Merge pull request #116 from Libensemble/release/v0.4.1

Release/v0.4.1

.travis.yml

@@ -16,7 +16,7 @@ env:
     - OMPI_MCA_rmaps_base_oversubscribe=yes  
   matrix:
     - MPI=mpich
-    - MPI=openmpi
+    #- MPI=openmpi
 
 matrix:
   allow_failures:
@@ -45,30 +45,31 @@ before_install:
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
+  - conda update -q -y conda
   - conda info -a # For debugging any issues with conda
   - conda config --add channels conda-forge  
   - conda create --yes --name condaenv python=$TRAVIS_PYTHON_VERSION 
   - source activate condaenv
 
 install:
+  - conda install gcc_linux-64
   - conda install $MPI
-  - pip install numpy
-  - pip install scipy
-  - pip install mpi4py
-  - pip install petsc petsc4py
+  - conda install --no-update-deps scipy # includes numpy
+  - conda install --no-update-deps mpi4py
+  - conda install --no-update-deps petsc4py petsc
+  - conda install --no-update-deps nlopt
+  # pip install these as the conda installs downgrade pytest on python3.4
   - pip install pytest
   - pip install pytest-cov
-  - pip install pytest-timeout 
+  - pip install pytest-timeout
   - pip install mock
   - pip install coveralls
-  - conda install --no-deps nlopt  
   # For confirmation of MPI library being used.
   - python conda/find_mpi.py #locate compilers
   - mpiexec --version #Show MPI library details
   - pip install -e .
 
-# Run test
+# Run test (-z show output)
 script:
   - libensemble/tests/run-tests.sh -z
 

conda/conda-install-deps.sh

@@ -1,27 +1,62 @@
 #!/usr/bin/env bash
 
-#Note - This assumes miniconda - with anaconda some will already be installed
-#You must have installed miniconda: https://conda.io/docs/install/quick.html
+# Install dependencies for libEnsemble and tests in Conda.
+# Note: libEnsemble itself is currently not in Conda
+# To replicate travis builds - see directory run_travis_locally/
 
-#To create and activate new environment called py3.6
-#> conda create --name py3.6 python=3.6
-#> source activate py3.6
+# Note - This assumes miniconda - with anaconda some will already be installed
+# You must have installed miniconda: https://conda.io/docs/install/quick.html
 
-#To come out of env: source deactivate
-#To see envs: conda info --envs
+# To isolate from local installs run this before activating environment
+# export PYTHONNOUSERSITE=1
+
+# To create and activate new environment called py3.6
+# > conda create --name py3.6 python=3.6
+# > source activate py3.6
+# To enable running this script without prompts:
+# > conda config --set always_yes yes
+# Then source this script: . ./conda-install-deps.sh
+
+# To come out of env: source deactivate
+# To see envs: conda info --envs
+
+# You may need to add the conda-forge chanel
+# conda config --add channels conda-forge
 
 #--------------------------------------------------------------------------
 
-#Install packages for libensemble. Do in this order!!!
-  conda install --yes mpi4py
-  conda install --yes -c conda-forge petsc4py
-  conda install --yes -c conda-forge nlopt
-  conda install --yes pytest pytest-cov 
-  conda install --yes scipy 
-
-  #To use dev version of mpi4py
-  #conda install --yes cython
-  #pip install git+https://bitbucket.org/mpi4py/mpi4py.git@master
-
-  echo -e "\nDo 'conda list' to see installed packages"
-  echo -e "Do './run-tests.sh' to run the tests\n"
+# Install packages for libensemble. Do in this order!!!
+
+# This should work for mpich as of v0.4.1
+# For other MPI libraries, some packages, such as mpi4py and PETSc may
+# need to be pip installed.
+
+export MPI=MPICH
+export LIBE_BRANCH=master
+
+conda install gcc_linux-64 || return
+conda install $MPI || return
+#conda install numpy || return #scipy includes numpy
+conda install --no-update-deps scipy || return
+conda install --no-update-deps  mpi4py || return
+conda install --no-update-deps petsc4py petsc || return
+conda install --no-update-deps nlopt || return
+
+# pip install these as the conda installs downgrade pytest on python3.4
+pip install pytest || return
+pip install pytest-cov || return
+pip install pytest-timeout || return
+pip install mock || return
+# pip install coveralls || return # for online
+
+# Install libEnsemble
+
+# From source
+git clone -b $LIBE_BRANCH https://github.com/Libensemble/libensemble.git || return
+cd libensemble/ || return
+pip install -e . || return
+# OR
+# pip install libEnsemble
+
+echo -e "\nDo 'conda list' to see installed packages"
+echo -e "Do 'libensemble/tests/run-tests.sh' to run the tests\n"

conda/run_travis_locally/build_mpich_libE.sh

@@ -0,0 +1,83 @@
+# Conda build of dependencies using mpich.
+# Source script to maintain environment after running. Script stops if installs fail.
+# Note for other MPIs may need to install some packages from source (eg. petsc)
+
+# -x echo commands
+set -x # problem with this - loads of conda internal commands shown - overwhelming.
+
+export PYTHON_VERSION=3.7       # default - override with -p <version>
+export LIBE_BRANCH="develop"    # default - override with -b <branchname>
+
+export MPI=MPICH
+export HYDRA_LAUNCHER=fork
+
+# Allow user to optionally set python version and branch
+# E.g: ". ./build_mpich_libE.sh -p 3.4 -b feature/myfeature"
+while getopts ":p:b:" opt; do
+  case $opt in
+    p)
+      echo "Parameter supplied for Python version: $OPTARG" >&2
+      PYTHON_VERSION=$OPTARG
+      ;;
+    b)
+      echo "Parameter supplied for branch name: $OPTARG" >&2
+      LIBE_BRANCH=${OPTARG}
+      ;;
+    \?)
+      echo "Invalid option supplied: -$OPTARG" >&2
+      exit 1
+      ;;
+    :)
+      echo "Option -$OPTARG requires an argument." >&2
+      exit 1
+      ;;
+  esac
+done
+
+echo -e "\nBuilding libE with python $PYTHON_VERSION and branch ${LIBE_BRANCH}\n"
+
+sudo apt-get update
+
+# This works if not sourced but if sourced its no good.
+# set -e
+
+sudo apt install gfortran || return
+sudo apt install libblas-dev || return
+sudo apt-get install liblapack-dev || return
+
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh || return
+bash miniconda.sh -b -p $HOME/miniconda || return
+export PATH="$HOME/miniconda/bin:$PATH" || return
+conda update -q -y  conda
+
+conda config --add channels conda-forge || return
+conda config --set always_yes yes --set changeps1 no || return
+conda create --yes --name condaenv python=$PYTHON_VERSION || return
+
+source activate condaenv || return
+wait
+
+conda install gcc_linux-64 || return
+conda install $MPI || return
+#conda install numpy || return #scipy includes numpy
+conda install --no-update-deps scipy || return
+conda install --no-update-deps  mpi4py || return
+conda install --no-update-deps petsc4py petsc || return
+conda install --no-update-deps nlopt || return
+
+# pip install these as the conda installs downgrade pytest on python3.4
+pip install pytest || return
+pip install pytest-cov || return
+pip install pytest-timeout || return
+pip install mock || return
+pip install coveralls || return
+
+# Not required on travis
+git clone -b $LIBE_BRANCH https://github.com/Libensemble/libensemble.git || return
+cd libensemble/ || return
+pip install -e . || return
+
+libensemble/tests/run-tests.sh
+
+echo -e "\n\nScript completed...\n\n"
+set +ex