Merge pull request #64 from ghammond86/master

Updates to make interface compatible with PFLOTRAN v3.0 + PETSc v3.11

.travis.yml

@@ -19,24 +19,24 @@ branches:
 compiler:
   - gcc
 
-install: travis_wait 60 ./.install-$TRAVIS_OS_NAME-deps.sh
+install: travis_wait 60 ./.travis/install-$TRAVIS_OS_NAME-deps.sh
 
 env:
-  - BUILD_TYPE=Debug PETSC_DIR=$PWD/petsc PETSC_ARCH=petsc_debug DEBUG=1
-  - BUILD_TYPE=Release PETSC_DIR=$PWD/petsc PETSC_ARCH=petsc_opt DEBUG=0
+  global:
+    - ALQUIMIA_DIR=$PWD
+    - THIRD_PARTY_LIB_DIR=$HOME
+    - CRUNCHTOPE_DIR=$THIRD_PARTY_LIB_DIR/crunchtope-dev
+    - PETSC_DIR=$THIRD_PARTY_LIB_DIR/petsc
+    - PFLOTRAN_DIR=$THIRD_PARTY_LIB_DIR/pflotran
+  jobs:
+  - BUILD_TYPE=Debug PETSC_ARCH=petsc_debug DEBUG=1
+  - BUILD_TYPE=Release PETSC_ARCH=petsc_opt DEBUG=0
 
 script: 
-  - mkdir build && cd build
-  - ls $PETSC_DIR
-  - ls $PETSC_DIR/$PETSC_ARCH
-  - ls $PETSC_DIR/$PETSC_ARCH/lib
-  - export TMPDIR=/tmp
-  - cmake .. -DCMAKE_INSTALL_PREFIX=$PWD/../alquimia-install -DCMAKE_C_COMPILER=`which mpicc` -DCMAKE_CXX_COMPILER=`which mpicxx` -DCMAKE_Fortran_COMPILER=`which mpif90` -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DXSDK_WITH_PFLOTRAN=ON -DTPL_PFLOTRAN_LIBRARIES=$PETSC_DIR/$PETSC_ARCH/externalpackages/git.pflotran/src/pflotran/libpflotranchem.a -DTPL_PFLOTRAN_INCLUDE_DIRS=$PETSC_DIR/$PETSC_ARCH/externalpackages/git.pflotran/src/pflotran -DXSDK_WITH_CRUNCHFLOW=ON -DTPL_CRUNCHFLOW_LIBRARIES=$PETSC_DIR/$PETSC_ARCH/externalpackages/crunchtope-dev/source/libcrunchchem.a -DTPL_CRUNCHFLOW_INCLUDE_DIRS=$PETSC_DIR/$PETSC_ARCH/externalpackages/crunchtope-dev/source
-  - make -j4
-  - make test
-  - make install
-  - make test_install
-  - cd ..
+  - ./.travis/install-petsc.sh
+  - ./.travis/install-crunchtope.sh
+  - ./.travis/install-pflotran.sh
+  - ./.travis/install-alquimia.sh
 
 after_failure: 
-  - cat build/Testing/Temporary/LastTest.log
+  - cat $ALQUIMIA_DIR/build/Testing/Temporary/LastTest.log

.travis/install-alquimia.sh

@@ -0,0 +1,20 @@
+#!/bin/sh
+
+cd $ALQUIMIA_DIR
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=$PWD/../alquimia-install \
+         -DCMAKE_C_COMPILER=`which mpicc` \
+         -DCMAKE_CXX_COMPILER=`which mpicxx` \
+         -DCMAKE_Fortran_COMPILER=`which mpif90` \
+         -DCMAKE_BUILD_TYPE=$BUILD_TYPE \
+         -DXSDK_WITH_PFLOTRAN=ON \
+         -DTPL_PFLOTRAN_LIBRARIES=$PFLOTRAN_DIR/src/pflotran/libpflotranchem.a \
+         -DTPL_PFLOTRAN_INCLUDE_DIRS=$PFLOTRAN_DIR/src/pflotran \
+         -DXSDK_WITH_CRUNCHFLOW=ON \
+         -DTPL_CRUNCHFLOW_LIBRARIES=$CRUNCHTOPE_DIR/source/libcrunchchem.a \
+         -DTPL_CRUNCHFLOW_INCLUDE_DIRS=$CRUNCHTOPE_DIR/source
+make -j4
+make test
+make install
+make test_install

.travis/install-crunchtope.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+
+git clone https://bitbucket.org/crunchflow/crunchtope-dev.git --branch petsc-upgrade $CRUNCHTOPE_DIR
+cd $CRUNCHTOPE_DIR/source
+git apply MakefileForAlquimia.patch
+make libcrunchchem.a

.travis/install-linux-deps.sh

@@ -0,0 +1,4 @@
+# Install necessary software.
+sudo apt-get update -qq
+sudo apt-get install -y cmake gcc libopenmpi-dev openmpi-bin liblapack-dev gfortran git
+

.travis/install-osx-deps.sh

@@ -0,0 +1,20 @@
+# Install required software
+brew cask uninstall oclint
+brew update
+brew install openmpi
+export TMPDIR=/tmp
+
+# Make sure the weird gfortran library links are in place.
+ln -s /usr/local/lib/gcc/7/libgfortran.dylib /usr/local/lib/libgfortran.dylib
+ln -s /usr/local/lib/gcc/7/libgfortran.a /usr/local/lib/libgfortran.a
+
+# Go get PETSc 3.6.x and build it.
+git clone https://bitbucket.org/petsc/petsc petsc
+pushd $PETSC_DIR
+./configure --with-mpi=1 --download-hdf5 --with-debug=$DEBUG --with-shared-libraries=1 --download-pflotran --download-pflotran-commit=origin/master
+make
+make test
+popd
+
+# Go get pflotran and build it.
+# -already installed under PETSc

.travis/install-petsc.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+
+git clone https://gitlab.com/petsc/petsc.git $PETSC_DIR
+cd $PETSC_DIR
+git checkout v3.11.3
+./configure --with-mpi=1 --with-debug=1 --with-shared-libraries=1 --download-fblaslapack=1 --with-debug=$DEBUG
+make

.travis/install-pflotran.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+
+git clone https://bitbucket.org/pflotran/pflotran $PFLOTRAN_DIR
+cd $PFLOTRAN_DIR/src/pflotran
+git checkout v3.0
+git apply $ALQUIMIA_DIR/.travis/pflotran_version_patch.txt
+make libpflotranchem.a

.travis/pflotran_version_patch.txt

@@ -0,0 +1,13 @@
+diff --git a/src/pflotran/pflotran_constants.F90 b/src/pflotran/pflotran_constants.F90
+index dd88e7265..86d0816c4 100644
+--- a/src/pflotran/pflotran_constants.F90
++++ b/src/pflotran/pflotran_constants.F90
+@@ -16,7 +16,7 @@ module PFLOTRAN_Constants_module
+   PetscInt, parameter :: PFLOTRAN_VERSION_PATCH = 0 ! (alpha < -1; beta = -1)
+
+ #define VMAJOR 3
+-#define VMINOR 13
++#define VMINOR 11
+ #define VSUBMINOR 0
+ #if (PETSC_VERSION_MAJOR < VMAJOR ||                    \
+      (PETSC_VERSION_MAJOR == VMAJOR &&                  \