Merge pull request #457 from pdziekan/avg_edge_sclr

bcond: Avg edge sclr

Author: pdziekan

.travis.yml

@@ -48,6 +48,8 @@ env:
 #    - TEST_SUITE=UWLCM MPI=mvapich2
 
 cache:
+  packages: true
+  pip: true
   directories:
     - ${TRAVIS_BUILD_DIR}/deps/mvapich2-2.3b
     - ${TRAVIS_BUILD_DIR}/deps/boost
@@ -63,12 +65,8 @@ cache:
 aliases:
   - &precache_default
     stage: precache
-    # os: linux
-    # dist: xenial
-    # language: cpp
-    # compiler: gcc
     install: 
-      - . ./.travis_scripts/install_common.sh
+      - . ./.travis_scripts/deps_install/install_common.sh
     script: echo "Preparing cache finished"
 
 jobs:
@@ -140,20 +138,7 @@ before_install:
     - if [[ $TRAVIS_OS_NAME == 'linux' && $CXX == 'clang++' ]]; then export COMPILER=clang++; fi
     - if [[ $TRAVIS_OS_NAME == 'linux' && $CXX == 'g++'     ]]; then export COMPILER=g++; fi
     - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then export COMPILER=clang++; fi # only clang on osx
-
-# to avoid python lib/interpreter mismatch; https://github.com/travis-ci/travis-ci/issues/5326
-#    - if [[ $TRAVIS_OS_NAME == 'linux' ]]; then export PATH=$(echo $PATH | tr ':' "\n" | sed '/\/opt\/python/d' | tr "\n" ":" | sed "s|::|:|g"); fi
-#    - if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo add-apt-repository "deb http://archive.ubuntu.com/ubuntu/ trusty main universe multiverse"; fi
-#    - if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo apt-get update; fi
     - if [[ $TRAVIS_OS_NAME == 'linux' ]]; then export apt_get_install="apt-get install --no-install-recommends -t xenial -y"; fi
-#    - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then brew update; fi
-
-    # - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then brew tap homebrew/science; fi
-    # - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then rvm get stable; fi #see https://github.com/travis-ci/travis-ci/issues/6307
-    
-    # Workaround for upgrading gcc, see https://github.com/travis-ci/travis-ci/issues/8826
-    # Seems like this is now done by Travis, but leaving it (commented out) for now
-    #- if [[ $TRAVIS_OS_NAME == 'osx' ]]; then brew cask uninstall oclint; fi
 
     # gnuplot-iostream
     - git clone -n https://github.com/dstahlke/gnuplot-iostream && cd gnuplot-iostream
@@ -183,18 +168,13 @@ before_install:
     # testing Python 3 on Linux
     - export PY3DEB=""
     - if [[ $TRAVIS_OS_NAME == 'linux' ]]; then PY3DEB=3; fi
-#    - PY3DEB=3 # had problems with building h5py using python3-pip
-#    - if [[ $PY3DEB != '' ]]; then sudo apt-get install python3-dev; fi
 
     # upgrade pip
-    #- if [[ $TRAVIS_OS_NAME == 'osx' ]]; then sudo pip install --upgrade pip; fi 
     - sudo pip$PY3DEB install --upgrade pip
 
 install:
-    - . ./.travis_scripts/install_common.sh
+    - . ./.travis_scripts/deps_install/install_common.sh
 
-#    - if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo $apt_get_install  -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" libpango-1.0-0 libpangocairo-1.0-0 libhdf5-dev; fi
-#    - if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo $apt_get_install hdf5-tools; fi
     - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then brew install hdf5; fi
 
     - if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo $apt_get_install gnuplot-nox; fi

.travis_scripts/UWLCM.sh

@@ -11,22 +11,6 @@ cd libmpdata++/build
 sudo make install
 cd ../..
 
-# making Python 2 back the default if needed - TODO: support Python3 in libcloudph++
-if [[ $PY3DEB != '' ]]; then sudo update-alternatives --remove python /usr/bin/python3; fi
-if [[ $PY3DEB != '' ]]; then sudo update-alternatives --install /usr/bin/python python /usr/bin/python2 10; fi
-
-# libcloudph++'s dependencies
-#if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo $apt_get_install libboost-python1.55-dev python-numpy; fi
-if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo $apt_get_install python-numpy; fi
-if [[ $TRAVIS_OS_NAME == 'osx' ]]; then brew install boost-python; fi
-
-# odeint
-if [[ $TRAVIS_OS_NAME == 'linux' ]]; then git clone --depth=1 https://github.com/boostorg/odeint.git; fi # get boost odeint > 1.58
-if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo rm -f /usr/include/boost/numeric/odeint.hpp; fi
-if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo rm -rf /usr/include/boost/numeric/odeint; fi
-if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo ln -s `pwd`/odeint/include/boost/numeric/odeint.hpp /usr/include/boost/numeric/odeint.hpp; fi
-if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo ln -s `pwd`/odeint/include/boost/numeric/odeint  /usr/include/boost/numeric/; fi
-
 # newest thrust
 git clone --depth=1 git://github.com/thrust/thrust.git;
 sudo ln -s `pwd`/thrust/thrust /usr/local/include/thrust;

.travis_scripts/install_common.sh …s_scripts/deps_install/install_common.sh.travis_scripts/install_common.sh renamed to .travis_scripts/deps_install/install_common.sh .travis_scripts/install_common.sh renamed to .travis_scripts/deps_install/install_common.sh

@@ -18,15 +18,6 @@ if [[ $TRAVIS_OS_NAME == 'linux' && $COMPILER == 'g++'     ]]; then export CXX=g
 # downloads and setups local clang on osx
 if [[ $TEST_SUITE == 'osx_local_clang' ]]; then . ./.travis_scripts/setup_local_clang.sh; fi
 
-#<<<<<<< HEAD
-    # add a definition -DBOOST_HAS_INT128=1 to clang calls on linux to avoid errors with boost.atomic (https://svn.boost.org/trac/boost/ticket/9610)
-#    if [[ $TRAVIS_OS_NAME == 'linux' && $CXX == 'clang++' ]]; then mkdir /tmp/bin; fi
-#    if [[ $TRAVIS_OS_NAME == 'linux' && $CXX == 'clang++' ]]; then printf "#!/bin/sh\nexec /usr/bin/clang++ -DBOOST_HAS_INT128=1 \"\$@\"" > /tmp/bin/clang++; fi
-#    if [[ $TRAVIS_OS_NAME == 'linux' && $CXX == 'clang++' ]]; then chmod +x /tmp/bin/clang++; fi
-#    if [[ $TRAVIS_OS_NAME == 'linux' && $CXX == 'clang++' ]]; then sudo ln -sf /tmp/bin/clang++ /usr/bin/clang++; fi
-    # put /usr/bin first to use clang++-3.5 instead of the default 3.4
-    #if [[ $TRAVIS_OS_NAME == 'linux' && $CXX == 'clang++' ]]; then export PATH=/usr/bin:$PATH; fi
-
 if [[ $TRAVIS_OS_NAME == 'linux' && $CXX == 'clang++' ]]; then export CXXFLAGS="-DBOOST_HAS_INT128=1 ${CXXFLAGS}"; fi
 
 # cmake 
@@ -61,47 +52,45 @@ if [[ $MPI == 'openmpi'  ]]; then sudo $apt_get_install openmpi-bin libopenmpi-d
 if [[ $MPI != 'none'    ]]; then export CXX=${DEPS_DIR}/mvapich2-2.3b/bin/mpic++ ; fi # full path, since libtool in hdf5 installation does not understand PATH set above (?)
 if [[ $MPI != 'none'    ]]; then export CC=${DEPS_DIR}/mvapich2-2.3b/bin/mpicc ; fi
 
-# boost
-#if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo $apt_get_install libboost-thread1.55-dev libboost-timer1.55-dev libboost-iostreams1.55-dev libboost-filesystem1.55-dev; fi
-#if [[ $TRAVIS_OS_NAME == 'linux' && $MPI != 'none' ]]; then sudo $apt_get_install libboost-mpi1.55-dev; fi
-#if [[ $TRAVIS_OS_NAME == 'osx' ]]; then brew reinstall boost --c++11; fi          # ...what takes too long :(
-
-# no MPI get boost from the repository
-if [[ $TRAVIS_OS_NAME == 'linux' && $MPI == 'none' ]]; then sudo $apt_get_install boost1.61; fi
+# no MPI
+if [[ $TRAVIS_OS_NAME == 'linux' && $MPI == 'none' ]]; then 
+  sudo $apt_get_install boost1.61
+  sudo ln -s /usr/lib/x86_64-linux-gnu/libboost_python-py35.so /usr/lib/x86_64-linux-gnu/libboost_python3.so # different naming conventions for boost python with python 3
+fi
 
 # for MPI we need boost>=1.59 with mpi support, boost installation based on https://github.com/boostorg/compute/blob/master/.travis.yml
-  if [[ $TRAVIS_OS_NAME == 'linux' && $MPI != 'none' ]]; then 
-    ls -A ${DEPS_DIR}/boost
-    if [[ -z "$(ls -A ${DEPS_DIR}/boost)" ]]; then
-      wget http://sourceforge.net/projects/boost/files/boost/1.65.1/boost_1_65_1.tar.gz 
-      tar xf boost_1_65_1.tar.gz
-      cd boost_1_65_1
-      # configure and install
-      if [[ $COMPILER == 'g++' ]]; then echo "using gcc : 6.2 : g++-6 ;" > $HOME/user-config.jam; fi
-      if [[ $COMPILER == 'clang++' ]]; then echo "using clang : 5.0 : clang++-5.0 ;" > $HOME/user-config.jam; fi
-      echo "using mpi : $CC ;" >> $HOME/user-config.jam
-      cat $HOME/user-config.jam
-      if [[ $COMPILER == 'g++' ]]; then
-        ./bootstrap.sh --prefix=${DEPS_DIR}/boost/ --with-libraries=serialization,mpi,thread,date_time,system,iostreams,timer,filesystem
-        ./b2 -d0 install
-      fi
-      if [[ $COMPILER == 'clang++' ]]; then 
-        #clang installation taken from https://gist.github.com/jimporter/10442880
-        ./bootstrap.sh --prefix=${DEPS_DIR}/boost/ --with-libraries=serialization,mpi,thread,date_time,system,iostreams,timer,filesystem --with-toolset=clang
-        ./b2 clean
-        ./b2 toolset=clang cxxflags="-std=c++14 -stdlib=libc++" linkflags="-stdlib=libc++" --prefix=${DEPS_DIR}/boost/ -j 4 stage release
-        ./b2 install toolset=clang cxxflags="-std=c++14 -stdlib=libc++" linkflags="-stdlib=libc++" --prefix=${DEPS_DIR}/boost/
-      fi
-      cd ..
-    else
-      echo "Using cached boost."
+if [[ $TRAVIS_OS_NAME == 'linux' && $MPI != 'none' ]]; then 
+  ls -A ${DEPS_DIR}/boost
+  if [[ -z "$(ls -A ${DEPS_DIR}/boost)" ]]; then
+    wget http://sourceforge.net/projects/boost/files/boost/1.65.1/boost_1_65_1.tar.gz 
+    tar xf boost_1_65_1.tar.gz
+    cd boost_1_65_1
+    # configure and install
+    if [[ $COMPILER == 'g++' ]]; then echo "using gcc : 6.2 : g++-6 ;" > $HOME/user-config.jam; fi
+    if [[ $COMPILER == 'clang++' ]]; then echo "using clang : 5.0 : clang++-5.0 ;" > $HOME/user-config.jam; fi
+    echo "using mpi : $CC ;" >> $HOME/user-config.jam
+    cat $HOME/user-config.jam
+    if [[ $COMPILER == 'g++' ]]; then
+      ./bootstrap.sh --prefix=${DEPS_DIR}/boost/ --with-libraries=serialization,mpi,thread,date_time,system,iostreams,timer,filesystem
+      ./b2 -d0 install
+    fi
+    if [[ $COMPILER == 'clang++' ]]; then 
+      #clang installation taken from https://gist.github.com/jimporter/10442880
+      ./bootstrap.sh --prefix=${DEPS_DIR}/boost/ --with-libraries=serialization,mpi,thread,date_time,system,iostreams,timer,filesystem --with-toolset=clang
+      ./b2 clean
+      ./b2 toolset=clang cxxflags="-std=c++14 -stdlib=libc++" linkflags="-stdlib=libc++" --prefix=${DEPS_DIR}/boost/ -j 4 stage release
+      ./b2 install toolset=clang cxxflags="-std=c++14 -stdlib=libc++" linkflags="-stdlib=libc++" --prefix=${DEPS_DIR}/boost/
     fi
-    export BOOST_ROOT=${DEPS_DIR}/boost
-    export LD_LIBRARY_PATH=${DEPS_DIR}/boost/lib:${LD_LIBRARY_PATH}
-    export LD_RUN_PATH=${DEPS_DIR}/boost/lib:${LD_RUN_PATH}
-    export LIBRARY_PATH=${DEPS_DIR}/boost/lib:${LIBRARY_PATH}
-    export CPATH=${DEPS_DIR}/boost/include:${CPATH}
+    cd ..
+  else
+    echo "Using cached boost."
   fi
+  export BOOST_ROOT=${DEPS_DIR}/boost
+  export LD_LIBRARY_PATH=${DEPS_DIR}/boost/lib:${LD_LIBRARY_PATH}
+  export LD_RUN_PATH=${DEPS_DIR}/boost/lib:${LD_RUN_PATH}
+  export LIBRARY_PATH=${DEPS_DIR}/boost/lib:${LIBRARY_PATH}
+  export CPATH=${DEPS_DIR}/boost/include:${CPATH}
+fi
 
 # blitz
 if [[ $TRAVIS_OS_NAME == 'osx' ]]; then brew install blitz; fi

libmpdata++/bcond/cyclic_1d.hpp

@@ -40,6 +40,20 @@ namespace libmpdataxx
       {
         fill_halos_vctr_alng(av, ad);
       }
+
+      void copy_edge_sclr_to_halo1_cyclic(arr_t &a)
+      {
+        assert(halo>=1);
+
+        a(this->left_halo_sclr.last()) = a(this->rght_edge_sclr);
+      }
+
+      void avg_edge_and_halo1_sclr_cyclic(arr_t &a)
+      {
+        assert(halo>=1);
+
+        a(this->left_edge_sclr) = ( a(this->left_edge_sclr) + a(this->left_halo_sclr.last()) ) / real_t(2); 
+      }
     };
 
     template <typename real_t, int halo, bcond_e knd, drctn_e dir, int n_dims, int dim>
@@ -71,6 +85,20 @@ namespace libmpdataxx
       {
         fill_halos_vctr_alng(av, ad);
       }
+
+      void copy_edge_sclr_to_halo1_cyclic(arr_t &a)
+      {
+        assert(halo>=1);
+
+        a(this->rght_halo_sclr.first()) = a(this->left_edge_sclr);
+      }
+
+      void avg_edge_and_halo1_sclr_cyclic(arr_t &a)
+      {
+        assert(halo>=1);
+
+        a(this->rght_edge_sclr) = ( a(this->rght_edge_sclr) + a(this->rght_halo_sclr.first()) ) / real_t(2); 
+      }
     };
   } // namespace bcond
 } // namespace libmpdataxx

libmpdata++/bcond/cyclic_2d.hpp

@@ -78,6 +78,22 @@ namespace libmpdataxx
       {
         fill_halos_vctr_nrml(a, j);
       }
+
+      void copy_edge_sclr_to_halo1_cyclic(arr_t &a, const rng_t &j)
+      {
+        using namespace idxperm;
+        assert(halo>=1);
+
+        a(pi<d>(this->left_halo_sclr.last(), j)) = a(pi<d>(this->rght_edge_sclr, j));
+      }
+
+      void avg_edge_and_halo1_sclr_cyclic(arr_t &a, const rng_t &j)
+      {
+        using namespace idxperm;
+        assert(halo>=1);
+
+        a(pi<d>(this->left_edge_sclr, j)) = ( a(pi<d>(this->left_edge_sclr, j)) + a(pi<d>(this->left_halo_sclr.last(), j)) ) / real_t(2); 
+      }
     };
 
     template <typename real_t, int halo, bcond_e knd, drctn_e dir, int n_dims, int d>
@@ -147,6 +163,22 @@ namespace libmpdataxx
       {
         fill_halos_vctr_nrml(a, j);
       }
+
+      void copy_edge_sclr_to_halo1_cyclic(arr_t &a, const rng_t &j)
+      {
+        using namespace idxperm;
+        assert(halo>=1);
+
+        a(pi<d>(this->rght_halo_sclr.first(), j)) = a(pi<d>(this->left_edge_sclr, j));
+      }
+
+      void avg_edge_and_halo1_sclr_cyclic(arr_t &a, const rng_t &j)
+      {
+        using namespace idxperm;
+        assert(halo>=1);
+
+        a(pi<d>(this->rght_edge_sclr, j)) = ( a(pi<d>(this->rght_edge_sclr, j)) + a(pi<d>(this->rght_halo_sclr.first(), j)) ) / real_t(2); 
+      }
     };
   } // namespace bcond
 } // namespace libmpdataxx

libmpdata++/bcond/cyclic_3d.hpp

@@ -78,6 +78,22 @@ namespace libmpdataxx
       {
         fill_halos_vctr_nrml(a, j, k);
       }
+
+      void copy_edge_sclr_to_halo1_cyclic(arr_t &a, const rng_t &j, const rng_t &k)
+      {
+        using namespace idxperm;
+        assert(halo>=1);
+
+        a(pi<d>(this->left_halo_sclr.last(), j, k)) = a(pi<d>(this->rght_edge_sclr, j, k));
+      }
+
+      void avg_edge_and_halo1_sclr_cyclic(arr_t &a, const rng_t &j, const rng_t &k)
+      {
+        using namespace idxperm;
+        assert(halo>=1);
+
+        a(pi<d>(this->left_edge_sclr, j, k)) = ( a(pi<d>(this->left_edge_sclr, j, k)) + a(pi<d>(this->left_halo_sclr.last(), j, k)) ) / real_t(2); 
+      }
     };
 
     template <typename real_t, int halo, bcond_e knd, drctn_e dir, int n_dims, int d>
@@ -147,6 +163,22 @@ namespace libmpdataxx
       {
         fill_halos_vctr_nrml(a, j, k);
       }
+
+      void copy_edge_sclr_to_halo1_cyclic(arr_t &a, const rng_t &j, const rng_t &k)
+      {
+        using namespace idxperm;
+        assert(halo>=1);
+
+        a(pi<d>(this->rght_halo_sclr.first(), j, k)) = a(pi<d>(this->left_edge_sclr, j, k));
+      }
+
+      void avg_edge_and_halo1_sclr_cyclic(arr_t &a, const rng_t &j, const rng_t &k)
+      {
+        using namespace idxperm;
+        assert(halo>=1);
+
+        a(pi<d>(this->rght_edge_sclr, j, k)) = ( a(pi<d>(this->rght_edge_sclr, j, k)) + a(pi<d>(this->rght_halo_sclr.first(), j, k)) ) / real_t(2); 
+      }
     };
   } // namespace bcond
 } // namespace libmpdataxx

libmpdata++/bcond/detail/bcond_common.hpp

@@ -56,6 +56,12 @@ namespace libmpdataxx
         virtual void fill_halos_vctr_alng_cyclic(arrvec_t<blitz::Array<real_t, 1>> &, const bool ad = false)
         {};
 
+        virtual void copy_edge_sclr_to_halo1_cyclic(arr_1d_t &)
+        {};
+
+        virtual void avg_edge_and_halo1_sclr_cyclic(arr_1d_t &)
+        {};
+
         // 2D
         virtual void fill_halos_sclr(arr_2d_t &, const rng_t &, const bool deriv = false)
         {
@@ -111,6 +117,12 @@ namespace libmpdataxx
         virtual void fill_halos_flux(arrvec_t<blitz::Array<real_t, 2>> &, const rng_t &)
         {};
 
+        virtual void copy_edge_sclr_to_halo1_cyclic(arr_2d_t &, const rng_t &)
+        {};
+
+        virtual void avg_edge_and_halo1_sclr_cyclic(arr_2d_t &, const rng_t &)
+        {};
+
         // 3D
         virtual void fill_halos_sclr(arr_3d_t &, const rng_t &, const rng_t &, const bool deriv = false)
         {
@@ -175,6 +187,12 @@ namespace libmpdataxx
         virtual void fill_halos_flux(arrvec_t<blitz::Array<real_t, 3>> &, const rng_t &, const rng_t &)
         {};
 
+        virtual void copy_edge_sclr_to_halo1_cyclic(arr_3d_t &, const rng_t &, const rng_t &)
+        {};
+
+        virtual void avg_edge_and_halo1_sclr_cyclic(arr_3d_t &, const rng_t &, const rng_t &)
+        {};
+
         protected:
           // sclr
         int