created an ubuntu Eclipse CDT development container for C++.

CMakeLists.txt

@@ -35,7 +35,7 @@ elseif (LINUX)
 endif()
 
 project(numerics)
-cmake_minimum_required(VERSION 2.8.9)
+cmake_minimum_required(VERSION 3.0)
 enable_language(CXX)
 enable_language(C)
 enable_language(Fortran)

VCell/src/SimTool.cpp

@@ -895,6 +895,7 @@ void SimTool::start1() {
 		if (duration >= 2){
 			percentile = (simulation->getTime_sec() - simStartTime)/(simEndTime - simStartTime);
 			if (percentile - lastSentPercentile >= increment) {
+				std::cout << "SimTool.start1() sending JOB_PROGRESS to SimulationMessaging: percentile=" << percentile << ", time=" << simulation->getTime_sec() << std::endl;
 				SimulationMessaging::getInstVar()->setWorkerEvent(new WorkerEvent(JOB_PROGRESS, percentile, simulation->getTime_sec()));
 				lastSentPercentile = percentile;
 				oldTime = currentTime;

VagrantBoxes/linux64-ubuntu/Vagrantfile

@@ -2,26 +2,16 @@
 # vi: set ft=ruby :
 
 Vagrant.configure("2") do |config|
-  config.vm.box = "ubuntu/trusty64"
+  config.vm.box = "ubuntu/xenial64"
   config.vm.synced_folder "../..", "/vagrant_numerics"
+  config.ssh.forward_x11 = true
   config.vm.provider "virtualbox" do |vb|
   	vb.name = "vcell-solvers-ubuntu64"
   end
 
   config.vm.provision "shell", inline: <<-SHELL
-    sudo apt-get install -y -qq -o=Dpkg::Use-Pty=0  build-essential
-    sudo apt-get install -y -qq -o=Dpkg::Use-Pty=0  gfortran
-    sudo apt-get install -y -qq -o=Dpkg::Use-Pty=0  zlib1g-dev
-    sudo apt-get install -y -qq -o=Dpkg::Use-Pty=0  libhdf5-dev    
-    
-    #wget https://cmake.org/files/v3.8/cmake-3.8.1.tar.gz
-    #sudo tar xzf cmake-3.8.1.tar.gz
-    #cd cmake-3.8.1
-    #sudo ./configure --prefix=/opt/cmake
-    #sudo make --quiet 
-    #sudo make --quiet install
-    
-    sudo apt-get install -y -qq -o=Dpkg::Use-Pty=0  cmake3    
-    
+    apt-get -y update && apt-get install -y apt-utils && \
+    apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran zlib1g-dev \
+    libhdf5-dev libcurl4-openssl-dev libboost-dev cmake    
 SHELL
 end

docker/Dockerfile-ide

@@ -0,0 +1,33 @@
+FROM ubuntu:xenial as build
+
+RUN apt-get -y update && apt-get install -y apt-utils && \
+    apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran gdb cmake expect
+
+RUN apt-get install -y software-properties-common  python-software-properties
+
+RUN add-apt-repository ppa:ubuntu-desktop/ubuntu-make
+RUN	apt -y update
+RUN apt-get install -y ubuntu-make
+
+#RUN umake -v ide eclipse-cpp
+RUN export COMMAND="spawn umake ide eclipse-cpp;" \
+    SLEEP="sleep 3;" \
+    EXPECT_PROMPT="expect -re \"Choose installation path: /root/.local/share/umake/ide/eclipse-cpp\";" \
+    SEND="send \"\r\n\";" \
+    TIMEOUT="set timeout -1;" \
+    EXPECT_DONE="expect -re \"Installation done\";" && \
+    expect -c "$COMMAND $SLEEP $EXPECT_PROMPT $SEND $TIMEOUT $EXPECT_DONE"
+
+
+RUN apt-get install -y -qq -o=Dpkg::Use-Pty=0 zlib1g-dev libhdf5-dev libcurl4-openssl-dev libboost-dev
+
+
+# RUN useradd -ms /bin/bash  developer
+# USER developer
+# ENV HOME /home/developer
+WORKDIR /workspace/build-docker
+
+VOLUME /workspace
+
+CMD /root/.local/share/umake/ide/eclipse-cpp/eclipse -data /workspace
+

docker/build.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+DIR="$(cd "$(dirname "$0")"; pwd)"
+echo "dir is $DIR"
+
+cd $DIR
+
+image_name="localhost:5000/vcell-solvers-ide:dev"
+
+docker build -f ./Dockerfile-ide --tag $image_name .
+

docker/cmake.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+mkdir -p /workspace/vcell-solvers-build
+cd /workspace/vcell-solvers-build
+
+cmake \
+    -G "Eclipse CDT4 - Unix Makefiles" \
+    -DCMAKE_BUILD_TYPE="Debug" \
+    -DOPTION_TARGET_MESSAGING=ON \
+    -DOPTION_TARGET_PARALLEL=OFF \
+    -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
+    -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
+    -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
+    -DOPTION_TARGET_FV_SOLVER=ON \
+    -DOPTION_TARGET_STOCHASTIC_SOLVER=OFF \
+    -DOPTION_TARGET_NFSIM_SOLVER=OFF \
+    -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
+    -DOPTION_TARGET_SUNDIALS_SOLVER=OFF \
+    -DOPTION_TARGET_HY3S_SOLVERS=OFF \
+    ../vcell-solvers
+
+

docker/eclipse.sh

@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+
+THIS_DIR="$(cd "$(dirname "$0")"; pwd)"
+PROJECT_DIR="$(cd "$(dirname "$0")"; cd ..; pwd)"
+WORKSPACE_DIR="$(cd "$(dirname "$0")"; cd ..; cd ..; pwd)"
+echo "dir is $THIS_DIR"
+echo "projectDir is $PROJECT_DIR"
+echo "workspaceDir is $WORKSPACE_DIR"
+
+
+# https://cntnr.io/running-guis-with-docker-on-mac-os-x-a14df6a76efc
+# https://blog.alexellis.io/linux-desktop-on-mac/
+
+# > brew install socat
+# > socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\"
+
+# to test ability to run an X program:
+#   docker run -e DISPLAY=$IP gns3/xeyes
+
+# (socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\") &
+
+IP=$(ifconfig en0 | grep inet | awk '$1=="inet" {print $2}')
+
+image_name="localhost:5000/vcell-solvers-ide:dev"
+WORKSPACE_DIR=/Users/schaff/Documents/workspace-modular
+ECLIPSE="/root/.local/share/umake/ide/eclipse-cpp/eclipse"
+
+docker run -it  \
+  -v "$WORKSPACE_DIR:/workspace" -e DISPLAY=$IP:0 $image_name \
+  $ECLIPSE -data /workspace

docker/run.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+THIS_DIR="$(cd "$(dirname "$0")"; pwd)"
+PROJECT_DIR="$(cd "$(dirname "$0")"; cd ..; pwd)"
+WORKSPACE_DIR="$(cd "$(dirname "$0")"; cd ..; cd ..; pwd)"
+echo "dir is $THIS_DIR"
+echo "projectDir is $PROJECT_DIR"
+echo "workspaceDir is $WORKSPACE_DIR"
+
+
+# https://cntnr.io/running-guis-with-docker-on-mac-os-x-a14df6a76efc
+# https://blog.alexellis.io/linux-desktop-on-mac/
+
+# > brew install socat
+# > socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\"
+
+# to test ability to run an X program:
+#   docker run -e DISPLAY=$IP gns3/xeyes
+
+# (socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\") &
+
+IP=$(ifconfig en0 | grep inet | awk '$1=="inet" {print $2}')
+
+image_name="localhost:5000/vcell-solvers-ide:dev"
+
+echo docker run -it \
+  -v "$WORKSPACE_DIR:/workspace" -e DISPLAY=$IP:0 $image_name /bin/bash