base_v3/Dockerfile

@@ -16,6 +16,8 @@ RUN apt-get install git curl sudo nano -y
 
 RUN cd /opt/ && git clone https://github.com/lofar-astron/LOFARBeam.git
 RUN mkdir /opt/LOFARBeam/build && cd /opt/LOFARBeam/build && cmake -DCMAKE_INSTALL_PREFIX=/opt/lofarsoft -DPYTHON_EXECUTABLE=$(which python) -DCASACORE_INCLUDE_DIRS=/opt/lofarsoft/include/casacore/ -DCASACORE_LIBRARIES=/opt/lofarsoft/lib/ -DCASACORE_ROOT_DIR=/opt/lofarsoft/ ../ && make -j16 && make install 
+
+
 #------------------------
 # Lofar user
 #------------------------
@@ -37,10 +39,63 @@ COPY data/input_data /input_data
 COPY data/output_data /output_data
 RUN chown lofar:lofar /home/lofar && chown -R lofar:lofar /input_data && chown -R lofar:lofar /output_data
 
-# This is required mainly for Singularity
-RUN mv /home/lofar /home/vanilla_lofar
-RUN ln -s /tmp/lofarhome /home/lofar
-RUN rm -rf /tmp/lofarhome
+
+#----------------------
+# Minimal Desktop
+#----------------------
+
+# Utilities
+RUN apt-get install -y telnet unzip wget supervisor build-essential python-dev git-core openjdk-8-jre
+
+# Global Supervisord conf
+COPY files/supervisord.conf /etc/supervisor/
+
+# Install xvfb that triggers minimal install of X base packages and xterm
+RUN apt-get install xvfb xterm  -y
+
+# Install base packages for VNC server and headless desktop (2)
+RUN cd /opt && wget https://bintray.com/tigervnc/stable/download_file?file_path=tigervnc-1.8.0.x86_64.tar.gz -O tigervnc-1.8.0.x86_64.tar.gz \
+            && tar -zxvf tigervnc-1.8.0.x86_64.tar.gz \
+            && mv tigervnc-1.8.0.x86_64 tigervnc
+
+# Supervisord configuration
+COPY files/supervisord_vnc.conf /etc/supervisor/conf.d/
+COPY files/run_vnc.sh /etc/supervisor/conf.d/
+COPY files/run_novnc.sh /etc/supervisor/conf.d/
+RUN chmod 755 /etc/supervisor/conf.d/run_vnc.sh
+RUN chmod 755 /etc/supervisor/conf.d/run_novnc.sh
+
+# Web VNC (noVNC) v0.6.1.
+# NOTE: this is a custom version from Doro Wu (fcwu.tw@gmail.com).
+# TODO: Check differences and maybe move to 0.6.2
+COPY files/noVNC.tar.gz /usr/lib/
+RUN cd /usr/lib/ && tar -zxvf noVNC.tar.gz
+COPY files/index.html /usr/lib/noVNC
+
+RUN apt-get install -y net-tools
+
+# Supervisord configuration
+COPY files/supervisord_novnc.conf /etc/supervisor/conf.d/
+
+# X environment setup/startup
+RUN apt-get install fluxbox -y
+COPY files/xstartup /opt/tigervnc/
+RUN chmod 755 /opt/tigervnc/xstartup
+
+# Prepare for logs
+RUN mkdir /home/lofar/.logs && chown lofar:lofar /home/lofar/.logs
+
+# Add fluxbox customisations
+COPY files/dot_fluxbox /home/lofar/.fluxbox
+RUN chown -R lofar:lofar /home/lofar/.fluxbox
+COPY files/background.jpg /usr/share/images/fluxbox/background.jpg
+
+# Rename lofar home folder as a "vanilla" home folder
+RUN mv /home/lofar /lofar_home_vanilla
+
+# Give write access to anyone to the home folder so the entrypoint will be able
+# to copy over the /home/matauser_vanilla into /home/lofar (for Singularity)
+RUN chmod 777 /home
 
 
 #----------------------

base_v3/entrypoint.sh

 #!/bin/bash
 
-# Exit on any error. More complex thing could be done in future
+# Exit on any error. More complex stuff could be done in future
 # (see https://stackoverflow.com/questions/4381618/exit-a-script-on-error)
 set -e
 
-echo ""
-echo "[INFO] Executing entrypoint..."
 
-#echo "[INFO] Sourcing env in /opt/lofarsoft/lofarinit.sh..."
-source /opt/lofarsoft/lofarinit.sh
+if [ "x$SAFE_MODE" == "xTrue" ]; then
 
-echo "[INFO] Creating /tmp/lofarhome to be used as lofar home"
-mkdir /tmp/lofarhome
+    echo ""
+    echo "[INFO] Not executing entrypoint as we are in safe mode, just opening a Bash shell."
+    exec /bin/bash
 
-echo "[INFO] Initialising /tmp/lofarhome with configuration files"
-cp -aT /home/vanilla_lofar /tmp/lofarhome
+else
 
-echo "[INFO] Moving to /home/lofar and setting as home"
-cd /home/lofar
-export HOME=/home/lofar
+    echo ""
+    echo "[INFO] Executing entrypoint..."
+    
+    if [ "x$GUI" == "xTrue" ]; then
+	    if [ "x$BASE_PORT" == "x" ]; then
+	        echo "[INFO] No task base port set, will set noVNC port 8590 and VNC port 5900 with desktop id \"0\""  
+	    else 
+	        echo "[INFO] Task base port set, will set noVNC port $BASE_PORT and noVNC port $(($BASE_PORT+1)) with desktop id \"$(($BASE_PORT-5900+1))\""
+	    fi
+    fi
+    
+    #---------------------
+    #   Setup home
+    #---------------------
 
-echo "[INFO] Setting new prompt @$CONTAINER_NAME container"
-echo 'export PS1="${debian_chroot:+($debian_chroot)}\u@$CONTAINER_NAME@\h:\w\$ "' >> /tmp/lofarhome/.bashrc
+    if [ -f "/home/lofar/.initialized" ]; then
+        :
+    else
+        echo "[INFO] Setting up home"
+        mkdir -p /home/lofar
 
-# Set entrypoint command
-if [ "x$@" == "x" ]; then
-    COMMAND="/bin/bash"
-else
-    COMMAND="$@"
-fi
+        # Copy over vanilla home contents
+        for x in /lofar_home_vanilla/* /lofar_home_vanilla/.[!.]* /lofar_home_vanilla/..?*; do
+            if [ -e "$x" ]; then cp -a "$x" /home/lofar/; fi
+        done
+        
+        # Mark as initialized
+        touch /home/lofar/.initialized
+    fi
+    
 
+    #---------------------
+    #   Save env
+    #---------------------
+    echo "[INFO] Dumping env"
+    
+    # Save env vars for later usage (e.g. ssh)
+    
+    env | \
+    while read env_var; do
+      if [[ $env_var == HOME\=* ]]; then
+          : # Skip HOME var
+      elif [[ $env_var == PWD\=* ]]; then
+          : # Skip PWD var
+      else
+          echo "export $env_var" >> /tmp/env.sh
+      fi
+    done
+    
+    #---------------------
+    #   VNC Password
+    #---------------------
+    if [ "x$GUI" == "xTrue" ]; then
+	    if [ "x$AUTH_PASS" != "x" ]; then
+	        echo "[INFO] Setting up VNC password..."
+	        mkdir -p /home/lofar/.vnc
+	        /opt/tigervnc/usr/bin/vncpasswd -f <<< $AUTH_PASS > /home/lofar/.vnc/passwd
+	        chmod 600 /home/lofar/.vnc/passwd
+	        export VNC_AUTH=True
+	    else
+	        echo "[INFO] Not setting up any VNC password"
+	            
+	    fi
+    fi
+    
+	echo "[INFO] Creating /tmp/lofarhome to be used as lofar home"
+	mkdir /tmp/lofarhome
+	
+	echo "[INFO] Initializing /tmp/lofarhome with configuration files"
+	cp -aT /lofar_home_vanilla /tmp/lofarhome
+	
+	echo "[INFO] Moving to /home/lofar and setting as home"
+	cd /home/lofar
+	export HOME=/home/lofar
+	
+	echo "[INFO] Setting new prompt @$CONTAINER_NAME container"
+	echo 'export PS1="${debian_chroot:+($debian_chroot)}\u@$CONTAINER_NAME@\h:\w\$ "' >> /tmp/lofarhome/.bashrc
 
+    echo "[INFO] Sourcing env in /opt/lofarsoft/lofarinit.sh..."
+    source /opt/lofarsoft/lofarinit.sh
+    	
+			
+    # Set entrypoint command
+	if [ "x$@" == "x" ]; then
+	    if [ "x$GUI" == "xTrue" ]; then
+            COMMAND="supervisord -c /etc/supervisor/supervisord.conf"
+	    else
+	        COMMAND="/bin/bash"
+	    fi
+	else
+	    COMMAND="$@"
+	fi
+	
 
-# Start!
-echo -n "[INFO] Will execute entrypoint command: "
-echo $COMMAND
-echo ""
-echo "=============================================================="
-echo ""
-echo "      Welcome to the LOFAR-IT $CONTAINER_NAME container!"
-echo ""
-echo "=============================================================="
-echo ""
-echo "You are now in /home/lofar with write access as user \"$(whoami)\"."
-echo ""
-echo "Remember that contents inside this container, unless stored"
-echo "on a persistent volume mounted from you host machine, will"
-echo "be wiped out when exiting the container."
-echo ""
-
-exec $COMMAND
+    # Start!
+	echo -n "[INFO] Will execute entrypoint command: "
+	echo $COMMAND
+	echo ""
+	echo "=============================================================="
+	echo ""
+	echo "      Welcome to the LOFAR-IT $CONTAINER_NAME container!"
+	echo ""
+	echo "=============================================================="
+	echo ""
+	echo "You are now in /home/lofar with write access as user \"$(whoami)\"."
+	echo ""
+	echo "Remember that contents inside this container, unless stored"
+	echo "on a persistent volume mounted from you host machine, will"
+	echo "be wiped out when exiting the container."
+	echo ""
+	
+	exec $COMMAND
 
+fi

base_v3/files/dot_fluxbox/apps

+[app] (name=fbrun)
+  [Position]	(WINCENTER)	{0 0}
+  [Layer]	{2}
+[end]

base_v3/files/dot_fluxbox/init

+session.screen0.tabs.usePixmap:	true
+session.screen0.tabs.maxOver:	false
+session.screen0.tabs.intitlebar:	true
+session.screen0.clientMenu.usePixmap:	true
+session.screen0.iconbar.usePixmap:	true
+session.screen0.iconbar.iconTextPadding:	10
+session.screen0.iconbar.iconWidth:	128
+session.screen0.iconbar.alignment:	Relative
+session.screen0.iconbar.mode:	{static groups} (workspace)
+session.screen0.toolbar.visible:	true
+session.screen0.toolbar.height:	0
+session.screen0.toolbar.onhead:	1
+session.screen0.toolbar.widthPercent:	100
+session.screen0.toolbar.alpha:	255
+session.screen0.toolbar.maxOver:	false
+session.screen0.toolbar.autoHide:	false
+session.screen0.toolbar.layer:	Dock
+session.screen0.toolbar.placement:	BottomCenter
+#session.screen0.toolbar.tools:	prevworkspace, workspacename, nextworkspace, clock, prevwindow, nextwindow, iconbar, systemtray
+session.screen0.toolbar.tools: iconbar, systemtray
+session.screen0.menu.alpha:	255
+session.screen0.tab.placement:	TopLeft
+session.screen0.tab.width:	64
+session.screen0.titlebar.left:	Stick 
+session.screen0.titlebar.right:	Minimize Maximize Close 
+session.screen0.window.focus.alpha:	255
+session.screen0.window.unfocus.alpha:	255
+session.screen0.slit.alpha:	255
+session.screen0.slit.maxOver:	false
+session.screen0.slit.placement:	RightBottom
+session.screen0.slit.autoHide:	false
+session.screen0.slit.acceptKdeDockapps:	true
+session.screen0.slit.onhead:	0
+session.screen0.slit.layer:	Dock
+session.screen0.colPlacementDirection:	TopToBottom
+session.screen0.tabFocusModel:	ClickToTabFocus
+session.screen0.autoRaise:	true
+session.screen0.maxDisableMove:	false
+session.screen0.edgeSnapThreshold:	10
+session.screen0.tooltipDelay:	500
+session.screen0.opaqueMove:	true
+session.screen0.windowPlacement:	RowMinOverlapPlacement
+session.screen0.focusNewWindows:	true
+session.screen0.clickRaises:	true
+session.screen0.maxDisableResize:	false
+session.screen0.windowMenu:	/home/lofar/.fluxbox/windowmenu
+session.screen0.allowRemoteActions:	false
+session.screen0.strftimeFormat:	%d %b, %a %02k:%M:%S
+session.screen0.focusSameHead:	false
+session.screen0.workspacewarping:	true
+session.screen0.fullMaximization:	false
+session.screen0.defaultDeco:	NORMAL
+session.screen0.noFocusWhileTypingDelay:	0
+session.screen0.menuDelay:	200
+session.screen0.workspaceNames:	Workspace 1,Workspace 2,Workspace 3,Workspace 4,
+session.screen0.rowPlacementDirection:	LeftToRight
+session.screen0.focusModel:	ClickFocus
+session.screen0.showwindowposition:	false
+session.screen0.maxIgnoreIncrement:	true
+session.screen0.workspaces:	1
+session.styleOverlay:	/home/lofar/.fluxbox/overlay
+session.keyFile:	~/.fluxbox/keys
+session.cacheMax:	200
+session.tabsAttachArea:	Window
+session.slitlistFile:	/home/lofar/.fluxbox/slitlist
+session.forcePseudoTransparency:	false
+session.tabPadding:	0
+session.colorsPerChannel:	4
+session.styleFile:	/usr/share/fluxbox/styles//ubuntu-light
+session.autoRaiseDelay:	250
+session.cacheLife:	5
+session.appsFile:	/home/lofar/.fluxbox/apps
+session.ignoreBorder:	false
+session.configVersion:	13
+session.doubleClickInterval:	250
+session.menuFile:	~/.fluxbox/menu

base_v3/files/dot_fluxbox/keys

+# click on the desktop to get menus
+OnDesktop Mouse1 :HideMenus
+OnDesktop Mouse2 :WorkspaceMenu
+OnDesktop Mouse3 :RootMenu
+
+# scroll on the desktop to change workspaces
+OnDesktop Mouse4 :PrevWorkspace
+OnDesktop Mouse5 :NextWorkspace
+
+# scroll on the toolbar to change current window
+OnToolbar Mouse4 :PrevWindow {static groups} (iconhidden=no)
+OnToolbar Mouse5 :NextWindow {static groups} (iconhidden=no)
+
+# alt + left/right click to move/resize a window
+OnWindow Mod1 Mouse1 :MacroCmd {Raise} {Focus} {StartMoving}
+OnWindowBorder Move1 :StartMoving
+
+OnWindow Mod1 Mouse3 :MacroCmd {Raise} {Focus} {StartResizing NearestCorner}
+OnLeftGrip Move1 :StartResizing bottomleft
+OnRightGrip Move1 :StartResizing bottomright
+
+# alt + middle click to lower the window
+OnWindow Mod1 Mouse2 :Lower
+
+# control-click a window's titlebar and drag to attach windows
+OnTitlebar Control Mouse1 :StartTabbing
+
+# double click on the titlebar to shade
+OnTitlebar Double Mouse1 :Shade
+
+# left click on the titlebar to move the window
+OnTitlebar Mouse1 :MacroCmd {Raise} {Focus} {ActivateTab}
+OnTitlebar Move1  :StartMoving
+
+# middle click on the titlebar to lower
+OnTitlebar Mouse2 :Lower
+
+# right click on the titlebar for a menu of options
+OnTitlebar Mouse3 :WindowMenu
+
+# alt-tab
+Mod1 Tab :NextWindow {groups} (workspace=[current])
+Mod1 Shift Tab :PrevWindow {groups} (workspace=[current])
+
+# cycle through tabs in the current window
+Mod4 Tab :NextTab
+Mod4 Shift Tab :PrevTab
+
+# go to a specific tab in the current window
+Mod4 1 :Tab 1
+Mod4 2 :Tab 2
+Mod4 3 :Tab 3
+Mod4 4 :Tab 4
+Mod4 5 :Tab 5
+Mod4 6 :Tab 6
+Mod4 7 :Tab 7
+Mod4 8 :Tab 8
+Mod4 9 :Tab 9
+
+# open a terminal
+Mod1 F1 :Exec x-terminal-emulator
+
+# open a dialog to run programs
+Mod1 F2 :Exec fbrun
+
+# volume settings, using common keycodes
+# if these don't work, use xev to find out your real keycodes
+176 :Exec amixer sset Master,0 1+
+174 :Exec amixer sset Master,0 1-
+160 :Exec amixer sset Master,0 toggle
+
+# current window commands
+Mod1 F4 :Close
+Mod1 F5 :Kill
+Mod1 F9 :Minimize
+Mod1 F10 :Maximize
+Mod1 F11 :Fullscreen
+
+# open the window menu
+Mod1 space :WindowMenu
+
+# exit fluxbox
+Control Mod1 Delete :Exit
+
+# change to previous/next workspace
+Control Mod1 Left :PrevWorkspace
+Control Mod1 Right :NextWorkspace
+
+# send the current window to previous/next workspace
+Mod4 Left :SendToPrevWorkspace
+Mod4 Right :SendToNextWorkspace
+
+# send the current window and follow it to previous/next workspace
+Control Mod4 Left :TakeToPrevWorkspace
+Control Mod4 Right :TakeToNextWorkspace
+
+# change to a specific workspace
+Control F1 :Workspace 1
+Control F2 :Workspace 2
+Control F3 :Workspace 3
+Control F4 :Workspace 4
+Control F5 :Workspace 5
+Control F6 :Workspace 6
+Control F7 :Workspace 7
+Control F8 :Workspace 8
+Control F9 :Workspace 9
+Control F10 :Workspace 10
+Control F11 :Workspace 11
+Control F12 :Workspace 12
+
+# send the current window to a specific workspace
+Mod4 F1 :SendToWorkspace 1
+Mod4 F2 :SendToWorkspace 2
+Mod4 F3 :SendToWorkspace 3
+Mod4 F4 :SendToWorkspace 4
+Mod4 F5 :SendToWorkspace 5
+Mod4 F6 :SendToWorkspace 6
+Mod4 F7 :SendToWorkspace 7
+Mod4 F8 :SendToWorkspace 8
+Mod4 F9 :SendToWorkspace 9
+Mod4 F10 :SendToWorkspace 10
+Mod4 F11 :SendToWorkspace 11
+Mod4 F12 :SendToWorkspace 12
+
+# send the current window and change to a specific workspace
+Control Mod4 F1 :TakeToWorkspace 1
+Control Mod4 F2 :TakeToWorkspace 2
+Control Mod4 F3 :TakeToWorkspace 3
+Control Mod4 F4 :TakeToWorkspace 4
+Control Mod4 F5 :TakeToWorkspace 5
+Control Mod4 F6 :TakeToWorkspace 6
+Control Mod4 F7 :TakeToWorkspace 7
+Control Mod4 F8 :TakeToWorkspace 8
+Control Mod4 F9 :TakeToWorkspace 9
+Control Mod4 F10 :TakeToWorkspace 10
+Control Mod4 F11 :TakeToWorkspace 11
+Control Mod4 F12 :TakeToWorkspace 12

base_v3/files/dot_fluxbox/lastwallpaper

+$full $full|/usr/share/images/fluxbox/ubuntu-light.png|style|:0.0

base_v3/files/dot_fluxbox/menu

+[begin] (fluxbox)
+[include] (/etc/X11/fluxbox/fluxbox-menu)
+[end]

base_v3/files/dot_fluxbox/overlay

+! The following line will prevent styles from setting the background.
+! background: none
+background: aspect
+background.pixmap: /usr/share/images/fluxbox/background.jpg

base_v3/files/dot_fluxbox/windowmenu

+[begin]
+  [shade]
+  [stick]
+  [maximize]
+  [iconify]
+  [raise]
+  [lower]
+  [settitledialog]
+  [sendto]
+  [layer]
+  [alpha]
+  [extramenus]
+  [separator]
+  [close]
+[end]

base_v3/files/index.html

+<html>
+<head>
+<script type="text/javascript">
+function redirecter(){
+    window.location = "./vnc.html?autoconnect=true&resize=remote"
+}
+</script>
+</head>
+<body onLoad="redirecter()">
+Access VNC: click <a href="./vnc.html?autoconnect=true&resize=remote">here</a>.
+</body>
+</html>
\ No newline at end of file

base_v3/files/run_novnc.sh

+#!/bin/bash
+
+# Exec TigerVNC server 
+
+if [ "x$BASE_PORT" == "x" ]; then
+    /usr/lib/noVNC/utils/launch.sh --listen 8590
+    echo "Running noVNC on port 8590"
+else
+    /usr/lib/noVNC/utils/launch.sh --listen $BASE_PORT --vnc localhost:$(($BASE_PORT+1))
+    echo "Running noVNC on port $BASE_PORT and connecting to VNC on port $(($BASE_PORT+1))"
+
+fi

base_v3/files/run_vnc.sh

+#!/bin/bash
+
+# Exec TigerVNC server 
+
+if [ "x$BASE_PORT" == "x" ]; then
+    DESKTOP_NUMBER=0
+else
+    DESKTOP_NUMBER=$(($BASE_PORT-5900+1))
+fi
+
+if [ "x$VNC_AUTH" == "xTrue" ]; then
+    /opt/tigervnc/usr/bin/vncserver :$DESKTOP_NUMBER -SecurityTypes vncauth,tlsvnc -xstartup /opt/tigervnc/xstartup
+else
+    /opt/tigervnc/usr/bin/vncserver :$DESKTOP_NUMBER -SecurityTypes None -xstartup /opt/tigervnc/xstartup
+fi
+
+
+# Check it is running. If it is not, exit
+while true
+do
+
+    PSOUT=$(ps -ef | grep /opt/tigervnc/usr/bin/Xvnc | grep SecurityTypes) 
+
+    if [[ "x$PSOUT" == "x" ]] ; then
+        exit 1
+    fi
+
+	# Sleep other 10 secs before re-checking
+	sleep 10
+
+done

base_v3/files/supervisord.conf

+; supervisor config file (modified for our own purpose)
+
+[unix_http_server]
+file=/home/lofar/.supervisor.sock   ; (the path to the socket file)
+chmod=0700                             ; sockef file mode (default 0700)
+
+[supervisord]
+logfile=/home/lofar/.logs/supervisord.log   ; (main log file;default $CWD/supervisord.log)
+pidfile=/home/lofar/.logs/supervisord.pid   ; (supervisord pidfile;default supervisord.pid)
+childlogdir=/home/lofar/.logs               ; ('AUTO' child log dir, default $TEMP)
+nodaemon=true                                  ; Mandatory to run Supervisor in foreground and avoid Docker to exit!
+
+; The below section must remain in the config file for RPC
+; (supervisorctl/web interface) to work, additional interfaces may be
+; added by defining them in separate rpcinterface: sections
+[rpcinterface:supervisor]
+supervisor.rpcinterface_factory = supervisor.rpcinterface:make_main_rpcinterface
+
+[supervisorctl]
+serverurl=unix:///home/lofar/.supervisor.sock ; use a unix:// URL  for a unix socket
+
+; The [include] section can just contain the "files" setting.  This
+; setting can list multiple files (separated by whitespace or
+; newlines).  It can also contain wildcards.  The filenames are
+; interpreted as relative to this file.  Included files *cannot*
+; include files themselves.
+
+[include]
+files = /etc/supervisor/conf.d/*.conf

base_v3/files/supervisord_novnc.conf

+;=======================================
+; noVNC service
+;=======================================
+ 
+[program:novnc]
+ 
+; General
+directory     = /usr/lib/noVNC/
+command       = /etc/supervisor/conf.d/run_novnc.sh
+numprocs      = 1
+autostart     = true
+autorestart   = true
+startsecs     = 10
+stopwaitsecs  = 30
+process_name  = novnc
+ 
+; Standard out / error
+stdout_logfile          = /home/lofar/.logs/%(program_name)s.log
+stdout_logfile_maxbytes = 5MB
+stdout_logfile_backups  = 10
+stderr_logfile          = /home/lofar/.logs/%(program_name)s.log
+stderr_logfile_maxbytes = 5MB
+stderr_logfile_backups  = 10

base_v3/files/supervisord_vnc.conf

+;=======================================
+; VNC service
+;=======================================
+ 
+[program:vnc]
+ 
+; General
+directory     = /
+command       = /etc/supervisor/conf.d/run_vnc.sh
+numprocs      = 1
+autostart     = true
+autorestart   = true
+startsecs     = 10
+stopwaitsecs  = 30
+process_name  = vnc
+ 
+; Standard out / error
+stdout_logfile          = /home/lofar/.logs/%(program_name)s.log
+stdout_logfile_maxbytes = 5MB
+stdout_logfile_backups  = 10
+stderr_logfile          = /home/lofar/.logs/%(program_name)s.log
+stderr_logfile_maxbytes = 5MB
+stderr_logfile_backups  = 10

base_v3/files/xstartup

+#!/bin/sh
+
+cd /home/lofar
+
+unset SESSION_MANAGER
+unset DBUS_SESSION_BUS_ADDRESS
+OS=`uname -s`
+if [ $OS = 'Linux' ]; then
+  case "$WINDOWMANAGER" in
+    *gnome*)
+      if [ -e /etc/SuSE-release ]; then
+        PATH=$PATH:/opt/gnome/bin
+        export PATH
+      fi
+      ;;
+  esac
+fi
+if [ -x /etc/X11/xinit/xinitrc ]; then
+  exec /etc/X11/xinit/xinitrc
+fi
+if [ -f /etc/X11/xinit/xinitrc ]; then
+  exec sh /etc/X11/xinit/xinitrc
+fi
+[ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources
+#xsetroot -solid grey
+xterm -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" /bin/bash &
+
+#twm &
+fluxbox &

base_v4/Dockerfile

@@ -36,10 +36,63 @@ COPY data/input_data /input_data
 COPY data/output_data /output_data
 RUN chown lofar:lofar /home/lofar && chown -R lofar:lofar /input_data && chown -R lofar:lofar /output_data
 
-# This is required mainly for Singularity
-RUN mv /home/lofar /home/vanilla_lofar
-RUN ln -s /tmp/lofarhome /home/lofar
-RUN rm -rf /tmp/lofarhome
+
+#----------------------
+# Minimal Desktop
+#----------------------
+
+# Utilities
+RUN apt-get install -y telnet unzip wget supervisor build-essential python-dev git-core openjdk-8-jre
+
+# Global Supervisord conf
+COPY files/supervisord.conf /etc/supervisor/
+
+# Install xvfb that triggers minimal install of X base packages and xterm
+RUN apt-get install xvfb xterm  -y
+
+# Install base packages for VNC server and headless desktop (2)
+RUN cd /opt && wget https://bintray.com/tigervnc/stable/download_file?file_path=tigervnc-1.8.0.x86_64.tar.gz -O tigervnc-1.8.0.x86_64.tar.gz \
+            && tar -zxvf tigervnc-1.8.0.x86_64.tar.gz \
+            && mv tigervnc-1.8.0.x86_64 tigervnc
+
+# Supervisord configuration
+COPY files/supervisord_vnc.conf /etc/supervisor/conf.d/
+COPY files/run_vnc.sh /etc/supervisor/conf.d/
+COPY files/run_novnc.sh /etc/supervisor/conf.d/
+RUN chmod 755 /etc/supervisor/conf.d/run_vnc.sh
+RUN chmod 755 /etc/supervisor/conf.d/run_novnc.sh
+
+# Web VNC (noVNC) v0.6.1.
+# NOTE: this is a custom version from Doro Wu (fcwu.tw@gmail.com).
+# TODO: Check differences and maybe move to 0.6.2
+COPY files/noVNC.tar.gz /usr/lib/
+RUN cd /usr/lib/ && tar -zxvf noVNC.tar.gz
+COPY files/index.html /usr/lib/noVNC
+
+RUN apt-get install -y net-tools
+
+# Supervisord configuration
+COPY files/supervisord_novnc.conf /etc/supervisor/conf.d/
+
+# X environment setup/startup
+RUN apt-get install fluxbox -y
+COPY files/xstartup /opt/tigervnc/
+RUN chmod 755 /opt/tigervnc/xstartup
+
+# Prepare for logs
+RUN mkdir /home/lofar/.logs && chown lofar:lofar /home/lofar/.logs
+
+# Add fluxbox customisations
+COPY files/dot_fluxbox /home/lofar/.fluxbox
+RUN chown -R lofar:lofar /home/lofar/.fluxbox
+COPY files/background.jpg /usr/share/images/fluxbox/background.jpg
+
+# Rename lofar home folder as a "vanilla" home folder
+RUN mv /home/lofar /lofar_home_vanilla
+
+# Give write access to anyone to the home folder so the entrypoint will be able
+# to copy over the /home/matauser_vanilla into /home/lofar (for Singularity)
+RUN chmod 777 /home
 
 
 #----------------------

base_v4/entrypoint.sh

 #!/bin/bash
 
-# Exit on any error. More complex thing could be done in future
+# Exit on any error. More complex stuff could be done in future
 # (see https://stackoverflow.com/questions/4381618/exit-a-script-on-error)
 set -e
 
-echo ""
-echo "[INFO] Executing entrypoint..."
 
-#echo "[INFO] Sourcing env in /opt/lofarsoft/lofarinit.sh..."
-#source /opt/lofarsoft/lofarinit.sh
+if [ "x$SAFE_MODE" == "xTrue" ]; then
 
-echo "[INFO] Creating /tmp/lofarhome to be used as lofar home"
-mkdir /tmp/lofarhome
+    echo ""
+    echo "[INFO] Not executing entrypoint as we are in safe mode, just opening a Bash shell."
+    exec /bin/bash
 
-echo "[INFO] Initialising /tmp/lofarhome with configuration files"
-cp -aT /home/vanilla_lofar /tmp/lofarhome
+else
 
-echo "[INFO] Moving to /home/lofar and setting as home"
-cd /home/lofar
-export HOME=/home/lofar
+    echo ""
+    echo "[INFO] Executing entrypoint..."
+    
+    if [ "x$GUI" == "xTrue" ]; then
+	    if [ "x$BASE_PORT" == "x" ]; then
+	        echo "[INFO] No task base port set, will set noVNC port 8590 and VNC port 5900 with desktop id \"0\""  
+	    else 
+	        echo "[INFO] Task base port set, will set noVNC port $BASE_PORT and noVNC port $(($BASE_PORT+1)) with desktop id \"$(($BASE_PORT-5900+1))\""
+	    fi
+    fi
+    
+    #---------------------
+    #   Setup home
+    #---------------------
 
-echo "[INFO] Setting new prompt @$CONTAINER_NAME container"
-echo 'export PS1="${debian_chroot:+($debian_chroot)}\u@$CONTAINER_NAME@\h:\w\$ "' >> /tmp/lofarhome/.bashrc
+    if [ -f "/home/lofar/.initialized" ]; then
+        :
+    else
+        echo "[INFO] Setting up home"
+        mkdir -p /home/lofar
 
-# Set entrypoint command
-if [ "x$@" == "x" ]; then
-    COMMAND="/bin/bash"
-else
-    COMMAND="$@"
-fi
+        # Copy over vanilla home contents
+        for x in /lofar_home_vanilla/* /lofar_home_vanilla/.[!.]* /lofar_home_vanilla/..?*; do
+            if [ -e "$x" ]; then cp -a "$x" /home/lofar/; fi
+        done
+        
+        # Mark as initialized
+        touch /home/lofar/.initialized
+    fi
+    
 
+    #---------------------
+    #   Save env
+    #---------------------
+    echo "[INFO] Dumping env"
+    
+    # Save env vars for later usage (e.g. ssh)
+    
+    env | \
+    while read env_var; do
+      if [[ $env_var == HOME\=* ]]; then
+          : # Skip HOME var
+      elif [[ $env_var == PWD\=* ]]; then
+          : # Skip PWD var
+      else
+          echo "export $env_var" >> /tmp/env.sh
+      fi
+    done
+    
+    #---------------------
+    #   VNC Password
+    #---------------------
+    if [ "x$GUI" == "xTrue" ]; then
+	    if [ "x$AUTH_PASS" != "x" ]; then
+	        echo "[INFO] Setting up VNC password..."
+	        mkdir -p /home/lofar/.vnc
+	        /opt/tigervnc/usr/bin/vncpasswd -f <<< $AUTH_PASS > /home/lofar/.vnc/passwd
+	        chmod 600 /home/lofar/.vnc/passwd
+	        export VNC_AUTH=True
+	    else
+	        echo "[INFO] Not setting up any VNC password"
+	            
+	    fi
+    fi
+    
+	echo "[INFO] Creating /tmp/lofarhome to be used as lofar home"
+	mkdir /tmp/lofarhome
+	
+	echo "[INFO] Initializing /tmp/lofarhome with configuration files"
+	cp -aT /lofar_home_vanilla /tmp/lofarhome
+	
+	echo "[INFO] Moving to /home/lofar and setting as home"
+	cd /home/lofar
+	export HOME=/home/lofar
+	
+	echo "[INFO] Setting new prompt @$CONTAINER_NAME container"
+	echo 'export PS1="${debian_chroot:+($debian_chroot)}\u@$CONTAINER_NAME@\h:\w\$ "' >> /tmp/lofarhome/.bashrc
 
+	
+    # Set entrypoint command
+	if [ "x$@" == "x" ]; then
+	    if [ "x$GUI" == "xTrue" ]; then
+            COMMAND="supervisord -c /etc/supervisor/supervisord.conf"
+	    else
+	        COMMAND="/bin/bash"
+	    fi
+	else
+	    COMMAND="$@"
+	fi
+	
 
-# Start!
-echo -n "[INFO] Will execute entrypoint command: "
-echo $COMMAND
-echo ""
-echo "=============================================================="
-echo ""
-echo "      Welcome to the LOFAR-IT $CONTAINER_NAME container!"
-echo ""
-echo "=============================================================="
-echo ""
-echo "You are now in /home/lofar with write access as user \"$(whoami)\"."
-echo ""
-echo "Remember that contents inside this container, unless stored"
-echo "on a persistent volume mounted from you host machine, will"
-echo "be wiped out when exiting the container."
-echo ""
-
-exec $COMMAND
+    # Start!
+	echo -n "[INFO] Will execute entrypoint command: "
+	echo $COMMAND
+	echo ""
+	echo "=============================================================="
+	echo ""
+	echo "      Welcome to the LOFAR-IT $CONTAINER_NAME container!"
+	echo ""
+	echo "=============================================================="
+	echo ""
+	echo "You are now in /home/lofar with write access as user \"$(whoami)\"."
+	echo ""
+	echo "Remember that contents inside this container, unless stored"
+	echo "on a persistent volume mounted from you host machine, will"
+	echo "be wiped out when exiting the container."
+	echo ""
+	
+	exec $COMMAND
 
+fi