Building the ``kaiju`` software (serial only) on a Mac ========================================================== Introduction ------------ These instructions will walk you through the process of building and installing the ``kaiju`` software on an Intel-based Macintosh computer running the MacOS Ventura operating system. These instructions assume that the user is using the ``bash`` shell, and that no modifications have been made to the user "dotfiles" (``$HOME/.bashrc``, ``$HOME/.bash_profile``). If you have customized either of these files for your account, please carefully save and inspect the output from each command in the build process to ensure that no unexpected problems have crept in. To facilitate this practice, all of the commands shown below will illustrate how to save command output, and how to measure how long each step takes. The latter is a useful bit of information which can help identify build problems early in the process, avoiding much wasted time and effort later. Unlike most HPC systems, a Mac does not use the ``module`` system to manage the versions of software packages available to the user. Compilers and libraries must be installed by the user before starting on building the ``kaiju`` software. Building the serial version of the ``kaiju`` software --------------------------------------------------------- Step 1: Configure the required software ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Set environment variables for the Intel fortran compiler (adjust the path as needed for your machine): .. code-block:: shell export INTEL_HOME=/opt/intel export PATH=$INTEL_HOME/oneapi/compiler/latest/mac/bin/intel64:$PATH Set environment variables for CDF (adjust the paths as needed for your machine): .. code-block:: shell source $HOME/ventura/local/cdf/3.9.0/bin/definitions.B Set environment variables for HDF5 (adjust the paths as needed for your machine): .. code-block:: shell export HDF5_DIR=$HOME/ventura/local/hdf5/1.14.1-2 export PATH=$HDF5_DIR/bin:$PATH export HDF5_INCLUDE_DIRS=$HDF5_DIR/include export HDF5_LIBRARIES=$HDF5_DIR/lib export CPATH=$HDF5_INCLUDE_DIRS Step 2: Create the build directory ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Create a ``ventura``-specific build directory. .. code-block:: shell cd $HOME mkdir -p ventura cd ventura Then make an additional subdirectory level for the branch of the code you are building (the ``development`` branch is used as an example). This arrangement is useful when you need to maintain simultaneous builds of different branches. .. code-block:: shell mkdir development cd development Step 3: Clone the ``kaiju`` repository from BitBucket ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ NOTE: This step assumes you have been granted access to the ``kaiju`` repository on BitBucket, and that you have configured an SSH key pair for use with BitBucket. If you need help with these tasks, please contact a CGS team member for assistance. Clone the ``kaiju`` repository (or "repo") from BitBucket: .. code-block:: shell git clone git@bitbucket.org:aplkaiju/kaiju.git This process should take a minute or so. When complete, verify that the ``kaiju`` code exists in your directory (the actual directory contents may differ slightly from what is shown below): .. code-block:: shell ls kaiju analysis cmake CMakeLists.txt examples external gitHookScripts kaiju.sublime-project kaipy places pytests quickstart README.md scripts setup.py src testingScripts tests xml Now move down into the cloned repo, and switch to the branch of the code you wish to use. By default, the cloned repository provides the ``master`` branch, but we want the ``development`` branch: .. code-block:: shell cd kaiju git switch development Step 4: Run ``cmake`` to create the ``Makefile`` needed to build the software ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Since the ``kaiju`` code can be built in serial and MPI forms, we first make a directory in which to build the serial version of the code (use whatever name you prefer, but ``build_serial`` is simple and unambiguous): .. code-block:: shell mkdir build_serial cd build_serial Now run the ``cmake`` command. Save the ``cmake`` output, and use timestamps for each step. The options shown below direct the build process to use a recent version of the Intel Fortran compiler: .. code-block:: shell date; time FC=`which ifort` cmake -DALLOW_INVALID_COMPILERS=ON >& cmake.out; date This command usually takes less than 10 seconds, depending on system activity. Examine the output file ``cmake.out`` for problems. It *should* look something like this: .. code-block:: shell -- The Fortran compiler identification is Intel 2021.9.0.20230302 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /opt/intel/oneapi/compiler/latest/mac/bin/intel64/ifort - skipped -- Found HDF5: /Users/winteel1/ventura/local/hdf5/1.14.1-2/lib/libhdf5_fortran.dylib;/Users/winteel1/ventura/local/hdf5/1.14.1-2/lib/libhdf5.dylib;/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/lib/libz.tbd;/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/lib/libdl.tbd;/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/lib/libm.tbd (found version "1.14.1-2") found components: Fortran -- Found OpenMP_Fortran: -qopenmp (found version "5.0") -- Found OpenMP: TRUE (found version "5.0") found components: Fortran CMake Warning at cmake/compilers.cmake:61 (message): Setting default optimization to O2 to avoid certain Intel compiler bugs Call Stack (most recent call first): CMakeLists.txt:99 (include) ------------------------- Configuration summary ... System: C02FC1QCMD6T-ML OS: Darwin Processor: x86_64 Compiler: Intel / 2021.9.0.20230302 /opt/intel/oneapi/compiler/latest/mac/bin/intel64/ifort HDF5 Wrapper: /Users/winteel1/ventura/local/hdf5/1.14.1-2/bin/h5fc Version: 339707e4 / ewinter-python_environment_upgrade Build Type: Release Base Flags: -fPIC -Wl,-stack_size,0x40000000,-stack_addr,0xf0000000 -xHost -free -implicitnone -qopenmp Build Flags: -O2 -align array64byte -align rec32byte -no-prec-div -fast-transcendentals ------------------------- Adding CHIMP module ... EB IC file is /Users/winteel1/ventura/cgs/kaiju/ewinter-python_environment_upgrade/kaiju/src/chimp/ebICs/ebICstd.F90 TP IC file is /Users/winteel1/ventura/cgs/kaiju/ewinter-python_environment_upgrade/kaiju/src/chimp/tpICs/tpICstd.F90 Adding executable project.x Adding executable psd.x Adding executable push.x Adding executable slice.x Adding executable chop.x Adding executable trace.x Adding executable sctrack.x Adding executable calcdb.x Adding executable wpicheck.x Adding Gamera module ... Bricksize is 16 IC file is /Users/winteel1/ventura/cgs/kaiju/ewinter-python_environment_upgrade/kaiju/src/gamera/ICs/null.F90 Adding executable gamera.x Adding Gamera Helio module ... IC file is /Users/winteel1/ventura/cgs/kaiju/ewinter-python_environment_upgrade/kaiju/src/gamera/ICs/helio/wsa.F90 Adding executable gamhelio.x Adding ReMIX module ... Adding executable remix.x Adding RCM module ... RCM Grid is of size 180 x 361 x 160 Adding executable rcm.x Adding Voltron module ... IC file is /Users/winteel1/ventura/cgs/kaiju/ewinter-python_environment_upgrade/kaiju/src/voltron/ICs/earthcmi.F90 Adding executable voltron.x -- Configuring done (7.6s) -- Generating done (0.3s) -- Build files have been written to: /Users/winteel1/ventura/cgs/kaiju/ewinter-python_environment_upgrade/kaiju/build_serial Step 5: Compile the ``kaiju`` software ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Now use ``make`` to build the ``kaiju`` software, time-stamping and saving the output: .. code-block:: shell date; time make >& make.out; date This command should complete in about 3-4 minutes on a modern Mac. When the command is finished, check the output file ``make.out``. The file is long, but the last few lines should look something like this: .. code-block:: shell [ 99%] Linking Fortran static library libvoltlib.a [ 99%] Built target voltlib [100%] Building Fortran object CMakeFiles/voltron.x.dir/src/drivers/voltronx.F90.o [100%] Linking Fortran executable bin/voltron.x [100%] Built target voltron.x [100%] Built target voltron To verify that all of the ``kaiju`` programs have been built, examine the ``bin`` subdirectory of your ``build_serial`` directory (this list will evolve as more programs are added): .. code-block:: shell ls bin calcdb.x chop.x gamera.x gamhelio.x kaitoy.x project.x psd.x push.x rcm.x remix2rcm.x remix2remix.x remix.x sctrack.x slice.x trace.x voltron.x wpicheck.x Using the ``kaiju`` software -------------------------------- Once built, you must run the setup script before using the ``kaiju`` software: .. code-block:: shell source $KAIJU_HOME/scripts/setupEnvironment.sh This script will set environment variables needed by the ``kaiju`` software, including the ``KAIJUHOME`` environment variable. However, the path to the compiled programs is not added - you will need to specify the complete path when using compiled programs. For example, to run the serial version of ``gamera.x``: .. code-block:: shell $KAIJUHOME/build_serial/bin/gamera.x