Docker - with Ubuntu 16.04

.ci/install_petsc.sh

@@ -0,0 +1,21 @@
+#!/bin/bash -xe
+
+if [ ! -f ${ci_path}/petsc_cached ]; then
+    git clone -b maint https://gitlab.com/petsc/petsc.git
+    pushd petsc
+    git checkout 8695de0
+    ./configure --prefix=${ci_path}/usr \
+                --with-x=0 --with-debugging=0 \
+                CFLAGS="-O3 -DNDEBUG -ffast-math" \
+                --with-parmetis=1 \
+                --with-metis=1 \
+                --with-hypre=1 --download-hypre=yes \
+                --with-superlu_dist=1 --download-superlu_dist=yes \
+                --with-mumps=1 --download-mumps=yes \
+                --with-ml=1 --download-ml=yes \
+                --download-scalapack=yes --download-blacs=yes
+    make
+    make install
+    popd
+    touch petsc_cached
+fi

.ci/install_zoltan.sh

@@ -0,0 +1,14 @@
+#!/bin/bash -xe
+
+if [ ! -f ${ci_path}/zoltan_cached ]; then
+    wget http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions/zoltan_distrib_v3.83.tar.gz
+    tar xf zoltan_distrib_v3.83.tar.gz --warning=no-unknown-keyword
+    mkdir Zoltan_v3.83/zoltanBUILD
+    pushd Zoltan_v3.83/zoltanBUILD
+    ../configure --prefix=${ci_path}/usr \
+                 --with-parmetis --with-parmetis-incdir=/usr/include/ --with-parmetis-libdir=/usr/lib/
+    make everything
+    make install
+    popd
+    touch zoltan_cached
+fi

.ci/setup_travis.sh

@@ -0,0 +1,19 @@
+#!/bin/bash -xe
+
+
+ci_path=$HOME/ci-helper
+
+# Check whether cache exists
+if [ ! -d ${ci_path} ]; then
+    mkdir -p ${ci_path}
+fi
+mkdir -p ${ci_path}/usr
+
+pushd ${ci_path}
+
+# Set up petsc
+source $TRAVIS_BUILD_DIR/.ci/install_petsc.sh
+# Set up zoltan
+source $TRAVIS_BUILD_DIR/.ci/install_zoltan.sh
+
+popd

.travis.yml

@@ -1,57 +1,43 @@
-language: bash
+language: cpp
+compiler: gcc
+os: linux
+dist: xenial
 sudo: required
 
-before_install:
-  - sudo apt-get -qq update
-  - sudo apt-get install -y libblas-dev liblapack-dev gfortran libboost-dev mpi-default-bin mpi-default-dev libgmp-dev libopenmpi-dev
-
-install:
-  - mkdir PEITS_root
-  - cd PEITS_root
-
-  - git clone -b maint https://bitbucket.org/petsc/petsc petsc
-
-  - cd petsc
-  - git checkout 8695de0
-
-
-  - ./configure --prefix=$TRAVIS_BUILD_DIR/PEITS_root/petscBUILD --with-x=0 --with-debugging=0 -CFLAGS="-O3 -DNDEBUG -ffast-math" --with-parmetis=1 --download-parmetis=yes --with-hypre=1 --download-hypre=yes --with-superlu_dist=1 --download-superlu_dist=yes --with-mumps=1 --download-mumps=yes --with-ml=1 --download-ml=yes --with-metis=1 --download-metis=yes --download-scalapack=yes --download-blacs=yes && make all test && make install
-
-
-  - cd ..
-  - wget http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions/zoltan_distrib_v3.83.tar.gz
-  - tar xf zoltan_distrib_v3.83.tar.gz --warning=no-unknown-keyword
-
-  - mkdir Zoltan_v3.83/BUILD_DIR
-  - cd Zoltan_v3.83/BUILD_DIR
+addons:
+  apt:
+    packages:
+      - libblas-dev
+      - liblapack-dev
+      - gfortran
+      - libboost-dev
+      - mpi-default-bin
+      - mpi-default-dev
+      - libgmp-dev
+      - libopenmpi-dev
+      - autotools-dev
+      - automake
+      - libug-dev
+      - libmetis-dev
+      - libparmetis-dev
+cache:
+  directories:
+    - /$HOME/ci-helper
 
+before_install:
+  - test -n $CC  && unset CC
+  - test -n $CXX && unset CXX
 
-  - ../configure --prefix=$TRAVIS_BUILD_DIR/PEITS_root/Zoltan_v3.83/BUILD_DIR --with-parmetis --with-parmetis-incdir="$TRAVIS_BUILD_DIR/PEITS_root/petscBUILD/include" --with-parmetis-libdir="$TRAVIS_BUILD_DIR/PEITS_root/petscBUILD/lib"
+install:
+  - source ${TRAVIS_BUILD_DIR}/.ci/setup_travis.sh
 
-  - make everything
-  - make install
-
 script:
   - cd $TRAVIS_BUILD_DIR
-  - mv config.opts_example config.opts
-
-  - PETSCPATH=$TRAVIS_BUILD_DIR/PEITS_root/petscBUILD
-  - ZOLTANPATH=$TRAVIS_BUILD_DIR/PEITS_root/Zoltan_v3.83/BUILD_DIR
-
-  - sed -i "s,/home/username/PEITS_root/petscBUILD,$PETSCPATH,g" config.opts
-  - sed -i "s,/home/username/PEITS_root/Zoltan_v3.8/BUILD_DIR,$ZOLTANPATH,g" config.opts
-
-  - sh INSTALL
+  - cp config.opts_example config.opts
+  - sed -i -e '/^PETSCPATH/d' -e '/^ZOLTANPATH/d' config.opts
+  - sed -i -e "1 a PETSCPATH=${ci_path}/usr/lib" -e "1 a ZOLTANPATH=${ci_path}/usr" config.opts
+  - cat config.opts
+  - ./INSTALL.sh
   - cd tests
   - sh ./initial_test.sh
-  - cd ../data
-  # now download nn mesh and try it 
-  - wget https://zenodo.org/record/1313709/files/NNmesh_small.tar.gz
-  - tar xf NNmesh_small.tar.gz
-  - cp parameter parameterBU
-  - cp standardparams standardparamsBU
-  - cd ../tests
-  - travis_wait 30 sh ./nn_test.sh
   - travis_wait 30 sh ./nn_test.sh
-
-

Dockerfile

@@ -0,0 +1,61 @@
+FROM uclrits/cppdev:16.04
+
+USER root
+WORKDIR /build
+ENV LD_LIBRARY_PATH /usr/local/lib
+
+RUN docker-apt-install libblas-dev liblapack-dev gfortran libboost-dev \
+    mpi-default-bin mpi-default-dev libgmp-dev libopenmpi-dev gfortran \
+    libmetis-dev libparmetis-dev autotools-dev automake libug-dev
+
+########## Build PETSC ##########
+RUN git clone -b maint https://gitlab.com/petsc/petsc.git && \
+    cd petsc && git checkout 8695de0 && \
+    ./configure --prefix=/usr \
+                --with-x=0 --with-debugging=0 \
+                CFLAGS="-O3 -DNDEBUG -ffast-math" \
+                --with-parmetis=1 \
+                --with-metis=1 \
+                --with-hypre=1 --download-hypre=yes \
+                --with-superlu_dist=1 --download-superlu_dist=yes \
+                --with-mumps=1 --download-mumps=yes \
+                --with-ml=1 --download-ml=yes \
+                --download-scalapack=yes --download-blacs=yes && \
+    make all && make install
+
+########## Build Zoltan ##########
+# NOTE - Because Zoltan doesn't allow to build on the source directory, it needs to go into zoltanBUILD
+#      - why does it need the path to incdir and libdir? it doesn't know how to look in the right place?
+RUN wget http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions/zoltan_distrib_v3.83.tar.gz && \
+    tar xf zoltan_distrib_v3.83.tar.gz && \
+    mkdir Zoltan_v3.83/zoltanBUILD && cd Zoltan_v3.83/zoltanBUILD && \
+    ../configure --prefix=/usr \
+                 --with-parmetis -with-parmetis-incdir=/usr/include/ --with-parmetis-libdir=/usr/lib/ && \
+    make everything && \
+    make install
+
+RUN rm -rf {petsc,?oltan}
+
+# Copy the local files
+COPY . /build/PEITS/
+WORKDIR PEITS
+
+# Configure PEITS build
+RUN cp config.opts_example config.opts && \
+    sed -i -e '/^PETSCPATH/d' -e '/ZOLTANPATH/d' \
+        -e '/with-metis/d' -e '/with-parmetis/d' \
+        config.opts && \
+    sed -i -e '1 a PETSCPATH="/usr/lib"' \
+        config.opts
+
+# Build PEITS
+RUN bash ./INSTALL.sh
+
+# Create User and set environment
+RUN useradd -ms /bin/bash peitsier
+RUN chown -R peitsier:peitsier /build/PEITS
+USER peitsier
+ENV HOME /home/peitsier
+RUN cp /etc/zsh/newuser.zshrc.recommended /home/peitsier/.zshrc
+WORKDIR /mydata
+CMD ["bash"]

INSTALL.md

@@ -0,0 +1,154 @@
+# Downloading and installing the required modules (Tested on Ubuntu 16.04)
+
+1. Install required libraries.
+
+   ```bash
+   sudo apt-get update
+   sudo apt-get install git gcc build-essential clang make autotools-dev \
+                        autoconf automake libtool cmake scons pkg-config \
+                        libblas-dev liblapack-dev gfortran libboost-dev \
+                        mpi-default-bin mpi-default-dev libgmp-dev libopenmpi-dev \
+                        gfortran autotools-dev automake libug-dev \
+                        libmetis-dev libparmetis-dev
+   ```
+
+1. Create a new folder — e.g. PEITS_root (Parallel EIT Solver) where the modules
+   will be installed.
+
+   ```bash
+   PEITS_root=/path/where/you/want/to/install/PEITS_root
+   mkdir -p ${PEITS_root}
+   cd ${PEITS_root}
+   ```
+   **Important** Change the `PEITS_root=/path/where/you/want/to/install/PEITS_root`
+   variable to reflect the actual location of the PEITS installation. /e.g./,
+   `PEITS_root=${HOME}/PEITS_root`.
+
+1. Download the PETSc library:
+
+   ```bash
+   git clone -b maint https://gitlab.com/petsc/petsc.git
+   ```
+   This will create a `petsc` subfolder in the PEITS_root directory.
+
+1. The PETSc libary needs to be configured, from within the `pestc` folder.
+   Installation has been tested using a previous version of PETSc (commit
+   `8695de0` - the nearest release is v3.6.3), newer versions cause an error
+   during configuration:
+
+   ```bash
+   cd petsc
+   git checkout 8695de0
+   ./configure --prefix=${PEITS_root}/petscBUILD \
+               --with-x=0 --with-debugging=0 \
+               CFLAGS="-O3 -DNDEBUG -ffast-math" \
+               --with-parmetis=1 --download-parmetis=yes \
+               --with-metis=1 --download-metis=yes \
+               --with-hypre=1 --download-hypre=yes \
+               --with-superlu_dist=1 --download-superlu_dist=yes \
+               --with-mumps=1 --download-mumps=yes \
+               --with-ml=1 --download-ml=yes \
+               --download-scalapack=yes --download-blacs=yes
+   ```
+
+   The `petscBUILD` folder will be created during the configuration process.
+
+
+1. Build the PETSc source code.
+
+   ```bash
+   make all test
+   make install
+   ```
+
+1. Download Zoltan library (v3.83 required) and extract to the PEITS_root folder.
+
+   ```bash
+   cd ${PEITS_root}
+   wget http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions/zoltan_distrib_v3.83.tar.gz
+   tar xf zoltan_distrib_v3.83.tar.gz --warning=no-unknown-keyword
+   ```
+
+   There may be some warning messages `'Ignoring unknown extended header keyword'`, these can be ignored.
+   The Zoltan library can also be downloaded through [their website](http://www.cs.sandia.gov/~web1400/1400_download.html).
+
+1. Configure and build the Zoltan library, must be run in a build subdirectory:
+
+   ```bash
+   mkdir Zoltan_v3.83/BUILD_DIR
+   cd Zoltan_v3.83/BUILD_DIR
+   ../configure --prefix=${PEITS_root}/Zoltan_v3.83/BUILD_DIR \
+                --with-parmetis --with-parmetis-incdir=/usr/include/ \
+                --with-parmetis-libdir=/usr/lib
+   make everything
+   make install
+   ```
+
+1. Download Parallel EIT Solver (PEITS) code into PEITS_root folder:
+
+   ```bash
+   cd ${PEITS_root}
+   git clone https://github.com/EIT-team/PEITS
+   ```
+
+1. Edit the `PEITS/config.opts_example` file and change `PETSCPATH` and `ZOLTANPATH`
+   to the appropriate directories by replacing `/home/username/PEITS_root/` with
+   the directory where `PEITS_root` is located, save the edited file as
+   `config.opts`.
+
+   If you have installed metis and parmetis using the package manager as
+   described above, then you can remove the lines that refer to them: /i.e./,
+   `--with-metis=...` and `--with-parmetis=...`
+
+1. Run install script. Located in PEITS_root/PEITS/
+
+   ```bash
+   ./INSTALL.sh
+   ```
+
+   The most likely cause of failure at this step is errors in the `config.opts`
+   file, double check `PETSCPATH` and `ZOLTANPATH` if this step fails.
+
+1. Test installation.
+
+   A simple regression test is includes in the PEITS/tests folder. This will check
+   that the default configuration is producing the expected output (by comparing
+   file sizes).
+
+   ```bash
+   cd ${PEITS_root}/PEITS/tests
+   sh initial_test.sh
+   ```
+
+   If the test is successful, `file sizes match - test OK` will be displayed,
+   meaning the installation process _should_ have been carried out correctly.
+
+   If there is an error regarding loading `libparmetis.so` then we need to add the
+   petsc library directory to the environmental path:
+
+   ```bash
+   LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${PEITS_root}/petscBUILD/lib/
+   export LD_LIBRARY_PATH
+   ```
+
+1. Running PEITS. If installation has been completed successfully, the solver
+   can be called from the `${PEITS_root}/PEITS/src` folder:
+
+   ```bash
+   cd ${PEITS_root}/PEITS/src
+   mpirun -np 2 ./dune_peits
+   ```
+
+   where `-np` specifies the number of parallel processors the solver should be run
+   on.
+
+   If the solver needs an unreasonably long time for the assembly of the system
+   matrix, then the pre-allocation of memory in PETSc needs to be adjusted. In
+   _file `${PEITS_root}/PEITS/dune-fem-1.4.0/dune/fem/misc/petsc/petsccommon.hh` the
+   number of allocated non-zeros can be changed in the command
+   `MatMPIAIJSetPreallocation(mat,100,PETSC_NULL,40,PETSC_NULL)`. A safe way of
+   adjusting this is to use very high numbers (e.g. 1000 and 150) and then running
+   the solver with the option `-info`, which outputs the precise number of non-zeros
+   required on the used mesh. Also, on some meshes ML preconditioning fails on some
+   numbers of parallel processes. If this happens, either the number of processes
+   can be changed or hypre preconditioning can be used.