Yosemite Clang

Mac OSX Yosemite 10.10.5

Apple LLVM version 7.0.2 (clang-700.1.81)
XCode Version 7.2.1 (7C1002)
Use GNU Fortran (GCC) 5.1.0

Building MPICH

Version 3.1.4

  ./configure --prefix=/usr/local/mpich-3.1.4
  make -j 4
  make install

Building ZLib

Version 1.2.11

  CC=mpicc CFLAGS="-O3 -march=native" ./configure --64 --archs="-arch x86_64" --prefix=/usr/local/mpich-3.1.4
  make -j 4
  make install

Building Yaml

git clone [email protected]:jbeder/yaml-cpp.git

  GCC_MPI_DIR=/usr/local/mpich-3.1.4

  cmake \
      -DCMAKE_CXX_COMPILER:STRING=${GCC_MPI_DIR}/bin/mpicxx \
      -DCMAKE_CXX_FLAGS:STRING='-march=native -O3 -DNDEBUG' \
      -DCMAKE_C_COMPILER:STRING=${GCC_MPI_DIR}/bin/mpicc \
      -DCMAKE_C_FLAGS:STRING='-march=native -O3 -DNDEBUG' \
      -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/mpich-3.1.4 \
      -DCMAKE_BUILD_TYPE:STRING=Release \
      -DBUILD_SHARED_LIBS:BOOL=ON \
      -DYAML_CPP_BUILD_TOOLS:BOOL=OFF \
  ..

  make -j 4
  make install

Need to edit the rpath after the dylib is installed

  install_name_tool -id /usr/local/mpich-3.1.4/lib/libyaml-cpp.0.5.3.dylib /usr/local/mpich-3.1.4/lib/libyaml-cpp.0.5.3.dylib

Building HDF5

Version 1.10.0-patch1

  ./configure CC=mpicc FC=mpifort CXX=mpicxx CXXFLAGS="-fPIC -march=native -O3" CFLAGS="-fPIC -march=native -O3" FCFLAGS="-fPIC -march=native -Wa,-q -O3" LDFLAGS="-fPIC -L/usr/local/mpich-3.1.4/lib -march=native -O3" --enable-parallel --with-zlib=/usr/local/mpich-3.1.4 --prefix=/usr/local/mpich-3.1.4
  make -j 4
  make install

Building parallel-netcdf

Version 1.8.1

Configure and build:

  ./configure --prefix=/usr/local/mpich-3.1.4 CC=/usr/local/mpich-3.1.4/bin/mpicc \
  FC=/usr/local/mpich-3.1.4/bin/mpifort CXX=/usr/local/mpich-3.1.4/bin/mpicxx \
  CXXFLAGS="-O3 -march=native -fPIC" CFLAGS="-O3 -march=native -fPIC" FFLAGS="-O3 -march=native -fPIC" \
  FCFLAGS="-O3 -march=native -fPIC"

  make -j 4 
  make install

Building Netcdf

Version 4.4.1.1

Edit the file include/netcdf.h. Make the following edits near line 265:

  #define NC_MAX_DIMS    65536    /* max dimensions per file */
  #define NC_MAX_ATTRS    8192
  #define NC_MAX_VARS   524288    /* max variables per file */
  #define NC_MAX_NAME   256
  #define NC_MAX_VAR_DIMS      8     /* max per variable dimensions */

Build

  ./configure --prefix=/usr/local/mpich-3.1.4 CC=mpicc FC=mpifort CXX=mpicxx \
  CFLAGS="-fPIC -I/usr/local/mpich-3.1.4/include -march=native -O3" \
  CXXFLAGS="-fPIC -I/usr/local/mpich-3.1.4/include -march=native -O3" \
  FCFLAGS="-fPIC -I/usr/local/mpich-3.1.4/include -march=native -Wa,-q -O3" \
  LDFLAGS=-L/usr/local/mpich-3.1.4/lib --disable-fsync --disable-doxygen --enable-netcdf4 --enable-pnetcdf
  make -j 4 
  make install

Building Boost

Version 1.63.0

I could not figure out how to get the boost build to properly treat the "rpath" on Yosemite, so I hacked it. Please edit "tools/build/src/tools/darwin.jam", changing the following line to change the install name to include the install path:

  actions link.dll bind LIBRARIES
  {
      "$(CONFIG_COMMAND)" -dynamiclib -Wl,-single_module -install_name "/usr/local/mpich-3.1.4/lib/$(<:B)$(<:S)" -L"$(LINKPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(FRAMEWORK_PATH) -framework$(_)$(FRAMEWORK:D=:S=) $(OPTIONS) $(USER_OPTIONS)
  }

Build boost with the commands

  echo "using mpi : /usr/local/mpich-3.1.4/bin/mpicxx : <cxxflags>"-O3 -DNDEBUG -march=native" <include>/usr/local/mpich-3.1.4/include <library-path>/usr/local/mpich-3.1.4/lib <find-shared-library>mpi ;" > ~/user-config.jam
  echo 'using darwin : : : <compileflags>"-O3 -march=native" <library-path>/usr/local/mpich-3.1.4/lib <find-shared-library>mpi ;' >> ~/user-config.jam
  ./bootstrap.sh --with-libraries=signals,regex,filesystem,system,mpi,serialization,thread,program_options,exception,chrono,date_time --prefix=/usr/local/mpich-3.1.4
  ./b2 -j 4
  ./b2 -j 4 install

Building ParMetis

Version 4.0.3

Edit metis.h to use an IDXTYPEWIDTH of 64

  cd parmetis-4.0.3/metis/include
  vi metis.h
  #define IDXTYPEWIDTH 64

Run CMake to build metis

  cd /usr/local/src/parmetis-4.0.3/
  mkdir build
  cd build
  export metis=/usr/local/src/parmetis-4.0.3/metis
  cmake \
  -DCMAKE_INSTALL_PREFIX=/usr/local/mpich-3.1.4 \
  -DMETIS_PATH=$metis \
  -DGKLIB_PATH=$metis/GKlib \
  -DCMAKE_C_COMPILER=mpicc \
  -DCMAKE_C_FLAGS="-O3 -march=native -fPIC" \
  -DCMAKE_CXX_COMPILER=mpicxx \
  -DCMAKE_CXX_FLAGS="-O3 -march=native -fPIC" \
  ..
  make -j 4
  make install

  cp libmetis/libmetis.a /usr/local/mpich-3.1.4/lib
  cp /usr/local/src/parmetis-4.0.3/metis/include/metis.h /usr/local/mpich-3.1.4/include

SuperLU (optional)

SuperLU is optional in a Trilinos build.

Version 4.3 (later versions do not appear to be supported in Amesos currently)

  mkdir /usr/local/mpich-3.1.4/SuperLU_4.3
  mkdir /usr/local/mpich-3.1.4/SuperLU_4.3/include
  mkdir /usr/local/mpich-3.1.4/SuperLU_4.3/lib

Edit make.inc for your machine and environment

  SuperLUroot     = /usr/local/mpich-3.1.4/SuperLU_4.3
  SUPERLULIB      = $(SuperLUroot)/lib/libsuperlu_4.3.a

  TMGLIB          = libtmglib.a
  BLASDEF     = -DUSE_VENDOR_BLAS
  BLASLIB     = /System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Versions/Current/libblas.a

  LIBS            = $(SUPERLULIB) $(BLASLIB)

  ARCH         = ar
  ARCHFLAGS    = cr
  RANLIB       = ranlib

  CC           = mpicc 
  CFLAGS       = -fPIC -O3 -DPRNTlevel=0 -DNDEBUG
  NOOPTS       = -O0
  FORTRAN      = mpifort
  FFLAGS       = -fPIC -O3

  LOADER       = $(CC)
  LOADOPTS     =
  CDEFS        = -DAdd_

Build SuperLU

  make -j 4
  cd SRC
  cp *.h /usr/local/mpich-3.1.4/SuperLU_4.3/include

Version 5.2.1 (experimental - does not appear to build with Amesos currently)

  mkdir /usr/local/mpich-3.1.4/SuperLU_5.2.1
  mkdir /usr/local/mpich-3.1.4/SuperLU_5.2.1/include
  mkdir /usr/local/mpich-3.1.4/SuperLU_5.2.1/lib

Edit make.inc for your machine and environment

  SuperLUroot     = /usr/local/mpich-3.1.4/SuperLU_5.2.1
  SUPERLULIB      = $(SuperLUroot)/lib/libsuperlu.a

  TMGLIB          = libtmglib.a
  BLASDEF     = -DUSE_VENDOR_BLAS
  BLASLIB     = /System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Versions/Current/libblas.a

  LIBS            = $(SUPERLULIB) $(BLASLIB)

  ARCH         = /usr/bin/ar
  ARCHFLAGS    = cr
  RANLIB       = /usr/bin/ranlib

  CC           = mpicc
  CFLAGS       = -fPIC -DNDEBUG -O3 -DPRNTlevel=0 -DAdd_
  NOOPTS       = -O0
  FORTRAN      = mpifort
  FFLAGS       = -fPIC -O3

  LOADER       = $(CC)
  LOADOPTS     =

Build SuperLU

  make -j 4
  cd SRC
  cp *.h /usr/local/mpich-3.1.4/SuperLU_5.2.1/include

Build Trilinos

do-configure script in the Albany Repo
Make a build directory at the top level of your Trilinos repo clone
```
  cd Trilinos
  mkdir build
  cd build
```
Download the above file as "do-configure" in the above build directory, then make it executable
```
  chmod +x ./do-configure
```
Edit the do-configure script to match your system and above TPL builds

Configure and build Trilinos

  ./do-configure
  make -j 4
  make -j 4 install

Build Albany

CMake configure script in the Albany Repo
Make a "build" directory at the top level of the Albany repo clone, download the "do-configure" file, and edit as appropriate
Do the build:
```
  ./do-configure
  make -j 4
  ctest
```

Misc utilities in Yosemite

MacVim

Instructions at http://colinwhite.net/dropplets/MacVim

Get recent MacVim

  git clone https://github.com/b4winckler/macvim

Build it

  cd macvim/src

  LDFLAGS=-L/usr/lib ./configure --with-features=huge \
  	--enable-rubyinterp \
  	--enable-pythoninterp \
  	--enable-perlinterp \
  	--enable-cscope

  make -j 4

Copy macvim/src/MacVim/build/Release/MacVim.app to Applications folder

OpenSSH (SFTP) with History and Filename Completion

Get OpenSSH 6.9p1

  wget http://openbsd.mirrorcatalogs.com/pub/OpenBSD/OpenSSH/portable/openssh-6.9p1.tar.gz

Edit source according to https://trac.macports.org/browser/trunk/dports/net/openssh/files/launchd.patch?rev=121205

Download patch file

Build OpenSSH

  ./configure --with-zlib=/usr/local/mpich-3.1.4/lib --prefix=/usr/local --with-xauth=/opt/X11/bin/xauth --with-libedit
  make -j 4
  make -j 4 install

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Yosemite Clang

Mac OSX Yosemite 10.10.5

Building MPICH

Building ZLib

Building Yaml

Building HDF5

Building parallel-netcdf

Building Netcdf

Building Boost

Building ParMetis

SuperLU (optional)

Build Trilinos

Build Albany

Misc utilities in Yosemite

MacVim

OpenSSH (SFTP) with History and Filename Completion

Docker Image

SPACK Package

ToDo List

Albany FAQs

Capabilities

Sub-Projects

Compiling

Nightly Tests

Code HowTo

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