technical:recipes:mcfost

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technical:recipes:mcfost [2023-03-03 11:33] – created freytechnical:recipes:mcfost [2023-03-24 23:03] (current) – frey
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 +====== Building MCFOST on Caviness ======
  
 +Two distinct use cases are described in this document.  The first represents a build of the MCFOST program alone.  The result of this scheme is the ''mcfost'' executable for stand-alone usage.
 +
 +The second integrates the MCFOST program into a Python virtual environment (virtualenv).  In this scheme, the ''mcfost'' executable can be used as a computational driver under scripted Python code.
 +
 +The following recipes reflect a user's building and managing MCFOST in their home directory.  The environment variable ''MCFOST_PREFIX'' will be used throughout and could instead point to a workgroup's storage to create versions shared by all members of the workgroup.  The value of ''MCFOST_PACKAGE'' will vary:  for the stand-alone scheme, ''mcfost'' will suffice.  For Python virtualenv integrations something indicative of the nature of that virtualenv is appropriate.  For example, a simple virtualenv which includes **astropy** might be ''mcfost-astropy'', while a Python program using multiple Python modules (like **astropy**) that models cooling of a stellar body might be ''stellar-cooling''((I do not profess to know exactly for what calculations MCFOST typically gets used.)).  Finally, code revisions must be balanced against working milestones in the development, so the ''MCFOST_VERSION'' environment variable will be used in that regard.
 +
 +===== Stand-alone =====
 +
 +The recipe begins by setting-up a directory to contain all versions of MCFOST to be built in stand-alone fashion:
 +
 +<code bash>
 +$ export MCFOST_PACKAGE="mcfost"
 +$ export MCFOST_PREFIX="$(echo ~/sw/${MCFOST_PACKAGE})"
 +$ mkdir -p "$MCFOST_PREFIX"
 +$ cd "$MCFOST_PREFIX"
 +</code>
 +
 +To build from the head of the master branch of the MCFOST source, it is easier to version the software by compilation date; the actual release version can be aliased to the date-based version after the fact in the VALET package definition.  So the next step is to create a version by date, change into that directory, and clone the source:
 +
 +<code bash>
 +$ export MCFOST_VERSION="$(date +%Y.%m.%d)"
 +$ mkdir -p "${MCFOST_PREFIX}/${MCFOST_VERSION}"
 +$ cd "${MCFOST_PREFIX}/${MCFOST_VERSION}"
 +$ git clone https://github.com/cpinte/mcfost.git src
 +$ cd src
 +</code>
 +
 +The next step is to build the program.
 +
 +==== Build Procedure ====
 +
 +MCFOST has two components to its build:  library dependencies and the ''mcfost'' executable.  The library dependencies is a scripted procedure that downloads source and builds static libraries that ''mcfost'' will link against.  Several environment variables are used to communicate compiler variant and options to the MCFOST build system.  The entire procedure can be scripted:
 +
 +<file bash SWMGR-build.sh>
 +#!/bin/bash -l
 +
 +vpkg_require intel-oneapi/2022
 +
 +export MCFOST_INSTALL="${MCFOST_PREFIX}/${MCFOST_VERSION}"
 +export MCFOST_GIT=1
 +export MCFOST_AUTO_UPDATE=0
 +
 +export SYSTEM=ifort
 +#export MCFOST_XGBOST=yes
 +
 +# Start with the library build:
 +pushd lib
 +    ./install.sh
 +    if [ $? -ne 0 ]; then
 +        exit 1
 +    fi
 +    # Remove the HDF5 fake install root that install.sh created:
 +    [ -d ~/hdf5_install_tmp ] && rm -rf ~/hdf5_install_tmp
 +popd
 +
 +# Move to the executable build:
 +pushd src
 +    make
 +    if [ $? -ne 0 ]; then
 +        exit 1
 +    fi
 +
 +    # There is no "install" target, so just do it ourself:
 +    mkdir -p "${MCFOST_INSTALL}/bin"
 +    cp mcfost "${MCFOST_INSTALL}/bin"
 +popd
 +
 +# Add a symlink to the utils directory to the install prefix, too;
 +# we'll set MCFOST_UTILS to point to that:
 +ln -s "$(realpath --relative-to="$MCFOST_INSTALL" ./utils)" "${MCFOST_INSTALL}/utils"
 +
 +</file>
 +
 +The library dependencies and ''mcfost'' are built with the Intel oneAPI 2022 compiler suite for best-performance on Caviness.  Parallelization of MCFOST is via OpenMP — there is no support for multinode parallelism e.g. with MPI.  Saving the ''SWMGR-build.sh'' script to the ''src'' directory (where the procedure left off above) and making it executable, it can be executed therein:
 +
 +<code bash>
 +$ chmod +x SWMGR-build.sh
 +$ ./SWMGR-build.sh
 +Adding dependency `binutils/2.38` to your environment
 +Adding package `intel-oneapi/2022.3.0.8767` to your environment
 +~/sw/mcfost/2023.03.03/src/lib ~/sw/mcfost/2023.03.03/src
 +Building MCFOST libraries with ifort
 +~/sw/mcfost/2023.03.03/src/lib ~/sw/mcfost/2023.03.03/src/lib
 +--2023-03-03 10:48:05--  http://sprng.org/Version2.0/sprng2.0b.tar.gz
 +Resolving sprng.org (sprng.org)... 204.85.28.65
 +Connecting to sprng.org (sprng.org)|204.85.28.65|:80... connected.
 +
 +  :
 +  
 +Compiling MCFOST for ifort system...........
 +
 +ifort -fpp -O3 -no-prec-div -fp-model fast=2 -traceback -axSSE2,SSSE3,SSE4.1,SSE4.2,AVX,CORE-AVX2,CORE-AVX512 -fopenmp -o mcfost mcfost_env.o parameters.o constants.o healpix_mod.o sha.o messages.o operating_system.o random_numbers.o utils.o sort.o fits_utils.o grains.o read1d_models.o cylindrical_grid.o spherical_grid.o kdtree2.o elements_type.o Voronoi.o grid.o wavelengths.o stars.o read_DustEM.o Temperature.o density.o read_opacity.o scattering.o read_fargo3d.o hdf5_utils.o utils_hdf5.o read_athena++.o readVTK.o read_idefix.o read_pluto.o coated_sphere.o dust_prop.o molecular_emission.o PAH.o input.o benchmarks.o atom_type.o wavelengths_gas.o broad.o read_param.o dust_ray_tracing.o uplow.o abo.o occupation_probability.o lte.o radiation_field.o thermal_emission.o diffusion.o io_prodimo.o disk_physics.o gas_contopac.o voigts.o opacity_atom.o optical_depth.o ML_prodimo.o output.o mem.o init_mcfost.o io_phantom_infiles.o io_phantom_utils.o mess_up_SPH.o read_phantom.o read_gadget2.o SPH2mcfost.o mhd2mcfost.o dust_transfer.o mol_transfer.o collision_atom.o io_atom.o electron_density.o see.o atom_transfer.o voro++_wrapper.o no_xgboost_wrapper.o mcfost.o -L/home/1001/sw/mcfost/2023.03.03/lib/ifort -L/home/1001/sw/mcfost/2023.03.03/lib/ifort -cxxlib -lcfitsio -lvoro++ -lsprng  -lhdf5_fortran -lhdf5 -lz -ldl
 +~/sw/mcfost/2023.03.03/src
 +</code>
 +
 +If successful (as above), the ''${MCFOST_PREFIX}/${MCFOST_VERSION}'' directory will be setup with the standard Linux subdirectories (''bin'', ''lib'') and the compiled targets:
 +
 +<code bash>
 +$ ls -l "${MCFOST_PREFIX}/${MCFOST_VERSION}"
 +total 42
 +drwxr-xr-x  2 frey everyone  3 Mar  3 11:07 bin
 +drwxr-xr-x  5 frey everyone  8 Mar  3 11:07 include
 +drwxr-xr-x  3 frey everyone  3 Mar  3 11:07 lib
 +drwxr-xr-x 10 frey everyone 15 Mar  3 11:26 src
 +lrwxrwxrwx  1 frey everyone  9 Mar  3 11:07 utils -> src/utils
 +
 +$ ls -l "${MCFOST_PREFIX}/${MCFOST_VERSION}/bin"
 +total 15003
 +-rwxr-xr-x 1 frey everyone 28472712 Mar  3 11:07 mcfost
 +</code>
 +
 +With this version of MCFOST built, the next step is to setup a VALET package definition to manage it in the user's environment.
 +
 +==== VALET Integration ====
 +
 +For a user building and managing MCFOST on their own, the VALET package definition file should be placed in ''~/.valet''.  If the software were being maintained for an entire workgroup the appropriate directory for the package definition file would be ''$WORKDIR/sw/valet''.  The file should be named ''mcfost.vpkg_yaml''.  Before editing that file the value of ''MCFOST_PREFIX'' and ''MCFOST_VERSION'' must be noted:
 +
 +<code bash>
 +$ echo $MCFOST_PREFIX ; echo $MCFOST_VERSION
 +/home/1001/sw/mcfost
 +2023.03.03
 +</code>
 +
 +With those values, ''~/.valet/mcfost.vpkg_yaml'' can be created:
 +
 +<file yaml mcfost.vpkg_yaml>
 +mcfost:
 +    prefix: /home/1001/sw/mcfost
 +    description: 3D continuum and line radiative transfer
 +    url: "https://mcfost.readthedocs.io/"
 +
 +    default-version: 2023.03.03
 +
 +    actions:
 +        - variable: MCFOST_INSTALL
 +          value: ${VALET_PATH_PREFIX}
 +        - variable: MCFOST_UTILS
 +          value: ${VALET_PATH_PREFIX}/utils
 +
 +    versions:
 +        2023.03.03:
 +            description: git master branch as of 2023-03-03, compiled with Intel oneAPI 2022
 +            dependencies:
 +                - intel-oneapi/2022
 +
 +</file>
 +
 +Once created, the syntax can be checked:
 +
 +<code bash>
 +[frey@login01.caviness ~]$ vpkg_check ~/.valet/mcfost.vpkg_yaml 
 +/home/1001/.valet/mcfost.vpkg_yaml is OK
 +   :
 +</code>
 +
 +When additional versions/variants of the program are built and added to ''$MCFOST_PREFIX'' a new version dictionary can be added to ''mcfost.vpkg_yaml''.
 +
 +Finally, the package can be added to the environment and the release version can be determined:
 +
 +<code bash>
 +$ vpkg_require mcfost/2023.03.03
 +Adding dependency `binutils/2.38` to your environment
 +Adding dependency `intel-oneapi/2022.3.0.8767` to your environment
 +Adding package `mcfost/2023.03.03` to your environment
 +
 +$ mcfost -version
 + You are running MCFOST 4.0.00
 + Git SHA = fe87f0e2c32ffcc897687d1a7a9a90e3ed2f02eb
 + Binary compiled the Mar 03 2023 at 10:01:05
 + with INTEL compiler version 2021
 +  
 + Checking last version ...
 + MCFOST is up-to-date
 +</code>
 +
 +Ah ha!  Version 4.0.00, so let's add an alias to the VALET package definition:
 +
 +<code yaml>
 +mcfost:
 +    prefix: /home/1001/sw/mcfost
 +    description: 3D continuum and line radiative transfer
 +    url: "https://mcfost.readthedocs.io/"
 +
 +    default-version: 2023.03.03
 +
 +    actions:
 +        - variable: MCFOST_INSTALL
 +          value: ${VALET_PATH_PREFIX}
 +        - variable: MCFOST_UTILS
 +          value: ${VALET_PATH_PREFIX}/utils
 +
 +    versions:
 +        2023.03.03:
 +            description: git master branch as of 2023-03-03, compiled with Intel oneAPI 2022
 +            dependencies:
 +                - intel-oneapi/2022
 +        4.0.00:
 +            alias-to: 2023.03.03
 +
 +</code>
 +
 +Having done that, the versions of MCFOST available are queried by doing:
 +
 +<code bash>
 +$ vpkg_versions mcfost
 +
 +Available versions in package (* = default version):
 +
 +[/home/1001/.valet/mcfost.vpkg_yaml]
 +mcfost        3D continuum and line radiative transfer
 +  4.0.00      alias to mcfost/2023.03.03
 +* 2023.03.03  git master branch as of 2023-03-03, compiled with Intel oneAPI 2022
 +</code>
 +
 +==== Using MCFOST ====
 +
 +With the build completed and the VALET package definition created, job scripts can now load a version of MCFOST into the runtime environment by doing
 +
 +<code bash>
 +   :
 +
 +vpkg_require mcfost/4.0.00
 +
 +   :
 +</code>
 +
 +The program is parallelized with OpenMP, so ''/opt/templates/slurm/generic/threads.qs'' can be used as the basis for job scripts.  Making a copy of that template, the tail end of the script can be altered:
 +
 +<code bash>
 +#
 +# If you have VALET packages to load into the job environment,
 +# uncomment and edit the following line:
 +#
 +vpkg_require mcfost/4.0.00
 +
 +#
 +# Do standard OpenMP environment setup:
 +#
 +. /opt/shared/slurm/templates/libexec/openmp.sh
 +
 +#
 +# [EDIT] Execute MCFOST:
 +#
 +MCFOST_ARGS=(-tmp_dir "${TMPDIR:-./}")
 +if [ -n "$SLURM_MEM_PER_NODE" ]; then
 +    MCFOST_ARGS+=(-max_mem "$((SLURM_MEM_PER_NODE/1024))")
 +elif [ -n "$SLURM_MEM_PER_CPU" ]; then
 +    MCFOST_ARGS+=(-max_mem "$((SLURM_MEM_PER_CPU*SLURM_JOB_CPUS_PER_NODE/1024))")
 +fi
 +mcfost "${MCFOST_ARGS[@]}" ...any other flags for this job...
 +mcfost_rc=$?
 +
 +# Add any cleanup commands here...
 +
 +exit $mcfost_rc
 +</code>
 +
 +===== Virtualenv Integration =====
 +
 +The recipe shown here for integration with a Python virtualenv is a real-world example provided by a Caviness user.  As with the stand-alone scheme, it begins with setting-up the directory that will hold the software:
 +
 +<code bash>
 +$ export MCFOST_PACKAGE="stellar-cooling"
 +$ export MCFOST_PREFIX="$(echo ~/sw/${MCFOST_PACKAGE})"
 +$ mkdir -p "$MCFOST_PREFIX"
 +$ cd "$MCFOST_PREFIX"
 +</code>
 +
 +For this recipe the new Intel oneAPI compilers will be used.  As of March 20, 2023, the MCFOST code included support for the traditional Intel Fortran compiler and the GNU Fortran compiler.  When writing this recipe, IT RCI staff added support for the Intel oneAPI Fortran compiler and contributed those changes back to the MCFOST developers; as of March 21, 2023, that code has been merged into the official MCFOST source.  A date-based versioning will be used for this recipe, as well:
 +
 +<code bash>
 +$ export MCFOST_VERSION="$(date +%Y.%m.%d)"
 +$ mkdir -p "${MCFOST_PREFIX}"
 +</code>
 +
 +==== Build the Virtual Environment ====
 +
 +At the very least a Python ''conda'' tool will be necessary in addition to the Intel Fortran compiler.  The oneAPI toolchain includes Intel Distribution for Python, so adding the ''intel-oneapi/2022'' package to the environment satisfies both requirements.
 +
 +The recipe presented here also requires Open MPI and HDF5 support.  Since MCFOST is Fortran code, the MPI-IO variant of HDF5 is not usable, therefore:
 +
 +<code bash>
 +$ vpkg_devrequire hdf5/1.10.9:intel-oneapi-2022
 +$ vpkg_require openmpi/4.1.4:intel-oneapi-2022
 +</code>
 +
 +The virtual environment will require a few modules that are compiled against local libraries
 +
 +  * mpi4py
 +  * schwimmbad
 +  * image_registration
 +  * FITS_tools
 +  * h5py
 +  * DebrisDiskFM
 +
 +the following (compiled) modules provided by the Intel channel
 +
 +  * numpy
 +  * scipy
 +  * astropy
 +  * matplotlib
 +  * zipp
 +  * pluggy
 +  * atomicwrites
 +
 +and a few standard PyPI modules
 +
 +  * emcee
 +  * corner
 +  * pyklip
 +
 +The process follows:
 +
 +<code bash>
 +$ conda create --prefix "${MCFOST_PREFIX}/${MCFOST_VERSION}" --channel intel numpy scipy astropy matplotlib pip zipp pluggy atomicwrites
 +$ conda activate "${MCFOST_PREFIX}/${MCFOST_VERSION}"
 +$ conda uninstall --force-remove impi_rt
 +$ pip install --upgrade pip
 +$ pip install --no-binary :all: --compile mpi4py 
 +$ pip install --compile emcee corner pyklip
 +$ pip install --no-binary :all: --compile schwimmbad image_registration FITS_tools
 +$ CC="icx" HDF5_DIR="$HDF5_PREFIX"  pip install --no-binary :all: --compile h5py
 +</code>
 +
 +<note important>Note the forced removal of the Intel MPI runtime library:  without doing that, the build of mpi4py will end up compiling against Open MPI but will link against the Intel `libmpi.so` in the virtualenv.  At runtime you will end up getting unresolved symbol errors (for Open MPI functions that Intel MPI isn't providing).  This works okay in this instance because none of the modules that wanted the Intel MPI runtime are going to be used in that way by this virtualenv.</note>
 +
 +If successful, the DebrisDiskFM module can be built; there is no PyPI or conda channel packaging of DebrisDiskFM so it must be built from source:
 +
 +<code bash>
 +$ mkdir -p "${MCFOST_PREFIX}/${MCFOST_VERSION}/src"
 +$ cd "${MCFOST_PREFIX}/${MCFOST_VERSION}/src"
 +$ git clone https://github.com/seawander/DebrisDiskFM.git
 +$ cd DebrisDiskFM
 +$ python setup.py install --compile
 +</code>
 +
 +At this point all of the Python components of the virtualenv have been completed.  The next step is to build and install MCFOST into the virtualenv, as well.
 +
 +==== Build MCFOST ====
 +
 +Akin to the procedure outlined above:
 +
 +<code bash>
 +$ cd "${MCFOST_PREFIX}/${MCFOST_VERSION}/src"
 +$ git clone https://github.com/cpinte/mcfost.git
 +$ cd mcfost
 +</code>
 +
 +The procedure is again scripted:
 +
 +<file bash SWMGR-build.sh>
 +#!/bin/bash -l
 +
 +vpkg_require hdf5/1.10.9:intel-oneapi-2022
 +
 +export MCFOST_INSTALL="${MCFOST_PREFIX}/${MCFOST_VERSION}"
 +export MCFOST_GIT=1
 +export MCFOST_AUTO_UPDATE=0
 +
 +export SYSTEM=ifx
 +#export MCFOST_XGBOST=yes
 +export SKIP_HDF5=yes
 +export HDF5_DIR="$HDF5_PREFIX"
 +
 +# Start with the library build:
 +pushd lib
 +    ./install.sh
 +    if [ $? -ne 0 ]; then
 +        exit 1
 +    fi
 +    # Remove the HDF5 fake install root that install.sh created:
 +    [ -d ~/hdf5_install_tmp ] && rm -rf ~/hdf5_install_tmp
 +popd
 +
 +# Move to the executable build:
 +pushd src
 +    make
 +    if [ $? -ne 0 ]; then
 +        exit 1
 +    fi
 +
 +    # There is no "install" target, so just do it ourself:
 +    mkdir -p "${MCFOST_INSTALL}/bin"
 +    cp mcfost "${MCFOST_INSTALL}/bin"
 +popd
 +
 +# Add a symlink to the utils directory to the install prefix, too;
 +# we'll set MCFOST_UTILS to point to that:
 +ln -s "$(realpath --relative-to="$MCFOST_INSTALL" ./utils)" "${MCFOST_INSTALL}/utils"
 +
 +</file>
 +
 +As in the stand-alone recipe, the ''SWMGR-build.sh'' file is saved to the MCFOST source directory and executed from there:
 +
 +<code bash>
 +$ chmod +x SWMGR-build.sh
 +$ ./SWMGR-build.sh
 +</code>
 +
 +If successful, the ''mcfost'' executable will be present in the ''${MCFOST_PREFIX}/${MCFOST_VERSION}/bin'' directory with the other executables associated with the virtualenv:
 +
 +<code bash>
 +$ which mcfost
 +/home/1001/sw/stellar-cooling/2023.03.21/bin/mcfost
 +</code>
 +
 +Henceforth additional Python modules can be added, either using the ''conda'' command or ''pip.''  Some care must be exercised to ensure the existing modules are not upgraded/downgraded.  Using the virtualenv is straightforward by means of a VALET package definition.
 +
 +==== VALET Integration ====
 +
 +For a user building and managing MCFOST on their own, the VALET package definition file should be placed in ''~/.valet''.  If the software were being maintained for an entire workgroup the appropriate directory for the package definition file would be ''$WORKDIR/sw/valet''.  The file for this project will be named ''stellar-cooling.vpkg_yaml''.  Before editing that file the value of ''MCFOST_PREFIX'' and ''MCFOST_VERSION'' must be noted:
 +
 +<code bash>
 +$ echo $MCFOST_PREFIX ; echo $MCFOST_VERSION
 +/home/1001/sw/stellar-cooling
 +2023.03.21
 +</code>
 +
 +With those values, ''~/.valet/${MCFOST_PACKAGE}.vpkg_yaml'' can be created:
 +
 +<file yaml stellar-cooling.vpkg_yaml>
 +stellar-cooling:
 +    prefix: /home/1001/sw/stellar-cooling
 +    description: 3D continuum and line radiative transfer
 +    url: "https://mcfost.readthedocs.io/"
 +
 +    default-version: 2023.03.21
 +
 +    actions:
 +        - variable: MCFOST_INSTALL
 +          value: ${VALET_PATH_PREFIX}
 +        - variable: MCFOST_UTILS
 +          value: ${VALET_PATH_PREFIX}/utils
 +
 +    versions:
 +        2023.03.21:
 +            description: build from 4.0.00 source with Python virtualenv
 +            dependencies:
 +                - hdf5/1.10.9:intel-oneapi-2022
 +                - openmpi/4.1.4:intel-oneapi-2022
 +            actions:
 +                - action: source
 +                  script:
 +                      sh: intel-python.sh
 +                  success: 0
 +</file>
 +
 +Once created, the syntax can be checked:
 +
 +<code bash>
 +[frey@login01.caviness ~]$ vpkg_check ~/.valet/stellar-cooling.vpkg_yaml 
 +/home/1001/.valet/stellar-cooling.vpkg_yaml is OK
 +   :
 +</code>
 +
 +When additional versions/variants of the virtualenv are built and added to ''$MCFOST_PREFIX'' a new version dictionary can be added to ''stellar-cooling.vpkg_yaml''.  Each version/variant is usable by means of ''vpkg_require'', as above.  In addition to the ''mcfost'' command's being present on the path, the virtualenv's Python interpreter is available as ''python''.  Python scripts written to make use of this environment should either be executed as an argument to ''python'':
 +
 +<code bash>
 +python my_script.py …
 +</code>
 +
 +or as an executable itself should include the following hash-bang on the first line of the file:
 +
 +<code bash>
 +#!/usr/bin/env python
 +</code>