Switch to github org 'quinoacomputing' from personal 'jbakosi'

Also fix static-alpine docker Charm++ build, see
https://lists.cs.illinois.edu/lists/arc/charm/2016-05/msg00013.html.

README.md

@@ -1,4 +1,4 @@
-[![Join the chat at https://gitter.im/jbakosi/quinoa](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/jbakosi/quinoa?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Join the chat at https://gitter.im/quinoacomputing/quinoa](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/quinoacomputing/quinoa?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 ## What is Quinoa?
 
@@ -7,27 +7,27 @@ Quinoa is a set of computational tools that enables research and numerical analy
 ## Organization
 
 Currently, Quinoa consists of the following tools:
-  - [<B>inciter</B>](https://jbakosi.github.io/quinoa/inciter_doc.html) - Solve a PDE on an unstructured mesh using overdecomposition
-  - [<B>walker</B>](https://jbakosi.github.io/quinoa/walker_doc.html) - Random walker for stochastic differential equations
-  - [<B>rngtest</B>](https://jbakosi.github.io/quinoa/rngtest_doc.html) - Random number generator test suite
-  - [<B>unittest</B>](https://jbakosi.github.io/quinoa/unittest_doc.html) - Unit test suite
-  - [<B>meshconv</B>](https://jbakosi.github.io/quinoa/meshconv_doc.html) - Mesh file converter
+  - [<B>inciter</B>](https://quinoacomputing.github.io/quinoa/inciter_doc.html) - Solve a PDE on an unstructured mesh using overdecomposition
+  - [<B>walker</B>](https://quinoacomputing.github.io/quinoa/walker_doc.html) - Random walker for stochastic differential equations
+  - [<B>rngtest</B>](https://quinoacomputing.github.io/quinoa/rngtest_doc.html) - Random number generator test suite
+  - [<B>unittest</B>](https://quinoacomputing.github.io/quinoa/unittest_doc.html) - Unit test suite
+  - [<B>meshconv</B>](https://quinoacomputing.github.io/quinoa/meshconv_doc.html) - Mesh file converter
 
 ## Goals
 
-  - [<B>Designed for the exascale era</B>](https://jbakosi.github.io/quinoa/why.html#exascale)
-  - [<B>Verified and proven to be correct</B>](https://jbakosi.github.io/quinoa/why.html#correct)
-  - [<B>Optimized for performance, power, and reliability</B>](https://jbakosi.github.io/quinoa/why.html#optimized)
-  - [<B>Advanced computer science outsourced to experts</B>](https://jbakosi.github.io/quinoa/why.html#outsource)
-  - [<B>Using a language that can cope with complexity</B>](https://jbakosi.github.io/quinoa/why.html#language)
-  - [<B>Highly-valued programmer productivity</B>](https://jbakosi.github.io/quinoa/why.html#productivity)
-  - [<B>User and developer friendly</B>](https://jbakosi.github.io/quinoa/why.html#friendly)
-  - [<B>Well documented</B>](https://jbakosi.github.io/quinoa/why.html#documented)
-  - [<B>Fun to work on</B>](https://jbakosi.github.io/quinoa/why.html#fun)
+  - [<B>Designed for the exascale era</B>](https://quinoacomputing.github.io/quinoa/why.html#exascale)
+  - [<B>Verified and proven to be correct</B>](https://quinoacomputing.github.io/quinoa/why.html#correct)
+  - [<B>Optimized for performance, power, and reliability</B>](https://quinoacomputing.github.io/quinoa/why.html#optimized)
+  - [<B>Advanced computer science outsourced to experts</B>](https://quinoacomputing.github.io/quinoa/why.html#outsource)
+  - [<B>Using a language that can cope with complexity</B>](https://quinoacomputing.github.io/quinoa/why.html#language)
+  - [<B>Highly-valued programmer productivity</B>](https://quinoacomputing.github.io/quinoa/why.html#productivity)
+  - [<B>User and developer friendly</B>](https://quinoacomputing.github.io/quinoa/why.html#friendly)
+  - [<B>Well documented</B>](https://quinoacomputing.github.io/quinoa/why.html#documented)
+  - [<B>Fun to work on</B>](https://quinoacomputing.github.io/quinoa/why.html#fun)
 
 ## License
 
-See the [license](https://github.com/jbakosi/quinoa/blob/master/LICENSE)
+See the [license](https://github.com/quinoacomputing/quinoa/blob/master/LICENSE)
 
 ## Authors
 
@@ -54,10 +54,10 @@ Jozsef Bakosi (jbakosi@lanl.gov)
 ### 2. Clone, build third-party libraries, build & test
 
    ```
-   git clone https://github.com/jbakosi/quinoa.git; cd quinoa
+   git clone https://github.com/quinoacomputing/quinoa.git; cd quinoa
    mkdir tpl/build; cd tpl/build; cmake ..; make; cd -
    mkdir build; cd build; cmake ../src; make; ../script/run_tests.sh
    ```
 
    - All executables will be in <tt>quinoa/build/Main</tt>
-   - Browse the [documentation](http://jbakosi.github.io/quinoa/index.html)
+   - Browse the [documentation](http://quinoacomputing.github.io/quinoa/index.html)

doc/pages/git-subtree.dox

@@ -16,8 +16,8 @@ This page explains how to use git subtree to work with TPLs and tools. This
 setup is only required
 
  - if you expect to make changes to
-   [TPLs](https://github.com/jbakosi/quinoa/blob/master/tpl/src) or
-   [tools](https://github.com/jbakosi/quinoa/blob/master/tool/src) and want to
+   [TPLs](https://github.com/quinoacomputing/quinoa/blob/master/tpl/src) or
+   [tools](https://github.com/quinoacomputing/quinoa/blob/master/tool/src) and want to
    push those changes upstream to the TPL or tool, or
 
  - if you want to update a TPL or a tool to a new version.
@@ -115,7 +115,7 @@ If you are happy with the diff, push the changes to the TPL:
 
 <hr>
 <div><small>
-<em>Page last updated:</em> Fri 29 Apr 2016 08:51:22 AM MDT
+<em>Page last updated:</em> Thu 05 May 2016 11:20:50 AM MDT
 <em>Copyright 2012-2016, Jozsef Bakosi.</em>
 </small></div>
 */

doc/pages/licenses.dox

@@ -4,8 +4,8 @@
 
 Here are the links to full verbatim texts of the licenses of all third-party
 libraries (TPLs), and the list of compilers and tools used by Quinoa. The [TPL
-sources](https://github.com/jbakosi/quinoa/blob/master/tpl/src) as well as the
-[tools sources](https://github.com/jbakosi/quinoa/blob/master/tool/src) are part
+sources](https://github.com/quinoacomputing/quinoa/blob/master/tpl/src) as well as the
+[tools sources](https://github.com/quinoacomputing/quinoa/blob/master/tool/src) are part
 of the distribution. While the Quinoa executables link to TPLs, they do not link
 to the tools.
 
@@ -160,7 +160,7 @@ to the tools.
 
 <hr>
 <div><small>
-<em>Page last updated:</em> Sat Apr 30 09:42:47 2016
+<em>Page last updated:</em> Thu 05 May 2016 11:21:11 AM MDT
 <em>Copyright 2012-2016, Jozsef Bakosi.</em>
 </small></div>
 */

doc/pages/mainpage.dox

@@ -11,29 +11,27 @@ various algorithms using fully asynchronous runtime systems.
 ## Organization
 
 Currently, Quinoa consists of the following tools:
-  - [<B>inciter</B>](https://jbakosi.github.io/quinoa/inciter_doc.html) - Solve
-    a PDE on an unstructured mesh using overdecomposition
-  - [<B>walker</B>](https://jbakosi.github.io/quinoa/walker_doc.html) - Random
-    walker for stochastic differential equations
-  - [<B>rngtest</B>](https://jbakosi.github.io/quinoa/rngtest_doc.html) - Random number generator test suite
-  - [<B>unittest</B>](https://jbakosi.github.io/quinoa/unittest_doc.html) - Unit test suite
-  - [<B>meshconv</B>](https://jbakosi.github.io/quinoa/meshconv_doc.html) - Mesh file converter
+  - [<B>inciter</B>](https://quinoacomputing.github.io/quinoa/inciter_doc.html) - Solve a system of partial differential equations on an unstructured mesh using overdecomposition
+  - [<B>walker</B>](https://quinoacomputing.github.io/quinoa/walker_doc.html) - Random walker for stochastic differential equations
+  - [<B>rngtest</B>](https://quinoacomputing.github.io/quinoa/rngtest_doc.html) - Random number generator test suite
+  - [<B>unittest</B>](https://quinoacomputing.github.io/quinoa/unittest_doc.html) - Unit test suite
+  - [<B>meshconv</B>](https://quinoacomputing.github.io/quinoa/meshconv_doc.html) - Mesh file converter
 
 ## Goals
 
-  - [<B>Designed for the exascale era</B>](https://jbakosi.github.io/quinoa/why.html#exascale)
-  - [<B>Verified and proven to be correct</B>](https://jbakosi.github.io/quinoa/why.html#correct)
-  - [<B>Optimized for performance, power, and reliability</B>](https://jbakosi.github.io/quinoa/why.html#optimized)
-  - [<B>Advanced computer science outsourced to experts</B>](https://jbakosi.github.io/quinoa/why.html#outsource)
-  - [<B>Using a language that can cope with complexity</B>](https://jbakosi.github.io/quinoa/why.html#language)
-  - [<B>Highly-valued programmer productivity</B>](https://jbakosi.github.io/quinoa/why.html#productivity)
-  - [<B>User and developer friendly</B>](https://jbakosi.github.io/quinoa/why.html#friendly)
-  - [<B>Well documented</B>](https://jbakosi.github.io/quinoa/why.html#documented)
-  - [<B>Fun to work on</B>](https://jbakosi.github.io/quinoa/why.html#fun)
+  - [<B>Designed for the exascale era</B>](https://quinoacomputing.github.io/quinoa/why.html#exascale)
+  - [<B>Verified and proven to be correct</B>](https://quinoacomputing.github.io/quinoa/why.html#correct)
+  - [<B>Optimized for performance, power, and reliability</B>](https://quinoacomputing.github.io/quinoa/why.html#optimized)
+  - [<B>Advanced computer science outsourced to experts</B>](https://quinoacomputing.github.io/quinoa/why.html#outsource)
+  - [<B>Using a language that can cope with complexity</B>](https://quinoacomputing.github.io/quinoa/why.html#language)
+  - [<B>Highly-valued programmer productivity</B>](https://quinoacomputing.github.io/quinoa/why.html#productivity)
+  - [<B>User and developer friendly</B>](https://quinoacomputing.github.io/quinoa/why.html#friendly)
+  - [<B>Well documented</B>](https://quinoacomputing.github.io/quinoa/why.html#documented)
+  - [<B>Fun to work on</B>](https://quinoacomputing.github.io/quinoa/why.html#fun)
 
 ## License
 
-See the [LICENSE](https://github.com/jbakosi/quinoa/blob/master/LICENSE).
+See the [LICENSE](https://github.com/quinoacomputing/quinoa/blob/master/LICENSE).
 
 ## Authors
 
@@ -60,16 +58,16 @@ Jozsef Bakosi (jbakosi@lanl.gov)
 ### 2. Clone, build third-party libraries, build & test Quinoa
 
    \code{.sh}
-   git clone https://github.com/jbakosi/quinoa.git; cd quinoa
+   git clone https://github.com/quinoacomputing/quinoa.git; cd quinoa
    mkdir tpl/build; cd build; cmake ..; make; cd -
    mkdir build; cd build; cmake ../src; make; ../script/run_tests.sh
    \endcode
    - All executables will be in <tt>quinoa/build/Main</tt>
-   - Browse the [documentation](http://jbakosi.github.io/quinoa/index.html)
+   - Browse the [documentation](http://quinoacomputing.github.io/quinoa/index.html)
 
 <hr>
 <div><small>
-<em>Page last updated:</em> Wed 27 Apr 2016 07:24:02 AM MDT
+<em>Page last updated:</em> Thu 05 May 2016 11:23:24 AM MDT
 <em>Copyright 2012-2016, Jozsef Bakosi.</em>
 </small></div>
 */

docker/Dockerfile.quinoa-build-alpine

@@ -1,7 +1,7 @@
 # vim: filetype=dockerfile:
 #
 # Author:    J. Bakosi
-# Date:      Thu 05 May 2016 09:43:54 AM MDT
+# Date:      Thu 05 May 2016 11:26:07 AM MDT
 # Copyright: 2012-2016, Jozsef Bakosi.
 
 # Dockerfile for a static build of Quinoa. We start from the minimalistic
@@ -36,15 +36,16 @@ ENV MANPATH /opt/openmpi/share/man:$MANPATH
 # Remove /install - no more installs after this line
 RUN rm -rf /install
 
-# Set default interactive shell
-CMD ["/bin/bash"]
+# Create symbolic link to /lib/cpp for the charm++ build, see
+# https://lists.cs.illinois.edu/lists/arc/charm/2016-05/msg00013.html
+RUN ln -s /usr/bin/cpp /lib/cpp
 
 # Clone quinoa
-RUN git clone https://github.com/jbakosi/quinoa.git
+RUN git clone https://github.com/quinoacomputing/quinoa.git
 # Build TPLs
-#RUN cd quinoa && mkdir -p tpl/build && cd tpl/build && cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_Fortran_COMPILER=mpif90 -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=off .. && make -sj`cat /proc/cpuinfo | grep MHz | wc -l`
+RUN cd quinoa && mkdir -p tpl/build && cd tpl/build && cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_Fortran_COMPILER=mpif90 -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=off .. && make -sj`cat /proc/cpuinfo | grep MHz | wc -l`
 # Build & test
-#RUN cd quinoa && mkdir -p build && cd build && cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=off -DMPIRUN_BIND_ARGS="-bind-to none -map-by node --allow-run-as-root" -DCMAKE_CXX_FLAGS=-Werror ../src && make -sj`cat /proc/cpuinfo | grep MHz | wc -l` && ../script/run_tests.sh
+RUN cd quinoa && mkdir -p build && cd build && cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=off -DMPIRUN_BIND_ARGS="-bind-to none -map-by node --allow-run-as-root" -DCMAKE_CXX_FLAGS=-Werror ../src && make -sj`cat /proc/cpuinfo | grep MHz | wc -l` && ../script/run_tests.sh
 
 # Clean everything not needed to run quinoa
 #RUN sudo -E apt-get clean -y && sudo -E apt-get autoclean -y && sudo -E apt-get autoremove -y && sudo rm -rf /usr/share/locale/* && sudo rm -rf /var/cache/debconf/*-old && sudo rm -rf /var/lib/apt/lists/* && sudo rm -rf /usr/share/doc/*

docker/Dockerfile.quinoa-build-dynamic

@@ -1,7 +1,7 @@
 # vim: filetype=dockerfile:
 #
 # Author:    J. Bakosi
-# Date:      Thu 05 May 2016 09:14:19 AM MDT
+# Date:      Thu 05 May 2016 11:26:19 AM MDT
 # Copyright: 2012-2016, Jozsef Bakosi.
 
 # Dockerfile for a simple dynamic build of Quinoa using the native (system-wide
@@ -40,7 +40,7 @@ WORKDIR /home/quinoa
 CMD ["/bin/bash"]
 
 # Clone quinoa
-RUN git clone https://github.com/jbakosi/quinoa.git
+RUN git clone https://github.com/quinoacomputing/quinoa.git
 # Build TPLs
 RUN cd quinoa && mkdir -p tpl/build && cd tpl/build && cmake -DCMAKE_BUILD_TYPE=Release .. && make -sj`cat /proc/cpuinfo | grep MHz | wc -l`
 # Build & test

script/update_doc.sh

@@ -4,7 +4,7 @@
 # \author    J. Bakosi
 # \date      Sun 02 Aug 2015 10:06:34 PM MDT
 # \copyright 2012-2016, Jozsef Bakosi.
-# \brief     Update documentation and test coverage and upload to github pages
+# \brief     Update Thu 05 May 2016 11:25:42 AM MDT
 # \details   This script assumes that
 #   - a clone already exists and the TPLs are already built
 #   - the environment is setup for running cmake
@@ -43,7 +43,7 @@ mv doc/html/test_coverage /tmp
 rm * .ninja_* -rf
 
 # Start out in empty build-dir with a fresh clone of the gh-pages branch
-git clone git@github.com:jbakosi/quinoa.git --branch gh-pages --single-branch doc/html
+git clone git@github.com:quinoacomputing/quinoa.git --branch gh-pages --single-branch doc/html
 cd doc/html
 git rm -rf .
 cd -