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user-variables.scons.py
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user-variables.scons.py
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# Configuration for scons build system
#
# For each package the following variables are available:
# <PACKAGE>_DIR Location of the package, must contain subfolders "include" and "lib" or "lib64" with header and library files.
# <PACKAGE>_INC_DIR Location of (*.h) header files
# <PACKAGE>_LIB_DIR Location of (*.a) libraries
# <PACKAGE>_LIBS List of libraries, optional since the standard names are already hardcoded.
# <PACKAGE>_DOWNLOAD Download, build and use a local copy of the package.
# <PACKAGE>_REDOWNLOAD Force update of previously downloaded copy. For that <PACKAGE>_DOWNLOAD has to be also true.
# <PACKAGE>_REBUILD Force a new build of the package without redownloading it if already has been downloaded earlier.
#
# You do one of the following:
# 1. Not specify any of the variables. Then standard locations in dependencies as well as /usr, /usr/local are searched.
# 2. Specify <PACKAGE>_DIR to directly give the base directory to the package's location. Do this to e.g. use system provided libraries.
# 3. Specify <PACKAGE>_INC_DIR and <PACKAGE>_LIB_DIR to point to the header and library directories. They are usually named "include" and "lib".
# 4. Set <PACKAGE>_DOWNLOAD=True or additionally <PACKAGE>_REDOWNLOAD=True to let the build system download and install everything on their own.
# set compiler to use
cc = "gcc" # C compiler
CC = "g++" # C++ compiler
mpiCC = "mpic++" # MPI C++ wrapper
cmake="cmake" # cmake command
# PETSc, this also downloads and installs MUMPS (direct solver package) and its dependencies PT-Scotch, SCAlapack, ParMETIS, METIS
PETSC_DOWNLOAD = True
#PETSC_DIR = "/usr/lib/petsc/"
# Python 3.9, note that this also builds the C-API which is usually not included in the normal python3 installation of your system, therefore it is recommended that you leave it at 'True'
PYTHON_DOWNLOAD = True
# Python packages - they are now all combined with the option PYTHONPACKAGES_DOWNLOAD
PYTHONPACKAGES_DOWNLOAD = True
# Base64, encoding library for binary vtk (paraview) output files
BASE64_DOWNLOAD = True
# Google Test, testing framework, not needed on Hazelhen
GOOGLETEST_DOWNLOAD = True
# SEMT, library for symbolic differentiation
SEMT_DOWNLOAD = True
# EasyLoggingPP, provides logging facilities
EASYLOGGINGPP_DOWNLOAD = True
# ADIOS2, adaptable I/O library, needed for interfacing MegaMol
ADIOS_DOWNLOAD = True
# MegaMol, visualization framework of VISUS, optional, needs ADIOS2
MEGAMOL_DOWNLOAD = False # install MegaMol from official git repo, but needed is the private repo, ask Tobias Rau for access to use MegaMol with opendihu
# Vc, vectorization types and C++ utility to produce vectorized code (but does not support AVX-512)
# std::experimental::simd supports AVX-512, but requires C++17. Therefore the package std_simd includes a compatibility script that falls back to Vc, if C++17 is not available.
VC_DOWNLOAD = True
STD_SIMD_DOWNLOAD = True
# xbraid, used for parallel-in time methods (currently only on branch `xbraid`)
XBRAID_DOWNLOAD = True
# OpenCOR, utility to view CellML models and to convert them from xml format to c code
OPENCOR_DOWNLOAD = True
# preCICE coupling library, set both to True in order to use precice
LIBXML2_DOWNLOAD = True
PRECICE_DOWNLOAD = True
# MPI
# MPI is normally detected by running the mpicc command. If this is not available, you can provide the MPI_DIR manually.
#MPI_DIR = "/usr/lib/openmpi" # standard path for openmpi on ubuntu 16.04
MPI_DIR = "/usr/lib/x86_64-linux-gnu/openmpi" # standard path for openmpi on ubuntu >= 18.04
# Vectorized code for matrix assembly
# Set to True for fastest code, set to False for faster compilation, note this works only using the Vc code, not std::simd code (only for GCC < 9)
USE_VECTORIZED_FE_MATRIX_ASSEMBLY = False
if USE_VECTORIZED_FE_MATRIX_ASSEMBLY:
print("Note, USE_VECTORIZED_FE_MATRIX_ASSEMBLY is True in user-variables.scons.py, this means faster programs but longer compilation times.\n")
# Use the implementation of std::simd instead of Vc to support AVX-512. This automatically sets the C++ standard from C++14 to C++17
USE_STDSIMD = False
if USE_STDSIMD:
print("Note, USE_STDSIMD is True and, thus, c++17 will be used.");
# -------------------------------------------------------------------------
# automatically set MPI_DIR for other systems, like ubuntu 16.04 and Debian
try:
import lsb_release
lsb_info = lsb_release.get_lsb_information() # get information about ubuntu version, if available
if "RELEASE" in lsb_info:
if lsb_info["RELEASE"] == "16.04":
MPI_DIR="/usr/lib/openmpi" # this is the standard path on ubuntu 16.04
except:
pass
try:
import platform
if 'debian' in platform.dist():
MPI_DIR="/usr/lib/x86_64-linux-gnu/openmpi" # path for debian (on Aaron's workstation)
except:
pass
try:
# use value of environment variable 'MPI_HOME' if it is set
import os
if os.environ.get("MPI_HOME") is not None:
MPI_DIR = os.environ.get("MPI_HOME")
# for Travis CI, build MPI ourselves
if os.environ.get("TRAVIS") is not None:
print("Travis CI detected, del MPI_DIR")
del MPI_DIR
MPI_DOWNLOAD=True
import socket
# special settings on cluster "lead"
if "lead" in socket.gethostname():
MPI_DIR = os.environ["MPI_HOME"]
# special settings on supercomputer Hawk
elif "hawk" in os.environ["SITE_PLATFORM_NAME"]:
if "MPT_ROOT" in os.environ:
MPI_DIR = os.environ["MPT_ROOT"]
else:
MPI_DIR = os.environ["MPI_ROOT"]
MPI_IGNORE_MPICC = True
LAPACK_DOWNLOAD = False
PETSC_DOWNLOAD = False
PETSC_DIR = os.environ["PETSC_ROOT"]
PYTHONPACKAGES_DOWNLOAD = False
GOOGLETEST_DOWNLOAD = True
XBRAID_DOWNLOAD = True
ADIOS_DOWNLOAD = False
ADIOS_DIR = os.environ["ADIOS2_ROOT"]
except:
pass
# download and build debugging MPI version
if False:
del MPI_DIR
MPI_DOWNLOAD = True
MPI_IGNORE_MPICC = True # this downloads and builds openmpi
#PETSC_DEBUG = True # this enables debugging flags such that valgrind memcheck can track MPI errors
# specialized settings for supercomputer HazelHen, this is left here in case there will be another Cray supercomputer
import os
if os.environ.get("PE_ENV") is not None: # if on hazelhen
cc = "cc" # C compiler wrapper
CC = "CC" # C++ compiler wrapper
mpiCC = "CC" # mpi C++ compiler wrapper
cmake = "/lustre/cray/ws8/ws/icbbnmai-opendihu1/cmake/cmake-3.13.2-Linux-x86_64/bin/cmake"
# use cray-pat for profiling
USE_CRAY_PAT = False
# use -hpl option with cray compiler to create an optimization program library
USE_HPL = False
# do not use googletest
GOOGLETEST_DOWNLOAD = False
# do not use buggy python packages
PYTHONPACKAGES_DOWNLOAD = False
# steps for getting started on HazelHen:
# module swap PrgEnv-cray/6.0.4 PrgEnv-gnu # to switch to GNU programming environment, however also Intel and Cray environments work
# module load cray-libsci
# module load cray-petsc (or cray-petsc-64 for big data)