update to Ubuntu 18.04 (#104)

* additional packages for ubuntu18.04

* add path to local user binary directory

* Added vagrantfile for 18.04

* use ubuntu18.04 branch of SIRF-SuperBuild

* remove install of gcc 6

* updates

* remove checkout of ubuntu18.04 SIF-SuperBuild tag

* Use system boost

* use bento box

* Added 50Gb VDI disk image

https://www.virtualbox.org/manual/ch05.html

* builds VM with vagrant

currently doesn't find the system Boost.

* add port forwarding, add 32 Mb video ram, 50 Gb HDD

* use system boost

* delete sirf_disk.vdi

* removed links to specific VM and SuperBuild branches

requires SyneRBI/SIRF-SuperBuild#149 first

* use globbing for resetting *URL and *TAG

* set USE_ITK=ON

* created function find_boost_version

* moved shell provision script to file

closes #114

* install libhdf5-dev

* vram is in modifyvm section

https://www.virtualbox.org/manual/ch08.html

* indentation fix

* removed comment

* separate the install steps

* multi line install

* added bootstrap_ubuntu.sh script

* install missing boost libraries

* removes autosuspend notification

closes #118

* add info on 2.0rc1

* builds ubuntu18.04 SuperBuild

* build ubuntu18.04 branch of superbuild

* removed conflict message

* changed VM name

* uses SuperBuild master

* removed -V command

* checks if user and homedir is already created

* bugfix

* bugfix~~

* fix test dir existence

* install spyder and jupyter in pip script

* force spyder 3.2

* manual configure jupyter

* info on manual step to configure ip for jupyter

* add info on jupyter config

* removed reference to specific branches

* updated VM name

* add new version

* update doc

* clean up

CHANGES.md

@@ -1,5 +1,15 @@
 # ChangeLog
 
+## 2.0.0-rc.1
+- upgraded to Ubuntu 18.04
+- installs more recent Gadgetron https://github.com/gadgetron/gadgetron/commit/b6191eaaa72ccca6c6a5fe4c0fa3319694f512ab
+- add port forwarding (8888 -> 8888 for jupyter)
+- install jupyter notebook, with default password
+- installs spyder v3.2
+- does not install a browser
+- add cython for CIL
+
+
 ## 1.1.1
 - added nbstripout (https://github.com/kynan/nbstripout) to handle conflicts in SIRF-Exercises
 

VM_version.txt

@@ -1 +1 @@
-1.1.1
+2.0.0-rc.1

scripts/INSTALL_prerequisites_with_apt-get.sh

@@ -8,67 +8,76 @@
 # without asking any questions.
 # We use it for the CCP PETMR VM etc.
 # Use it with caution.
-
+set -e
 
 #if [ -z "SUDO" ]; then SUDO=sudo; fi
-
+export DEBIAN_FRONTEND=noninteractive
+SUDO=sudo
 echo "Installing Gadgetron pre-requisites..."
-
-$SUDO apt-get install -y --no-install-recommends libhdf5-serial-dev git-core cmake \
-      build-essential libfftw3-dev h5utils \
-      hdf5-tools hdfview liblapack-dev \
-      libarmadillo-dev libace-dev  \
-      libgtest-dev \
-      libopenblas-dev libatlas-base-dev \
-      libxml2-dev libxslt-dev \ # for siemens_to_ismrmrd
-      cython
-#      g++-6 gcc-6 
-# Gadgetron dependencies, not required (yet) by SIRF
-# only plplot install once https://github.com/gadgetron/gadgetron/issues/608 fixed
-# in the Gadgetron version that we use
-# libplplot-dev
+APT_GET_INSTALL="$SUDO apt-get install -y --no-install-recommends"
+${APT_GET_INSTALL} libhdf5-serial-dev git build-essential libfftw3-dev h5utils hdf5-tools \
+	hdfview liblapack-dev libarmadillo-dev libace-dev libgtest-dev libopenblas-dev \
+	libatlas-base-dev libatlas-base-dev libxml2-dev libxslt1-dev cython
 
 echo "Installing boost 1.65 or later"
 # first find current boost version (if any)
 # the 'tail' makes sure we use the last one listed by apt-cache in case there is more than 1 version
-tmp=`apt-cache search libboost|grep ALL|egrep libboost[1-9]|tail -n 1`
-boost_major=${tmp:8:1}
-boost_minor=${tmp:10:2}
+function find_boost_version() {
+  tmp=`apt-cache search libboost|grep ALL|egrep libboost[1-9]|tail -n 1`
+  boost_major=${tmp:8:1}
+  boost_minor=${tmp:10:2}
+}
+
+find_boost_version
+
 echo "Found Boost major version ${boost_major}, minor ${boost_minor}"
 if [ $boost_major -gt 1 -o $boost_minor -gt 64 ]
 then
+    echo "installing Boost ${boost_major}.${boost_minor} from system apt"
     $SUDO apt install -y libboost-dev
+    $SUDO apt install -y libboost-chrono-dev
+    $SUDO apt install -y libboost-filesystem-dev
+    $SUDO apt install -y libboost-thread-dev
+    $SUDO apt install -y libboost-date-time-dev
+    $SUDO apt install -y libboost-regex-dev
+    $SUDO apt install -y libboost-program-options-dev
+    $SUDO apt install -y libboost-atomic-dev
+    $SUDO apt install -y libboost-test-dev
+    $SUDO apt install -y libboost-timer-dev
 else    
     # packaged boost is too old
     # we need to find a ppa that has it. This is unsafe and likely prone to falling over
     # when the ppa is no longer maintained
-    $SUDO apt install -y software-properties-common
+    echo "trying to find boost from ppa:mhier/libboost-latest"
+    ${APT_GET_INSTALL} software-properties-common
     $SUDO add-apt-repository -y  ppa:mhier/libboost-latest
     $SUDO apt update
     # get rid of the default installed boost version
     $SUDO apt remove -y libboost-all-dev
     $SUDO apt auto-remove -y
     # TODO: find out which version is in the ppa
-    $SUDO apt install -y libboost1.68-dev
+    find_boost_version
+    echo "installing Boost ${boost_major}.${boost_minor} from system apt"
+    ${APT_GET_INSTALL} libboost${boost_major}.${boost_minor}-all-dev
 fi
 
 echo "Installing SWIG..."
 
-$SUDO apt-get install -y --no-install-recommends swig
+${APT_GET_INSTALL} --no-install-recommends swig
 
 echo "Installing doxygen related packages"
-$SUDO apt-get install -y --no-install-recommends doxygen graphviz
+${APT_GET_INSTALL} --no-install-recommends doxygen graphviz
 
 # replaced with pip install
 #echo "Installing python libraries etc"
 #$SUDO apt-get install -y --no-install-recommends  python-scipy python-docopt  python-numpy python-h5py python-matplotlib python-libxml2 python-psutil python-tk python-nose
 
 echo "installing glog"
-$SUDO apt-get install -y libgoogle-glog-dev
+${APT_GET_INSTALL} libgoogle-glog-dev
 
 echo "Installing python APT packages"
 # we will use pip for most
 # some extra package needed for jupyter
 qt=pyqt5
-$SUDO apt-get install -y python-dev python-pip python-tk python-${qt} python-${qt}.qtsvg python-${qt}.qtwebkit
+${APT_GET_INSTALL} python-dev python-pip python-tk python-${qt} python-${qt}.qtsvg python-${qt}.qtwebkit
 echo "Run INSTALL_python_packages.sh after this."

scripts/INSTALL_python_packages.sh

@@ -67,3 +67,4 @@ done
 
 $PYTHON -m pip install $PIPOPTIONS --upgrade pip wheel setuptools
 $PYTHON -m pip install $PIPOPTIONS --only-binary=numpy,scipy,matplotlib numpy scipy matplotlib nose coverage docopt
+$PYTHON -m pip install $PIPOPTIONS jupyter spyder==3.2

scripts/UPDATE.sh

@@ -132,17 +132,16 @@ SuperBuild(){
 
   cd buildVM
   cmake ../SIRF-SuperBuild \
-      -DCMAKE_INSTALL_PREFIX=${SIRF_INSTALL_PATH} \
-	  -USIRF_URL -USIRF_TAG -USTIR_URL -USTIR_TAG \
-	  -UGadgetron_URL -UGadgetron_TAG -UISMRMRD_URL \
-	  -UISMRMRD_TAG \
-	  -DUSE_SYSTEM_SWIG=On \
-	  -DUSE_SYSTEM_Boost=On \
-	  -DUSE_SYSTEM_Armadillo=On \
-	  -DUSE_SYSTEM_FFTW3=On \
-	  -DUSE_SYSTEM_HDF5=ON \
-	  -DBUILD_siemens_to_ismrmrd=On \
-	  -DDEVEL_BUILD=OFF
+        -DCMAKE_INSTALL_PREFIX=${SIRF_INSTALL_PATH} \
+        -U\*_URL -U\*_TAG \
+        -DUSE_SYSTEM_SWIG=On \
+        -DUSE_SYSTEM_Boost=On \
+        -DUSE_SYSTEM_Armadillo=On \
+        -DUSE_SYSTEM_FFTW3=On \
+        -DUSE_SYSTEM_HDF5=ON \
+        -DBUILD_siemens_to_ismrmrd=On \
+        -DUSE_ITK=ON \
+        -DDEVEL_BUILD=OFF
   make -j${num_parallel}
 
   if [ ! -f ${SIRF_INSTALL_PATH}/share/gadgetron/config/gadgetron.xml ]

scripts/bootstrap_ubuntu.sh

@@ -0,0 +1,82 @@
+#!/bin/bash    
+
+set -x
+SIRFUSERNAME=sirfuser
+SIRFPASS=virtual
+
+# check if user exists. if not create it. Useful for vagrant provision
+id -u $SIRFUSERNAME
+if [ $? -eq "1" ] ; then
+  adduser $SIRFUSERNAME
+  adduser $SIRFUSERNAME sudo
+  { echo $SIRFPASS; echo $SIRFPASS; } | passwd $SIRFUSERNAME 
+fi
+
+# fail hard on any step
+set -ex
+# update the apt-get database
+export DEBIAN_FRONTEND=noninteractive
+apt-get update && apt-get upgrade -y -o Dpkg::Options::=--force-confnew
+# upgrade the list of packages
+
+
+#install upgrades
+apt-get update && apt-get install -y --no-install-recommends wget git xorg xterm gdm3 menu policykit-1-gnome synaptic gnome-session gnome-panel metacity
+apt-get update && apt-get install -y at-spi2-core gnome-terminal gnome-control-center nautilus dmz-cursor-theme network-manager network-manager-gnome
+
+# start gnome display manager
+service gdm start
+
+# set the current locale, otherwise the gnome-terminal doesn't start
+sudo locale-gen en_GB.UTF-8
+sudo locale-gen en_US.UTF-8
+sudo locale-gen de_DE.UTF-8
+sudo locale-gen fr_FR.UTF-8
+sudo locale-gen es_ES.UTF-8
+sudo locale-gen it_IT.UTF-8
+sudo locale-gen pt_PT.UTF-8
+sudo locale-gen pt_BR.UTF-8
+sudo locale-gen ja_JP.UTF-8
+sudo locale-gen zh_CN.UTF-8
+sudo update-locale LANG=en_GB.UTF-8
+sudo localectl set-x11-keymap uk
+sudo localectl status
+
+
+# To hide vagrant from login screen:
+#  1. Log-in as vagrant
+#  2. In /var/lib/AccountsService/users/vagrant change 'SystemAccount=true'
+sudo echo '[User]' > vagrant
+sudo echo 'SystemAccount=true' >> vagrant
+sudo cp -v vagrant /var/lib/AccountsService/users/vagrant
+
+  # To remove the Ubuntu user from VM:
+#sudo deluser --remove-home ubuntu
+# Could add custom logos here: /etc/gdm3/greeter.dconf-defaults 
+
+userHOME=/home/$SIRFUSERNAME
+
+if [ ! -d $userHOME/devel ]; then
+  mkdir $userHOME/devel 
+fi
+cd $userHOME/devel
+
+if [ ! -d $userHOME/devel/CCPPETMR_VM ]; then
+  git clone https://github.com/CCPPETMR/CCPPETMR_VM.git
+  cd CCPPETMR_VM
+else
+  cd CCPPETMR_VM
+  git pull
+fi
+
+
+
+bash $userHOME/devel/CCPPETMR_VM/scripts/INSTALL_prerequisites_with_apt-get.sh
+bash $userHOME/devel/CCPPETMR_VM/scripts/INSTALL_CMake.sh /usr/local
+bash $userHOME/devel/CCPPETMR_VM/scripts/INSTALL_python_packages.sh
+
+# port 8888 is forwarded to 8888 so the user can use the host browser
+# Therefore no browser is installed on the VM
+
+chown -R $SIRFUSERNAME:users $userHOME
+sudo -u $SIRFUSERNAME -H bash $userHOME/devel/CCPPETMR_VM/scripts/UPDATE.sh

scripts/configure_gnome.sh

@@ -36,4 +36,7 @@ gsettings set org.gnome.desktop.screensaver lock-enabled false
 gsettings set org.gnome.desktop.screensaver idle-activation-enabled false
 # enlarge pointer size
 gsettings set org.gnome.desktop.interface cursor-size 120
+# remove autosuspend notification
+gsettings set org.gnome.settings-daemon.plugins.power sleep-inactive-ac-timeout '0'
+gsettings set org.gnome.settings-daemon.plugins.power sleep-inactive-battery-timeout '0'
 

scripts/first_run.sh

@@ -27,4 +27,13 @@ location=`dirname $0`
 
 $location/configure_gnome.sh
 
+# configure jupyter notebook
+mkdir ~/.jupyter
+jupyter notebook --generate-config
+# requires to set the following variable manually by editing the file
+# jupyter_notebook_config.py
+# c.NotebookApp.ip = '0.0.0.0'
+jupyter notebook password
+
 $location/zero_fill.sh
+

vagrant/Vagrantfile

@@ -20,7 +20,7 @@
 #=========================================================================
 
 Vagrant.configure("2") do |config|
-  config.vm.box = "ubuntu/xenial64"
+  config.vm.box = "bento/ubuntu-18.04"
   config.vm.synced_folder '.', '/vagrant', disabled: true
 
   # Disable automatic box update checking. If you disable this, then
@@ -31,8 +31,10 @@ Vagrant.configure("2") do |config|
   # Create a forwarded port mapping which allows access to a specific port
   # within the machine from a port on the host machine. In the example below,
   # accessing "localhost:8080" will access port 80 on the guest machine.
-  # config.vm.network "forwarded_port", guest: 80, host: 8080
 
+  # Forward port for jupyter notebooks
+  config.vm.network "forwarded_port", guest: 8888, host: 8888
+
   # Create a private network, which allows host-only access to the machine
   # using a specific IP.
   # config.vm.network "private_network", ip: "192.168.33.10"
@@ -52,6 +54,7 @@ Vagrant.configure("2") do |config|
   # backing providers for Vagrant. These expose provider-specific options.
   # Example for VirtualBox:
   #
+
   config.vm.provider "virtualbox" do |vb|
     # Display the VirtualBox GUI when booting the machine
     vb.gui = true
@@ -62,17 +65,17 @@ Vagrant.configure("2") do |config|
 
 	vb.customize "pre-boot", [
        "storageattach", :id,
-       "--storagectl", "IDE",
+       "--storagectl", "IDE Controller",
         "--port", "1",
        "--device", "0",
        "--type", "dvddrive",
-       "--medium", "emptydrive",
+       "--medium", "emptydrive"
        ]
-	vb.name = "SIRF_1.1.1"
+	vb.name = "SIRF_2.0.0-rc.1"
 	vb.customize ["modifyvm", :id, 
-	              "--clipboard", "bidirectional"]
-	#vb.customize [ "modifyvm", :id, 
-	#              "--uartmode1", "disconnected" ]
+	              "--clipboard", "bidirectional",
+                  "--vram", "32"]
+                  
   end
 
   #
@@ -90,73 +93,6 @@ Vagrant.configure("2") do |config|
   # Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
   # documentation for more information about their specific syntax and use.
 
-  config.vm.provision "shell", inline: <<-SHELL
-    SIRFUSERNAME=sirfuser
-    SIRFPASS=virtual
-
-    adduser $SIRFUSERNAME
-    adduser $SIRFUSERNAME sudo
-    { echo $SIRFPASS; echo $SIRFPASS; } | passwd $SIRFUSERNAME 
-
-	# remove serial port from grub configuration and update configuration
-	sed -i 's/ console=ttyS0//' /etc/default/grub.d/50-cloudimg-settings.cfg
-    update-grub
-	# update the apt-get database
-    apt-get update
-	# upgrade the list of packages
-	apt-get upgrade -y
-
-	#install upgrades
-	apt-get install -y wget git xorg xterm gdm menu gksu synaptic gnome-session gnome-panel metacity --no-install-recommends
-    apt-get install -y at-spi2-core gnome-terminal gnome-control-center nautilus dmz-cursor-theme network-manager network-manager-gnome
-    
-	# start gnome display manager
-	service gdm start
-    
-	# set the current locale, otherwise the gnome-terminal doesn't start
-	sudo locale-gen en_GB.UTF-8
-	sudo locale-gen en_US.UTF-8
-	sudo locale-gen de_DE.UTF-8
-	sudo locale-gen fr_FR.UTF-8
-	sudo locale-gen es_ES.UTF-8
-	sudo locale-gen it_IT.UTF-8
-	sudo locale-gen pt_PT.UTF-8
-	sudo locale-gen pt_BR.UTF-8
-	sudo locale-gen ja_JP.UTF-8
-	sudo locale-gen zh_CN.UTF-8
-	sudo update-locale LANG=en_GB.UTF-8
-	sudo localectl set-x11-keymap uk
-	sudo localectl status
-	
-	
-	# To hide vagrant from login screen:
-    #  1. Log-in as vagrant
-    #  2. In /var/lib/AccountsService/users/vagrant change 'SystemAccount=true'
-	sudo echo '[User]' > vagrant
-	sudo echo 'SystemAccount=true' >> vagrant
-	sudo cp -v vagrant /var/lib/AccountsService/users/vagrant
-
-	# To remove the Ubuntu user from VM:
-    sudo deluser --remove-home ubuntu
-    # Could add custom logos here: /etc/gdm3/greeter.dconf-defaults 
-
-    userHOME=/home/$SIRFUSERNAME
-    mkdir $userHOME/devel
-    cd $userHOME/devel
-	
-    git clone https://github.com/CCPPETMR/CCPPETMR_VM.git
-    cd CCPPETMR_VM
-    #git checkout ubuntu18.04
-    bash $userHOME/devel/CCPPETMR_VM/scripts/INSTALL_prerequisites_with_apt-get.sh
-    bash $userHOME/devel/CCPPETMR_VM/scripts/INSTALL_CMake.sh /usr/local
-    bash $userHOME/devel/CCPPETMR_VM/scripts/INSTALL_python_packages.sh
-
-    apt-get install -y firefox
-    python -m pip install jupyter
-    python -m pip install spyder
-    chown -R $SIRFUSERNAME:users $userHOME
-    sudo -u $SIRFUSERNAME -H bash $userHOME/devel/CCPPETMR_VM/scripts/UPDATE.sh
-    
-    
-   SHELL
+  config.vm.provision "shell", path: "../scripts/bootstrap_ubuntu.sh"
 end
+