def test_replace_var(self):
"""Tests whether the replace variable function works.
"""
# Test par file
parfile = os.path.join(DATA_DIR, "Par_file")
# Set new value
newval = 4
with tempfile.NamedTemporaryFile(mode='w+t') as tmpfile:
# Copy parfile content to temporary file.
print(tmpfile)
with open(parfile) as PF:
for line in PF:
tmpfile.write(line)
# Back to start of file
tmpfile.seek(0)
# Replace value
DATAFixer.replace_varval(tmpfile.name, "NCHUNKS", newval)
# Check if value is
val = DATAFixer.get_val(tmpfile.name, "NCHUNKS")
# Check if value has changed
self.assertTrue(newval == int(val))
def test_get_val(self):
""" Tests static method get_val"""
# Test par file
parfile = os.path.join(DATA_DIR, "Par_file")
# Solution
original_value = 6
# Get the value from the file
val = DATAFixer.get_val(parfile, 'NCHUNKS')
print(val)
# Check if values match
self.assertTrue(original_value == int(val))
def Fix_Specfem():
"""This Function uses the parameters found in
::
GCMT3D/workflow/params/SpecfemParams/SpecfemParams.yml
and
::
GCMT3D/workflow/params/SpecfemParams/CompilersAndModules.yml
to fix and recompile the software which is necessary for the simulation
and inversion of the data.
Since all data are taken from the parameter files. there are no in- and
outputs.
"""
# Define parameter directory
param_path = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "params")
specfemspec_path = os.path.join(param_path,
"SpecfemParams/SpecfemParams.yml")
comp_and_modules_path = os.path.\
join(param_path, "SpecfemParams/CompilersAndModules.yml")
# Load parameters
sf_dict = smart_read_yaml(specfemspec_path, mpi_mode=is_mpi_env())
cm_dict = smart_read_yaml(comp_and_modules_path, mpi_mode=is_mpi_env())
# Define the specfemdatafixer
df = DATAFixer(
sf_dict["SPECFEM_DIR"],
NEX_XI=sf_dict["NEX_XI"],
NEX_ETA=sf_dict["NEX_ETA"],
NPROC_XI=sf_dict["NPROC_XI"],
NPROC_ETA=sf_dict["NPROC_ETA"],
ROTATE_SEISMOGRAMS_RT=sf_dict["ROTATE_SEISMOGRAMS_RT"],
RECORD_LENGTH=sf_dict["RECORD_LENGTH"],
MODEL=sf_dict["MODEL"],
WRITE_SEISMOGRAMS_BY_MASTER=sf_dict["WRITE_SEISMOGRAMS_BY_MASTER"],
OUTPUT_SEISMOS_ASCII_TEXT=sf_dict["OUTPUT_SEISMOS_ASCII_TEXT"],
OUTPUT_SEISMOS_SAC_ALPHANUM=sf_dict["OUTPUT_SEISMOS_SAC_ALPHANUM"],
OUTPUT_SEISMOS_SAC_BINARY=sf_dict["OUTPUT_SEISMOS_SAC_BINARY"],
OUTPUT_SEISMOS_ASDF=sf_dict["OUTPUT_SEISMOS_ASDF"],
MOVIE_SURFACE=sf_dict["MOVIE_SURFACE"],
MOVIE_VOLUME=sf_dict["MOVIE_VOLUME"],
MOVIE_COARSE=sf_dict["MOVIE_COARSE"],
GPU_MODE=sf_dict["GPU_MODE"],
GPU_RUNTIME=sf_dict["GPU_RUNTIME"],
GPU_PLATFORM=sf_dict["GPU_PLATFORM"],
GPU_DEVICE=sf_dict["GPU_DEVICE"],
ADIOS_ENABLED=sf_dict["ADIOS_ENABLED"],
ADIOS_FOR_FORWARD_ARRAYS=sf_dict["ADIOS_FOR_FORWARD_ARRAYS"],
ADIOS_FOR_MPI_ARRAYS=sf_dict["ADIOS_FOR_MPI_ARRAYS"],
ADIOS_FOR_ARRAYS_SOLVER=sf_dict["ADIOS_FOR_ARRAYS_SOLVER"],
ADIOS_FOR_SOLVER_MESHFILES=sf_dict["ADIOS_FOR_SOLVER_MESHFILES"],
ADIOS_FOR_AVS_DX=sf_dict["ADIOS_FOR_AVS_DX"],
ADIOS_FOR_KERNELS=sf_dict["ADIOS_FOR_KERNELS"],
ADIOS_FOR_MODELS=sf_dict["ADIOS_FOR_MODELS"],
ADIOS_FOR_UNDO_ATTENUATION=sf_dict["ADIOS_FOR_UNDO_ATTENUATION"],
modules=cm_dict["modulelist"],
gpu_module=cm_dict["gpu_module"],
gpu_version=cm_dict["gpu_version"],
cc=cm_dict["cc"],
cpp=cm_dict["cpp"],
mpicc=cm_dict["mpicc"],
f90=cm_dict["f90"],
mpif90=cm_dict["mpif90"],
nodes=sf_dict["nodes"],
tasks=sf_dict["tasks"],
tasks_per_node=sf_dict["tasks_per_node"],
walltime=sf_dict["walltime"],
walltime_solver=sf_dict["walltime"],
memory_req=sf_dict["memory_req"],
verbose=sf_dict["verbose"])
# Run `Par_file` fixer.
df.fix_parfiles()
# Configure and compile
df.configure_and_make()
# Run the mesher to a slurm scheduler.
df.run_mesher()
def main():
"""This script controlls the compilation and setting up of
specfem3d_globe.
Usage:
In the command line
``00_Fix_Specfem_And_Recompile.py``
It uses the parameter files located in
``../params/SpecfemParams/SpecfemParams.yml``
and ``../params/SpecfemParams/CompAndModules.yaml`` to get all necessary
parameters.
"""
# Define parameter directory
param_path = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(
__file__))), "params")
specfemspec_path = os.path.join(param_path,
"SpecfemParams/SpecfemParams.yml")
comp_and_modules_path = os.path.join(param_path,
"SpecfemParams/CompilersAndModules.yml")
# Load parameters
sf_dict = smart_read_yaml(specfemspec_path, mpi_mode=is_mpi_env())
cm_dict = smart_read_yaml(comp_and_modules_path, mpi_mode=is_mpi_env())
# Define the specfemdatafixer
DF = DATAFixer(sf_dict["SPECFEM_DIR"],
NEX_XI=sf_dict["NEX_XI"], NEX_ETA=sf_dict["NEX_ETA"],
NPROC_XI=sf_dict["NPROC_XI"], NPROC_ETA=sf_dict["NPROC_ETA"],
ROTATE_SEISMOGRAMS_RT=sf_dict["ROTATE_SEISMOGRAMS_RT"],
RECORD_LENGTH=sf_dict["RECORD_LENGTH"],
MODEL=sf_dict["MODEL"],
WRITE_SEISMOGRAMS_BY_MASTER=sf_dict[
"WRITE_SEISMOGRAMS_BY_MASTER"],
OUTPUT_SEISMOS_ASCII_TEXT=sf_dict[
"OUTPUT_SEISMOS_ASCII_TEXT"],
OUTPUT_SEISMOS_SAC_ALPHANUM=sf_dict[
"OUTPUT_SEISMOS_SAC_ALPHANUM"],
OUTPUT_SEISMOS_SAC_BINARY=sf_dict[
"OUTPUT_SEISMOS_SAC_BINARY"],
OUTPUT_SEISMOS_ASDF=sf_dict["OUTPUT_SEISMOS_ASDF"],
MOVIE_SURFACE=sf_dict["MOVIE_SURFACE"],
MOVIE_VOLUME=sf_dict["MOVIE_VOLUME"],
MOVIE_COARSE=sf_dict["MOVIE_COARSE"],
GPU_MODE=sf_dict["GPU_MODE"],
GPU_RUNTIME=sf_dict["GPU_RUNTIME"],
GPU_PLATFORM=sf_dict["GPU_PLATFORM"],
GPU_DEVICE=sf_dict["GPU_DEVICE"],
ADIOS_ENABLED=sf_dict["ADIOS_ENABLED"],
ADIOS_FOR_FORWARD_ARRAYS=sf_dict["ADIOS_FOR_FORWARD_ARRAYS"],
ADIOS_FOR_MPI_ARRAYS=sf_dict["ADIOS_FOR_MPI_ARRAYS"],
ADIOS_FOR_ARRAYS_SOLVER=sf_dict["ADIOS_FOR_ARRAYS_SOLVER"],
ADIOS_FOR_SOLVER_MESHFILES=sf_dict[
"ADIOS_FOR_SOLVER_MESHFILES"],
ADIOS_FOR_AVS_DX=sf_dict["ADIOS_FOR_AVS_DX"],
ADIOS_FOR_KERNELS=sf_dict["ADIOS_FOR_KERNELS"],
ADIOS_FOR_MODELS=sf_dict["ADIOS_FOR_MODELS"],
ADIOS_FOR_UNDO_ATTENUATION=sf_dict[
"ADIOS_FOR_UNDO_ATTENUATION"],
modules=cm_dict["modulelist"],
gpu_module=cm_dict["gpu_module"],
gpu_version=cm_dict["gpu_version"],
cc=cm_dict["cc"],
cpp=cm_dict["cpp"],
mpicc=cm_dict["mpicc"],
f90=cm_dict["f90"],
mpif90=cm_dict["mpif90"],
nodes=sf_dict["nodes"],
tasks=sf_dict["tasks"],
tasks_per_node=sf_dict["tasks_per_node"],
walltime=sf_dict["walltime"],
walltime_solver=sf_dict["walltime_solver"],
memory_req=sf_dict["memory_req"],
verbose=sf_dict["verbose"])
# Run `Par_file` fixer.
DF.fix_parfiles()
# Configure and compile
DF.configure_and_make()
# Run the mesher to a slurm scheduler.
DF.run_mesher()
def main():
# Define parameter directory
param_path = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "params")
specfemspec_path = os.path.join(param_path,
"SpecfemParams/SpecfemParams.yml")
comp_and_modules_path = os.path.join(
param_path, "SpecfemParams/CompilersAndModules.yml")
# Load parameters
sf_dict = smart_read_yaml(specfemspec_path, mpi_mode=is_mpi_env())
cm_dict = smart_read_yaml(comp_and_modules_path, mpi_mode=is_mpi_env())
# Define the specfemdatafixer
DF = DATAFixer(
sf_dict["SPECFEM_DIR"],
NEX_XI=sf_dict["NEX_XI"],
NEX_ETA=sf_dict["NEX_ETA"],
NPROC_XI=sf_dict["NPROC_XI"],
NPROC_ETA=sf_dict["NPROC_ETA"],
ROTATE_SEISMOGRAMS_RT=sf_dict["ROTATE_SEISMOGRAMS_RT"],
RECORD_LENGTH=sf_dict["RECORD_LENGTH"],
MODEL=sf_dict["MODEL"],
WRITE_SEISMOGRAMS_BY_MASTER=sf_dict["WRITE_SEISMOGRAMS_BY_MASTER"],
OUTPUT_SEISMOS_ASCII_TEXT=sf_dict["OUTPUT_SEISMOS_ASCII_TEXT"],
OUTPUT_SEISMOS_SAC_ALPHANUM=sf_dict["OUTPUT_SEISMOS_SAC_ALPHANUM"],
OUTPUT_SEISMOS_SAC_BINARY=sf_dict["OUTPUT_SEISMOS_SAC_BINARY"],
OUTPUT_SEISMOS_ASDF=sf_dict["OUTPUT_SEISMOS_ASDF"],
MOVIE_SURFACE=sf_dict["MOVIE_SURFACE"],
MOVIE_VOLUME=sf_dict["MOVIE_VOLUME"],
MOVIE_COARSE=sf_dict["MOVIE_COARSE"],
GPU_MODE=sf_dict["GPU_MODE"],
GPU_RUNTIME=sf_dict["GPU_RUNTIME"],
GPU_PLATFORM=sf_dict["GPU_PLATFORM"],
GPU_DEVICE=sf_dict["GPU_DEVICE"],
ADIOS_ENABLED=sf_dict["ADIOS_ENABLED"],
ADIOS_FOR_FORWARD_ARRAYS=sf_dict["ADIOS_FOR_FORWARD_ARRAYS"],
ADIOS_FOR_MPI_ARRAYS=sf_dict["ADIOS_FOR_MPI_ARRAYS"],
ADIOS_FOR_ARRAYS_SOLVER=sf_dict["ADIOS_FOR_ARRAYS_SOLVER"],
ADIOS_FOR_SOLVER_MESHFILES=sf_dict["ADIOS_FOR_SOLVER_MESHFILES"],
ADIOS_FOR_AVS_DX=sf_dict["ADIOS_FOR_AVS_DX"],
ADIOS_FOR_KERNELS=sf_dict["ADIOS_FOR_KERNELS"],
ADIOS_FOR_MODELS=sf_dict["ADIOS_FOR_MODELS"],
ADIOS_FOR_UNDO_ATTENUATION=sf_dict["ADIOS_FOR_UNDO_ATTENUATION"],
modules=cm_dict["modulelist"],
gpu_module=cm_dict["gpu_module"],
gpu_version=cm_dict["gpu_version"],
cc=cm_dict["cc"],
cpp=cm_dict["cpp"],
mpicc=cm_dict["mpicc"],
f90=cm_dict["f90"],
mpif90=cm_dict["mpif90"],
nodes=sf_dict["nodes"],
tasks=sf_dict["tasks"],
tasks_per_node=sf_dict["tasks_per_node"],
walltime=sf_dict["walltime"],
walltime_solver=sf_dict["walltime_solver"],
memory_req=sf_dict["memory_req"],
verbose=sf_dict["verbose"])
# Run the mesher to a slurm scheduler.
DF.run_mesher()