Release 7.1.0 (#149)

* ROSS cleanup (#135)

This commit fixes warnings when building with -Wall and -Wextra.  In addition, removes old unused code related to prior pthread versions of ROSS as well as removing the ROSS_MEMORY related code, due to no longer being fully functional.

* fixing warnings when building with Wall, etc

* fixing warnings in buddy.c

* fixing warnings in the rest of ROSS core

* fixing warnings in instrumentation

* fixing warnings with phold

* fixing undefined reference causing linking error

* adding warning flags to Travis builds

* fixing some additional warnings that appear in release builds

* minor changes to travis builds

* removing old, unnecessary pthread related code

* fixing ifdefs for ROSS_MEMORY

* removing tw-memory related stuff for now

* removing some unused stuff and unnecessary function arguments

* lots of documentation for network-mpi and removing some unnecessary stuff

* keeping the ROSS models submodule from being used in Travis tests

* minor fix for C++ Travis build

* adding installing phold to bin

* adding some RPATH commands to CMakeLists.txt for Spack

* removed ROSS-Models and template model submodule

* update readme for submodule details

* rpath in pkg-config

* adding develop branch to Travis safelist

* simplifying the build of static or shared libraries (#147)

* Update to the way the build process grabs version number (#148)

* updating the way the version number is grabbed, so we can have the actual version and not the git commit

* fixing an error that caused coveralls to fail

* updating README and removing out-of-date README-vis (current info is on webpage)

* few more updates to README

* changing damaris submodule/directory to risa

* see if gcov and clang versions match (#150)

* see if gcov and clang versions match

* maybe we should be using lcov... since we apt-get it

* whitespace

* what version is llvm-cov?

* use llvm-cov

* llvm-cov gcov

* remove cov version checks

* removing ROSS_obj from Cmake build - no longer necessary with single library creation

* removing some files that are actually unnecessary for version numbers as well as having ROSS output both version number and commit, instead of just version

Author: caitlinross

.gitmodules

@@ -1,9 +1,3 @@
-[submodule "models/template-model"]
-	path = models/template-model
-	url = https://github.com/ROSS-org/template-model.git
-[submodule "models/ROSS-Models"]
-	path = models/ROSS-Models
-	url = https://github.com/carothersc/ROSS-Models
-[submodule "damaris"]
-	path = core/damaris
-	url = https://github.com/caitlinross/ROSS-damaris
+[submodule "risa"]
+	path = core/risa
+	url = https://github.com/ROSS-org/RISA

.travis.yml

@@ -10,6 +10,8 @@ notifications:
     on_failure: always
 env:
  - secure: "BbB1KVY0Yb6DJwxdfFDF1PJwSx9euNfNX94oDKftiH8LE0nEzfS6xZc2sBkWTWOThHml9ttBkDIx/NhxEThOjyVcX6uv4kibP6moV5EqxqC+kLoZSEZnVuAdTJfGRKBdzmRp66R5a/GiMzzz/F3+smdVFMb6XR06sPQa5TQZjEc="
+git:
+  submodules: false
 before_install:
  - sudo apt-add-repository -y ppa:libreoffice/libreoffice-4-2
  - sudo apt-get update -q
@@ -21,29 +23,31 @@ before_install:
  - mpirun --version
 script:
  - mkdir cxx-build && cd cxx-build
- - cmake -DCMAKE_BUILD_TYPE=Release ..
+ - cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_FLAGS="-Wall -Wextra" ..
  - export MPICH_CC=clang++
  - make
  - unset MPICH_CC
  - cd ..
  - mkdir release && cd release
- - MPICH_CC=clang cmake -DCMAKE_BUILD_TYPE=Release -DROSS_BUILD_MODELS=ON ..
+ - MPICH_CC=clang cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_FLAGS="-Wall -Wextra" -DROSS_BUILD_MODELS=ON ..
  - make
  - CTEST_OUTPUT_ON_FAILURE=1 make test
  - cd ..
  - mkdir build && cd build
- - MPICH_CC=clang cmake -DCOVERALLS=ON -DCMAKE_BUILD_TYPE=Debug -DROSS_BUILD_MODELS=ON ..
+ - MPICH_CC=clang cmake -DCOVERALLS=ON -DCMAKE_BUILD_TYPE=Debug -DCMAKE_C_FLAGS="-Wall -Wextra" -DROSS_BUILD_MODELS=ON ..
  - make
  - CTEST_OUTPUT_ON_FAILURE=1 make test
  - make coveralls
  - cd ..
  - mkdir build2 && cd build2
- - MPICH_CC=clang cmake -DAVL_TREE=OFF -DCOVERALLS=ON -DCMAKE_BUILD_TYPE=Debug -DROSS_BUILD_MODELS=ON ..
+ - MPICH_CC=clang cmake -DAVL_TREE=OFF -DCOVERALLS=ON -DCMAKE_BUILD_TYPE=Debug -DCMAKE_C_FLAGS="-Wall -Wextra" -DROSS_BUILD_MODELS=ON ..
  - make
  - CTEST_OUTPUT_ON_FAILURE=1 make test
  - make coveralls
 branches:
-  only: master
+  only:
+  - master
+  - develop
 after_success:
   - bash <(curl -s https://codecov.io/bash)
   - ## the following automatically builds the doxygen

CMakeLists.txt

@@ -10,6 +10,35 @@ INCLUDE(CTest)
 
 LIST(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/core/cmake/")
 
+# Follow section based on Spack doc: 
+# https://spack.readthedocs.io/en/latest/workflows.html#write-the-cmake-build
+# enable @rpath in the install name for any shared library being built
+# note: it is planned that a future version of CMake will enable this by default
+set(CMAKE_MACOSX_RPATH 1)
+
+# Always use full RPATH
+# http://www.cmake.org/Wiki/CMake_RPATH_handling
+# http://www.kitware.com/blog/home/post/510
+
+# use, i.e. don't skip the full RPATH for the build tree
+SET(CMAKE_SKIP_BUILD_RPATH  FALSE)
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# the RPATH to be used when installing, but only if it's not a system directory
+LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
+IF("${isSystemDir}" STREQUAL "-1")
+   SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+ENDIF("${isSystemDir}" STREQUAL "-1")
+
+# end of spack-related addition
+
 # We probably don't want this to run on every build.
 option(COVERALLS "Generate coveralls data" OFF)
 

README-vis.md

@@ -6,6 +6,8 @@ You may find the now-deprecated version at the [ROSS-Legacy tag](https://github.
 Using this repository you can compare files from the new `ROSS/core` to `ROSS/ross`.
 For a detailed list of changes between old ROSS and SR please visit [the wiki](https://github.com/ROSS-org/ROSS/wiki/Differences-between-Simplified-ROSS-and-ROSS-Legacy).
 
+For the most recent docs and other important posts about ROSS, see the [ROSS webpage](http://ross-org.github.io).
+
 [![Build Status](https://travis-ci.com/ROSS-org/ROSS.svg?branch=master)](https://travis-ci.com/ROSS-org/ROSS)
 [![codecov.io](http://codecov.io/github/ROSS-org/ROSS/coverage.svg?branch=master)](http://codecov.io/github/ROSS-org/ROSS?branch=master)
 [![Doxygen](https://img.shields.io/badge/doxygen-reference-blue.svg)](http://ross-org.github.io/ROSS-docs/docs/html)
@@ -27,7 +29,7 @@ Developed as Simplified ROSS ([gonsie/SR](http://github.com/gonsie/SR)), this ve
 ## Requirements
 
 1. ROSS is written in C standard and thus requires a C compiler (C11 is prefered, but not required).
-2. The build system is [CMake](http://cmake.org), and we require version 2.8 or higher.
+2. The build system is [CMake](http://cmake.org), and we require version 3.5 or higher.
 3. ROSS relies on MPI.
    We recommend the [MPICH](http://www.mpich.org) implementation.
 
@@ -46,18 +48,17 @@ Developed as Simplified ROSS ([gonsie/SR](http://github.com/gonsie/SR)), this ve
   git submodule init
   git submodule update
   ```
-  Currently, ROSS includes three submodules:
-  - [ROSS-Models](http://github.com/ROSS-org/ROSS-Models) is a set of existing models
-  - [template-model](http://github.com/ROSS-org/template-model) is a starting place for new models
+  Currently, ROSS includes one submodule:
+  - [RISA](https://github.com/ROSS-org/RISA) ROSS In Situ Analysis
 
 3. *Optional* Symlink your model to ROSS.
-Please [this wiki page](https://github.com/ROSS-org/ROSS/wiki/Constructing-the-Model) for details about creating and integrating a model with ROSS.
+Please [this blog post](https://ross-org.github.io/setup/build-model-with-ross.html) for details about creating and integrating a model with ROSS.
   ```
   ln -s ~/path-to/your-existing-model models/your-model-name
   ```
 
 4. Create a build directory.
-ROSS developers typically do out-of-tree builds.  See the [Installation page](https://github.com/ROSS-org/ROSS/wiki/Installation) for more details.
+ROSS developers typically do out-of-tree builds.  See the [Installation page](https://ross-org.github.io/setup/installation.html) for more details.
   ```
   cd ~/directory-of-builds/
   mkdir ROSS-build
@@ -73,7 +74,7 @@ ROSS developers typically do out-of-tree builds.  See the [Installation page](ht
   ```
 
 6. Run your model.
-See [this wiki page](https://github.com/ROSS-org/ROSS/wiki/Running-the-Simulator) for details about the ROSS command line options.
+See [this blog post](https://ross-org.github.io/setup/running-sim.html) for details about the ROSS command line options.
   ```
   cd ~/directory-of-builds/ROSS-build/models/your-model
   ./your-model --synch=1               // sequential mode