Merge branch 'master' of github.com:Tomographer/tomographer

Tomographer · Feb 22, 2017 · d9140b5 · d9140b5
2 parents ab60215 + 8bc457e
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,8 +3,8 @@
 # 
 # The MIT License (MIT)
 # 
-# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe
-# Faist
+# Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+# Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,7 +1,8 @@
 
 The MIT License (MIT)
 
-Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -66,25 +66,35 @@ anything else.
 
 To compile `tomorun` from source, you'll need:
 
-  - a recent C++ compiler (g++ >= 4.6, Intel ICC >= 14, LLVM/Clang++ >= 3.8)
-  - [CMake >= 3.1](http://www.cmake.org/)
-  - [Boost libraries >= 1.40](http://www.boost.org/)
-  - [Eigen3 library >= 3.3](http://eigen.tuxfamily.org/)
+  - a recent C++ compiler (g++ ≥ 4.6, Intel ICC ≥ 14, LLVM/Clang++ ≥ 3.8)
+  - [CMake ≥ 3.1](http://www.cmake.org/)
+  - [Boost libraries ≥ 1.40](http://www.boost.org/)
+  - [Eigen3 library ≥ 3.3](http://eigen.tuxfamily.org/)
   - [MatIO library](https://sourceforge.net/projects/matio/)
 
 To compile the python interface, you'll need:
 
-  - a recent C++ compiler (g++ >= 4.6, Intel ICC >= 14, LLVM/Clang++ >= 3.8)
-  - [CMake >= 3.1](http://www.cmake.org/)
-  - [Boost libraries >= 1.40, which includes boost::python](http://www.boost.org/)
-  - [Python 2 or Python 3](http://www.python.org/)
-  - [Eigen3 library >= 3.3](http://eigen.tuxfamily.org/)
+  - a recent C++ compiler (g++ ≥ 4.6, Intel ICC ≥ 14, LLVM/Clang++ ≥ 3.8)
+  - [Boost libraries ≥ 1.40, which includes boost::python](http://www.boost.org/)
+  - [Python 2.7 or Python 3](http://www.python.org/)
+  - [Eigen3 library ≥ 3.3](http://eigen.tuxfamily.org/)
 
 In both cases a recent C++ compiler is required as some C++11 features and
 elements of its standard library are used. Also, make sure it supports OpenMP or
 you won't benefit from parallelization. If you use LLVM/Clang++, you might need
 to install additional packages for OpenMP (e.g. `libomp`).
 
+NOTE: Apple's default compiler does not support OpenMP. To avoid tomographer
+from running tasks serially, you should install a recent version of LLVM/clang
+or g++ manually.
+
+Apple Mac OS X with [homebrew](https://brew.sh): the following commands will get
+you started with all the prerequisites and with homebrew's python3.
+
+    > brew tap homebrew/science
+    > brew install llvm eigen python3 libmatio boost
+    > brew install boost-python --with-python3
+
 Tested on Linux/Ubuntu, Mac OS X and Windows (MinGW32).
 
 
@@ -97,7 +107,7 @@ It is then ready for use.
 The rest of this section concerns compiling Tomographer/Tomorun from source.
 
 The configuration, compilation and installation process is done using CMake.
-(You'll need CMake >= 3.1. Don't worry, it's easy [install a binary
+(You'll need CMake ≥ 3.1. Don't worry, it's easy [install a binary
 release](https://cmake.org/download/).)  Download an official release of
 Tomographer, unpack it, and enter the unpacked directory.  Then, issue the
 commands:
@@ -251,7 +261,7 @@ existing code as much as possible.
 
 The API documentation of the Tomographer C++ Framework can be found
 [here][tomographer_apidoc].  You can also build the API documentation of the
-Tomographer C++ Framework using [Doxygen >= 1.8][doxygen]. You'll also need
+Tomographer C++ Framework using [Doxygen ≥ 1.8][doxygen]. You'll also need
 `dot` (from the `graphviz` suite). To build the documentation, simply run
 
     tomographer-X.X/build> make doc
@@ -340,6 +350,7 @@ Authors, Copyright, License
 Author: Philippe Faist, phfaist@caltech.edu.
 
 Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
-Copyright (c) 2016 Caltech, Philippe Faist
+
+Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 
 Released under the terms of the MIT License (see file LICENSE.txt)
diff --git a/cmake/CreateDoxyfile.cmake b/cmake/CreateDoxyfile.cmake
@@ -3,8 +3,8 @@
 # 
 # The MIT License (MIT)
 # 
-# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe
-# Faist
+# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+# Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/cmake/FindEigen3.cmake b/cmake/FindEigen3.cmake
@@ -13,6 +13,7 @@
 # Copyright (c) 2006, 2007 Montel Laurent, <montel@kde.org>
 # Copyright (c) 2008, 2009 Gael Guennebaud, <g.gael@free.fr>
 # Copyright (c) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
+#
 # Redistribution and use is allowed according to the terms of the 2-clause BSD
 # license:
 #

diff --git a/cmake/FindMatIO.cmake b/cmake/FindMatIO.cmake
@@ -3,8 +3,8 @@
 # 
 # The MIT License (MIT)
 # 
-# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe
-# Faist
+# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+# Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/cmake/FindNumPy.cmake b/cmake/FindNumPy.cmake
@@ -15,7 +15,7 @@
 #  NUMPY_INCLUDE_DIRS        - path to the NumPy include files
 
 #============================================================================
-# Copyright 2012 Continuum Analytics, Inc.
+# Copyright (c) 2012 Continuum Analytics, Inc.
 #
 # MIT License
 #

diff --git a/cmake/FindSphinx.cmake b/cmake/FindSphinx.cmake
@@ -1,3 +1,29 @@
+# This file is part of the Tomographer project, which is distributed under the
+# terms of the MIT license.
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+# Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
 
 
 find_program(SPHINX_BUILD_COMMAND

diff --git a/cmake/TomographerVersion.cmake b/cmake/TomographerVersion.cmake
@@ -3,8 +3,8 @@
 # 
 # The MIT License (MIT)
 # 
-# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe
-# Faist
+# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+# Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/cmake/UpdateTomographerGitVersion.cmake b/cmake/UpdateTomographerGitVersion.cmake
@@ -3,8 +3,8 @@
 # 
 # The MIT License (MIT)
 # 
-# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe
-# Faist
+# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+# Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/cmake/UpdateTomographerVersionHeader.cmake b/cmake/UpdateTomographerVersionHeader.cmake
@@ -3,8 +3,8 @@
 # 
 # The MIT License (MIT)
 # 
-# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe
-# Faist
+# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+# Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/cmake/Util.cmake b/cmake/Util.cmake
@@ -3,8 +3,8 @@
 # 
 # The MIT License (MIT)
 # 
-# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe
-# Faist
+# Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+# Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/cmake/vc/OptimizeForArchitecture.cmake b/cmake/vc/OptimizeForArchitecture.cmake
@@ -111,7 +111,7 @@ macro(AutodetectHostArchitecture)
             set(TARGET_ARCHITECTURE "knl")  # Knights Landing
          elseif(_cpu_model EQUAL 92)
             set(TARGET_ARCHITECTURE "goldmont")
-         elseif(_cpu_model EQUAL 90)
+         elseif(_cpu_model EQUAL 90 OR _cpu_model EQUAL 76)
             set(TARGET_ARCHITECTURE "silvermont")
          elseif(_cpu_model EQUAL 102)
             set(TARGET_ARCHITECTURE "cannonlake")
@@ -255,6 +255,15 @@ Other supported values are: \"none\", \"generic\", \"core\", \"merom\" (65nm Cor
       _broadwell()
       list(APPEND _available_vector_units_list "avx512f" "avx512pf" "avx512er" "avx512cd")
    endmacro()
+   macro(_silvermont)
+      list(APPEND _march_flag_list "silvermont")
+      _westmere()
+      list(APPEND _available_vector_units_list "rdrnd")
+   endmacro()
+   macro(_goldmont)
+      list(APPEND _march_flag_list "goldmont")
+      _silvermont()
+   endmacro()
 
    if(TARGET_ARCHITECTURE STREQUAL "core")
       list(APPEND _march_flag_list "core2")
@@ -294,6 +303,10 @@ Other supported values are: \"none\", \"generic\", \"core\", \"merom\" (65nm Cor
       _westmere()
    elseif(TARGET_ARCHITECTURE STREQUAL "nehalem")
       _nehalem()
+   elseif(TARGET_ARCHITECTURE STREQUAL "goldmont")
+      _goldmont()
+   elseif(TARGET_ARCHITECTURE STREQUAL "silvermont")
+      _silvermont()
    elseif(TARGET_ARCHITECTURE STREQUAL "atom")
       list(APPEND _march_flag_list "atom")
       list(APPEND _march_flag_list "core2")

diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
@@ -5,8 +5,8 @@
 # 
 # The MIT License (MIT)
 # 
-# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe
-# Faist
+# Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+# Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 # 
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/mainpage.cxx b/doc/doxdocs/mainpage.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/namespaces.cxx b/doc/doxdocs/namespaces.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/page_debugging.cxx b/doc/doxdocs/page_debugging.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/page_loggers.cxx b/doc/doxdocs/page_loggers.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/page_task_manager_dispatcher.cxx b/doc/doxdocs/page_task_manager_dispatcher.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/page_theory.cxx b/doc/doxdocs/page_theory.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/page_tomorun.cxx b/doc/doxdocs/page_tomorun.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/page_type_interfaces.cxx b/doc/doxdocs/page_type_interfaces.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/page_type_interfaces_densedm.cxx b/doc/doxdocs/page_type_interfaces_densedm.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxdocs/page_write_custom_logger.cxx b/doc/doxdocs/page_write_custom_logger.cxx
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/doxy_footer.html b/doc/doxy_footer.html
@@ -4,7 +4,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/tomographer_extra_css.css b/doc/tomographer_extra_css.css
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/tomographer_script_setup.js b/doc/tomographer_script_setup.js
@@ -3,7 +3,8 @@
  *
  * The MIT License (MIT)
  *
- * Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2016 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+ * Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/doc/tomographerlatexstyle.sty b/doc/tomographerlatexstyle.sty
@@ -3,8 +3,8 @@
 % 
 % The MIT License (MIT)
 % 
-% Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe
-% Faist
+% Copyright (c) 2015 ETH Zurich, Institute for Theoretical Physics, Philippe Faist
+% Copyright (c) 2017 Caltech, Institute for Quantum Information and Matter, Philippe Faist
 % 
 % Permission is hereby granted, free of charge, to any person obtaining a copy
 % of this software and associated documentation files (the "Software"), to deal