+git clone https://github.com/neuronsimulator/nrn
+git clone https://github.com/neuronsimulator/iv
+cd iv
+git checkout d4bb059
+./build.sh
+./configure
+make -j4
+sudo make install -j4
+cd ../nrn
+#git checkout be2997e
+./build.sh
+./configure --with-nrnpython=python3 --with-paranrn
+make -j4
+sudo PATH=$PATH:/usr/lib64/openmpi/bin make install -j4
+cd src/nrnpython
+sudo python3 setup.py install
+
+# move outside of nrn directories
+cd $startdir
+
+# cleanup the nrn and iv folders, since NEURON Has been installed
+sudo rm -rf iv
+sudo rm -rf nrn
+
+# setup HNN itself
+cd hnn
+# make compiles the mod files
+export CPU=$(uname -m)
+export PATH=$PATH:/usr/local/nrn/$CPU/bin
+make
+cd ..
+
+# delete the installed hnn folder in the event that it already exists
+sudo rm -rf /usr/local/hnn
+
+# move the hnn folder to the programs directory
+sudo mv hnn /usr/local
+
+# make the program accessable via the terminal command 'hnn'
+sudo ln -fs /usr/local/hnn/hnn /usr/local/bin/hnn
+
+# create the global session variables, make available for all users
+echo '# these lines define global session variables for HNN' | sudo tee -a /etc/profile.d/hnn.sh
+echo 'export CPU=$(uname -m)' | sudo tee -a /etc/profile.d/hnn.sh
+echo 'export PATH=$PATH:/usr/lib64/openmpi/bin:/usr/local/nrn/$CPU/bin' | sudo tee -a /etc/profile.d/hnn.sh
+
+# qt, pyqt, and supporting packages - needed for GUI
+# SIP unforutnately not available as a wheel for Python 3.4, so have to compile
+wget https://sourceforge.net/projects/pyqt/files/sip/sip-4.19.2/sip-4.19.2.tar.gz
+tar -zxf sip-4.19.2.tar.gz
+cd sip-4.19.2
+sudo python3 configure.py
+make -j4
+sudo make install -j4
+cd ..
+sudo rm -rf sip-4.19.2
+sudo rm -f sip-4.19.2.tar.gz
+
+sudo yum -y install qt-devel
+sudo yum -y install qt5-qtbase
+sudo yum -y install qt5-qtbase-devel
+
+# Have to use --no-deps to get it to install as no SIP wheel available for Python 3.4
+sudo pip3 install pyqt5 --no-deps
+
+# used by pqtgraph - for visualization
+sudo pip3 install PyOpenGL PyOpenGL_accelerate
+
+# pyqtgraph - only used for visualization
+sudo pip3 install pyqtgraph
+
+# needed for matplotlib
+sudo yum -y install python34-tkinter

installer/centos/uninstall.sh

@@ -0,0 +1,5 @@
+# Note: this removes HNN itself but none of its dependencies
+
+sudo rm -rf /usr/local/hnn
+sudo rm -f /usr/local/bin/hnn
+sudo rm -f /etc/profile.d/hnn.sh

installer/ubuntu/installer.sh

@@ -31,8 +31,8 @@ sudo pip3 install --upgrade matplotlib
 startdir=$(pwd)
 echo $startdir
 
-git clone https://github.com/nrnhines/nrn
-git clone https://github.com/nrnhines/iv
+git clone https://github.com/neuronsimulator/nrn
+git clone https://github.com/neuronsimulator/iv
 cd iv
 git checkout d4bb059
 ./build.sh