This project forked from krischer/lasif
An End-to-end Workflow for Adjoint Full Seismic Waveform Inversions, specifically designed for SALVUS. For a tutorial, please download the Jupyter notebook at https://github.com/solvithrastar/LASIF_tutorials
License: GNU General Public License v3.0
Hello, here I ran into one problem when using the irregular mesh from salvus smoothsem,
but get an error which is related to the domain identification:
/tmp/ipykernel_30620/1694013832.py in
1 events=lasif.api.list_events(lasif_root, output=True)
----> 2 submit_forward('1','buildmesh/japan_hindu.h5',events)
/tmp/ipykernel_30620/1399908083.py in submit_forward(iteration, modelfile, events)
41 event=event,
42 iteration=iteration,
---> 43 side_set="r1"
44 )
45 if i%5==0 and i!=0 :
~/Salvus/salvus_lasif_yjgao-main/LASIF_2.0/lasif/salvus_utils.py in create_salvus_forward_simulation(comm, event, iteration, mesh, side_set)
95 mesh, sim_set["absorbing_boundaries_in_km"]
96 )
---> 97 if not domain.is_global_domain():
98 absorbing = sc.boundary.Absorbing(
99 width_in_meters=comm.project.simulation_settings[
~/Salvus/salvus_lasif_yjgao-main/LASIF_2.0/lasif/domain.py in is_global_domain(self)
503 def is_global_domain(self):
504 if not self.is_read:
--> 505 self._read()
506
507 if self.is_global_mesh:
~/Salvus/salvus_lasif_yjgao-main/LASIF_2.0/lasif/domain.py in _read(self)
188 # the points on the boundary are arranged in a way that a proper
189 # polygon will be drawn.
--> 190 sorted_indices = self.get_sorted_edge_coords()
191 x, y, z = self.domain_edge_coords[np.append(sorted_indices, 0)].T
192 lats, lons, _ = xyz_to_lat_lon_radius(x[0], y[0], z[0])
~/Salvus/salvus_lasif_yjgao-main/LASIF_2.0/lasif/domain.py in get_sorted_edge_coords(self)
478 # start sorting with the first node
479 print(indices_sorted)
--> 480 indices_sorted[0] = 0
481 for i in range(num_edge_points)[1:]:
482 prev_idx = indices_sorted[i - 1]
IndexError: index 0 is out of bounds for axis 0 with size 0
Below is the mesh building:
sm = SmoothieSEM()
sm.basic.model = "csem"
sm.basic.min_period_in_seconds = 30.0
sm.basic.elements_per_wavelength = 2.0
sm.basic.number_of_lateral_elements = 24
sm.advanced.tensor_order = 1
sm.source.latitude = 40
sm.source.longitude = 140
sm.chunk.max_colatitude = 80.0
sm.spherical.min_radius = 4000.0
sm.topography.topography_file = "topography_earth2014_egm2008_lmax_10800.nc"
sm.topography.topography_varname = (
"topography_earth2014_egm2008_lmax_10800_lmax_4096"
)
sm.topography.moho_topography_file = "moho_topography_crust_1_0_egm2008.nc"
sm.topography.moho_topography_varname = (
"moho_topography_crust_1_0_egm2008_lmax_128"
)
sm.refinement.lateral_refinements = [
{
"theta_min": 40.0,
"theta_max": 70.0,
"r_min": 4500.0,
"phi_min": -15.0,
"phi_max": 15.0,
}
]
sm.source.azimuth = 290.0
from obspy.clients.fdsn import Client
source = sn.simple_config.source.seismology.SideSetMomentTensorPoint3D(
latitude=40,
longitude=140,
depth_in_m=120,
side_set_name="r1",
mrr=5.47e15,
mtt=-4.11e16,
mpp=3.56e16,
mrt=2.26e16,
mrp=-2.25e16,
mtp=1.92e16,
)
inv = Client("gfz").get_stations(
network="*", level="station", format="text",minlatitude=34.782,
maxlatitude=46.5322,minlongitude=66.3029, maxlongitude=88.2316)
inv2 = Client("iris").get_stations(
network="*", level="station", format="text",minlatitude=34.782,
maxlatitude=46.5322,minlongitude=66.3029, maxlongitude=88.2316)
receivers = sn.simple_config.receiver.seismology.parse(
inv, dimensions=3, fields=["displacement"]
)
receivers2 = sn.simple_config.receiver.seismology.parse(
inv2, dimensions=3, fields=["displacement"]
)
newreceivers=receivers+receivers2
event_collection = sn.EventCollection.from_sources(
sources=[source], receivers=newreceivers
)
sm.spherical.ellipticity = 0.0033528106647474805
from salvus.mesh.mask_generators import RayMaskGenerator
rmg = RayMaskGenerator(
event_collection,
phases=["P","pP","S","sS"],
number_of_points_per_ray=100,
distance_in_km=1000.0,
)
m= sm.create_mesh(mesh_processing_callback=rmg)
m.find_surface()
#print(m.side_sets)
m.get_element_nodes().shape
m.side_sets['r1']
m.map_nodal_fields_to_element_nodal()
m.attach_global_variable("reference_frame", "spherical")
m.attach_global_variable("rotation_convention", "Spherical")
m.write_h5('japan_hindu.h5')
Hi, I want to use LASIF but I wasn't able to install Salvus because it is subject to licensing fees that I can't afford right now.
Is there a tutorial on using LASIF with a solver other than Salvus?
Hey guys,
When I want to select events for a global mesh, the automatic event selection filters the entire catalogue for events that are actually within the mesh. This is of course a bit superfluous, as the mesh is global and all events in the catalogue should fall within it. I am guessing there are a few other operations within LASIF that filter on domain as well which aren't necessarily needed for global meshes.
One idea to speed up these kind of operations is by setting a field for a mesh being global, and skipping filtering. I'll look into this when I find the time.
Hi guys,
Problem: I tried reinstalling lasif2 (after foolishly removing my env without backup) and ran into issues with the typing library: AttributeError: type object 'Callable' has no attribute '_abc_registry'
Steps to reproduce:
conda update condagit clone https://github.com/dirkphilip/LASIF_2.0.gitconda env create -f environment.yml (where I have renamed the env to lasif2 to differentiate it from the old lasif which I have also installed on my system).conda activate lasif2cd LASIF_2.0; pip install -e .AttributeError: type object 'Callable' has no attribute '_abc_registry'Potential cause
I had a bit of a look around, and for example here and here are mentions of issues with python 3.7, the typing library (and maybe certain pip versions, but since typing is here not downloaded over pip I'm assuming that has nothing to do with my issue).
?Solution?
I solved this by removing typing: conda uninstall typing - then the installation ran without problem.
I also tested installing a test env with lasif where I'd simply removed typing from the environment.yml file. This seems to yield exactly the same result.
Question
I'm still marking this as an issue because I'm wondering where this issue popped up -- presumably you guys use py3.7 as well without this problem. Any ideas?
My full conda env, fwiw:
$ conda list
# packages in environment at /home/phlos/anaconda3/envs/lasif2:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
alabaster 0.7.12 py_0 conda-forge
attrs 19.3.0 py_0 conda-forge
babel 2.8.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bleach 3.1.5 pyh9f0ad1d_0 conda-forge
brotlipy 0.7.0 py37h8f50634_1000 conda-forge
ca-certificates 2020.4.5.1 hecc5488_0 conda-forge
cairo 1.16.0 hcf35c78_1003 conda-forge
cartopy 0.17.0 py37hd759880_1006 conda-forge
certifi 2020.4.5.1 py37hc8dfbb8_0 conda-forge
cffi 1.14.0 py37hd463f26_0 conda-forge
chardet 3.0.4 py37hc8dfbb8_1006 conda-forge
click 7.1.2 pypi_0 pypi
cmasher 1.3.1 pypi_0 pypi
colorama 0.4.3 py_0 conda-forge
colorspacious 1.1.2 pypi_0 pypi
cryptography 2.9.2 py37hb09aad4_0 conda-forge
cycler 0.10.0 py_2 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
dill 0.3.1.1 py37hc8dfbb8_1 conda-forge
docutils 0.16 py37hc8dfbb8_1 conda-forge
entrypoints 0.3 py37hc8dfbb8_1001 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
flake8 3.8.1 pypi_0 pypi
flask 1.1.2 pypi_0 pypi
flask-cache 0.13.1 pypi_0 pypi
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.2 he06d7ca_0 conda-forge
fribidi 1.0.9 h516909a_0 conda-forge
future 0.18.2 py37hc8dfbb8_1 conda-forge
geographiclib 1.50 pypi_0 pypi
geojson 2.5.0 pypi_0 pypi
geos 3.7.2 he1b5a44_2 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
glib 2.64.2 h6f030ca_1 conda-forge
graphite2 1.3.13 he1b5a44_1001 conda-forge
graphviz 2.42.3 h0511662_0 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
h5netcdf 0.8.0 pypi_0 pypi
h5py 2.10.0 nompi_py37h513d04c_102 conda-forge
harfbuzz 2.4.0 h9f30f68_3 conda-forge
hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge
html5lib 1.0.1 py_0 conda-forge
icu 64.2 he1b5a44_1 conda-forge
idna 2.9 py_1 conda-forge
imagesize 1.2.0 py_0 conda-forge
importlib-metadata 1.6.0 py37hc8dfbb8_0 conda-forge
importlib_metadata 1.6.0 0 conda-forge
ipydatawidgets 4.0.1 py_0 conda-forge
ipykernel 5.2.1 py37h43977f1_0 conda-forge
ipyscales 0.4.0 py_1 conda-forge
ipython 7.14.0 py37hc8dfbb8_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
isodate 0.6.0 py_1 conda-forge
itsdangerous 1.1.0 pypi_0 pypi
jedi 0.17.0 py37hc8dfbb8_0 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
joblib 0.15.1 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
jsonschema 3.2.0 py37hc8dfbb8_1 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 6.1.3 py_0 conda-forge
jupyter_console 6.1.0 py_1 conda-forge
jupyter_contrib_core 0.3.3 py_2 conda-forge
jupyter_contrib_nbextensions 0.5.1 py37_0 conda-forge
jupyter_core 4.6.3 py37hc8dfbb8_1 conda-forge
jupyter_highlight_selected_word 0.2.0 py37_1000 conda-forge
jupyter_latex_envs 1.4.6 py37_1000 conda-forge
jupyter_nbextensions_configurator 0.4.1 py37_0 conda-forge
jupytext 1.4.2 pyh9f0ad1d_0 conda-forge
keepalive 0.5 py_1 conda-forge
kiwisolver 1.2.0 py37h99015e2_0 conda-forge
lasif 0453b-dirty dev_0 <develop>
ld_impl_linux-64 2.34 h53a641e_1 conda-forge
libblas 3.8.0 16_openblas conda-forge
libcblas 3.8.0 16_openblas conda-forge
libclang 9.0.1 default_hde54327_0 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.5.0 hdf63c60_6 conda-forge
libiconv 1.15 h516909a_1006 conda-forge
liblapack 3.8.0 16_openblas conda-forge
libllvm9 9.0.1 he513fc3_1 conda-forge
libopenblas 0.3.9 h5ec1e0e_0 conda-forge
libpng 1.6.37 hed695b0_1 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libtiff 4.1.0 hc7e4089_6 conda-forge
libtool 2.4.6 h14c3975_1002 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp-base 1.1.0 h516909a_3 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxkbcommon 0.10.0 he1b5a44_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
libxslt 1.1.33 h31b3aaa_0 conda-forge
llvm-openmp 10.0.0 hc9558a2_0 conda-forge
lxml 4.5.1 py37he3881c9_0 conda-forge
lz4-c 1.9.2 he1b5a44_1 conda-forge
markupsafe 1.1.1 py37h8f50634_1 conda-forge
matplotlib 3.2.1 0 conda-forge
matplotlib-base 3.2.1 py37h30547a4_0 conda-forge
mccabe 0.6.1 pypi_0 pypi
mistune 0.8.4 py37h8f50634_1001 conda-forge
mock 4.0.2 py37hc8dfbb8_0 conda-forge
more-itertools 8.3.0 py_0 conda-forge
mpi 1.0 openmpi conda-forge
mpi4py 3.0.3 py37hbfacf26_1 conda-forge
nbconvert 5.6.1 py37hc8dfbb8_1 conda-forge
nbformat 5.0.6 py_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
networkx 2.4 py_1 conda-forge
nose 1.3.7 py37hc8dfbb8_1004 conda-forge
notebook 6.0.3 py37hc8dfbb8_0 conda-forge
nspr 4.25 he1b5a44_0 conda-forge
nss 3.47 he751ad9_0 conda-forge
numexpr 2.7.1 py37h0da4684_1 conda-forge
numpy 1.16.5 py37h95a1406_0 conda-forge
obspy 1.2.1 py37h03ebfcd_1 conda-forge
olefile 0.46 py_0 conda-forge
openmpi 4.0.3 hdf1f1ad_1 conda-forge
openssl 1.1.1g h516909a_0 conda-forge
owslib 0.19.2 py_0 conda-forge
packaging 20.4 pyh9f0ad1d_0 conda-forge
pandas 1.0.3 py37h0da4684_1 conda-forge
pandoc 2.9.2.1 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
pango 1.42.4 h7062337_4 conda-forge
parso 0.7.0 pyh9f0ad1d_0 conda-forge
pathlib 1.0.1 py37hc8dfbb8_2 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pexpect 4.8.0 py37hc8dfbb8_1 conda-forge
pickleshare 0.7.5 py37hc8dfbb8_1001 conda-forge
pillow 7.1.2 py37h718be6c_0 conda-forge
pip 20.1.1 pyh9f0ad1d_0 conda-forge
pixman 0.38.0 h516909a_1003 conda-forge
pluggy 0.13.1 py37hc8dfbb8_1 conda-forge
progressbar 2.5 py_0 conda-forge
proj4 5.2.0 he1b5a44_1006 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt-toolkit 3.0.5 py_0 conda-forge
prompt_toolkit 3.0.5 0 conda-forge
prov 1.5.3 py_1 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
py 1.8.1 py_0 conda-forge
pyasdf 0.6.1 pypi_0 pypi
pycodestyle 2.6.0 pypi_0 pypi
pycparser 2.20 py_0 conda-forge
pydot 1.4.1 py37hc8dfbb8_1002 conda-forge
pyepsg 0.4.0 py_0 conda-forge
pyexodus 0.1.3 pypi_0 pypi
pyflakes 2.2.0 pypi_0 pypi
pygments 2.6.1 py_0 conda-forge
pykdtree 1.3.1 py37h03ebfcd_1003 conda-forge
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyproj 1.9.6 py37h516909a_1002 conda-forge
pyqt 5.12.3 py37h8685d9f_3 conda-forge
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtchart 5.12 pypi_0 pypi
pyqtgraph 0.11.0rc0 py_0 conda-forge
pyqtwebengine 5.12.1 pypi_0 pypi
pyrsistent 0.16.0 py37h8f50634_0 conda-forge
pyshp 2.1.0 py_0 conda-forge
pysocks 1.7.1 py37hc8dfbb8_1 conda-forge
pytest 5.4.2 py37hc8dfbb8_0 conda-forge
python 3.7.6 h8356626_5_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.7 1_cp37m conda-forge
pythreejs 2.2.0 pyh8c360ce_0 conda-forge
pytz 2020.1 pyh9f0ad1d_0 conda-forge
pyyaml 5.3.1 py37h8f50634_0 conda-forge
pyzmq 19.0.1 py37hac76be4_0 conda-forge
qt 5.12.5 hd8c4c69_1 conda-forge
qtconsole 4.7.4 pyh9f0ad1d_0 conda-forge
qtpy 1.9.0 py_0 conda-forge
rdflib 5.0.0 py37hc8dfbb8_2 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.23.0 pyh8c360ce_2 conda-forge
salvus-seismo 0.0.0-gf867 dev_0 <develop>
scipy 1.4.1 py37ha3d9a3c_3 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 46.4.0 py37hc8dfbb8_0 conda-forge
shapely 1.6.4 py37hec07ddf_1006 conda-forge
six 1.14.0 py_1 conda-forge
snowballstemmer 2.0.0 py_0 conda-forge
sparqlwrapper 1.8.5 py37hc8dfbb8_1003 conda-forge
sphinx 3.0.3 py_0 conda-forge
sphinx_rtd_theme 0.4.3 py_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 1.0.3 py_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.4 py_0 conda-forge
sqlalchemy 1.3.17 py37h8f50634_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
sysroot_linux-64 2.12 h3a0023d_1 conda-forge
terminado 0.8.3 py37hc8dfbb8_1 conda-forge
testpath 0.4.4 py_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
toml 0.10.1 pypi_0 pypi
tornado 6.0.4 py37h8f50634_1 conda-forge
tqdm 4.46.0 pypi_0 pypi
traitlets 4.3.3 py37hc8dfbb8_1 conda-forge
traittypes 0.2.1 py_1 conda-forge
urllib3 1.25.9 py_0 conda-forge
wcwidth 0.1.9 pyh9f0ad1d_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
werkzeug 1.0.1 pypi_0 pypi
wheel 0.34.2 py_1 conda-forge
widgetsnbextension 3.5.1 py37_0 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.9 h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxpm 3.5.13 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-libxt 1.1.5 h516909a_1003 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.5 h516909a_0 conda-forge
yaml 0.2.4 h516909a_0 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
zstd 1.4.4 h6597ccf_3 conda-forgeSource idx 25 at location [ 1.69635e+06, 4.48826e+06, 4.19137e+06 ] was not attached. Please check the coordinates ...
Weird problem though the source are in the center of domain.
Hi, sorry to bother you guys, but I encountered some assertion errors when executing the py.test command after I install the LASIF_2.0 through pyenv(not anaconda).
I'm a rookie at Seismology. And I'm not sure what's wrong with my installation.
Here is some info about my env.
platform MacOS Monterey
Python 3.7.13
Python packages:
alabaster 0.7.12
appnope 0.1.3
attrs 22.2.0
Babel 2.11.0
backcall 0.2.0
Cartopy 0.20.3
certifi 2022.12.7
charset-normalizer 2.1.1
click 8.1.3
cmasher 1.6.3
colorama 0.4.6
colorspacious 1.1.2
cycler 0.11.0
debugpy 1.6.4
decorator 5.1.1
dill 0.3.6
docutils 0.17.1
e13tools 0.9.6
entrypoints 0.4
exceptiongroup 1.1.0
Flask 2.2.2
Flask-Cache 0.13.1
fonttools 4.38.0
geographiclib 2.0
geojson 2.5.0
greenlet 2.0.1
h5py 3.7.0
idna 3.4
imagesize 1.4.1
importlib-metadata 6.0.0
iniconfig 1.1.1
ipydatawidgets 4.3.2
ipykernel 6.16.2
ipython 7.34.0
ipywidgets 8.0.4
isodate 0.6.1
itsdangerous 2.1.2
jedi 0.18.2
Jinja2 3.1.2
joblib 1.2.0
jupyter_client 7.4.8
jupyter_core 4.12.0
jupyterlab-widgets 3.0.5
kiwisolver 1.4.4
lasif 0.0.1 /Users/yanghaote2/Documents/code/LASIF_2.0
lxml 4.9.2
MarkupSafe 2.1.1
matplotlib 3.5.3
matplotlib-inline 0.1.6
mock 5.0.0
nest-asyncio 1.5.6
networkx 2.6.3
nose 1.3.7
numexpr 2.8.4
numpy 1.21.6
obspy 1.3.1
packaging 22.0
pandas 1.3.5
parso 0.8.3
pathlib 1.0.1
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pip 22.3.1
pluggy 1.0.0
progressbar 2.5
prompt-toolkit 3.0.36
prov 2.0.0
psutil 5.9.4
ptyprocess 0.7.0
pyasdf 0.7.5
Pygments 2.14.0
pyparsing 3.0.9
pyproj 3.2.1
PyQt5 5.15.7
PyQt5-Qt5 5.15.2
PyQt5-sip 12.11.0
pyqtgraph 0.12.4
pyshp 2.3.1
pytest 7.2.0
python-dateutil 2.8.2
pythreejs 2.4.1
pytz 2022.7
pyzmq 24.0.1
rdflib 6.2.0
requests 2.28.1
scipy 1.7.3
seaborn 0.12.2
setuptools 47.1.0
Shapely 1.8.5
six 1.16.0
snowballstemmer 2.2.0
Sphinx 5.3.0
sphinx-rtd-theme 1.1.1
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
SQLAlchemy 1.4.46
toml 0.10.2
tomli 2.0.1
tornado 6.2
tqdm 4.64.1
traitlets 5.8.0
traittypes 0.2.1
typing_extensions 4.4.0
urllib3 1.26.13
wcwidth 0.2.5
Werkzeug 2.2.2
widgetsnbextension 4.0.4
zipp 3.11.0
AssertionError:
$LASIF_2.0 git:(master) py.test 3.7.13
Exception ignored in: <function Popen.__del__ at 0x10e332dd0>
Traceback (most recent call last):
File "/Users/yanghaote2/.pyenv/versions/3.7.13/lib/python3.7/subprocess.py", line 883, in __del__
ResourceWarning, source=self)
ResourceWarning: subprocess 75182 is still running
Exception ignored in: <function Popen.__del__ at 0x10e332dd0>
Traceback (most recent call last):
File "/Users/yanghaote2/.pyenv/versions/3.7.13/lib/python3.7/subprocess.py", line 883, in __del__
ResourceWarning, source=self)
ResourceWarning: subprocess 75183 is still running
============================================ test session starts ============================================
platform darwin -- Python 3.7.13, pytest-7.2.0, pluggy-1.0.0
rootdir: /Users/yanghaote2/Documents/code/LASIF_2.0, configfile: pytest.ini
collected 207 items
lasif/rotations.py .... [ 1%]
lasif/utils.py ... [ 3%]
lasif/window_selection.py . [ 3%]
lasif/components/events.py .. [ 4%]
lasif/components/iterations.py . [ 5%]
lasif/function_templates/process_data.py s [ 5%]
lasif/function_templates/window_picking_function.py s [ 6%]
lasif/tests/test_adjoint_sources.py .... [ 8%]
lasif/tests/test_api.py ............................. [ 22%]
lasif/tests/test_cli_interface.py .................s...... [ 33%]
lasif/tests/test_code_formatting.py s [ 34%]
lasif/tests/test_domain.py .......................................................................... [ 70%]
....................... [ 81%]
lasif/tests/test_rotations.py .. [ 82%]
lasif/tests/test_utils.py . [ 82%]
lasif/tests/test_window_selection.py . [ 83%]
lasif/tests/components/test_adjoint_sources_component.py .FF. [ 85%]
lasif/tests/components/test_downloads_component.py . [ 85%]
lasif/tests/components/test_events_component.py ...... [ 88%]
lasif/tests/components/test_iterations_component.py .... [ 90%]
lasif/tests/components/test_project_component.py F... [ 92%]
lasif/tests/components/test_query_component.py ... [ 93%]
lasif/tests/components/test_validator_component.py .. [ 94%]
lasif/tests/components/test_visualization_component.py ssssssss [ 98%]
lasif/tests/data/example_project/FUNCTIONS/process_data.py s [ 99%]
lasif/tests/data/example_project/FUNCTIONS/window_picking_function.py s [ 99%]
lasif/tools/adjoint/utils.py . [100%]
================================================= FAILURES ==================================================
_________________________________________ test_get_misfit_for_event _________________________________________
comm = <lasif.components.communicator.Communicator object at 0x13831f9d0>
def test_get_misfit_for_event(comm):
events = lasif.api.list_events(comm, output=True)
iteration = lasif.api.list_iterations(comm, output=True)[0]
lasif.api.calculate_adjoint_sources_multiprocessing(comm, iteration, "A")
misfit = comm.adj_sources.get_misfit_for_event(
event=events[0], iteration=iteration
)
> np.testing.assert_almost_equal(misfit, 1.301670132868937)
E AssertionError:
E Arrays are not almost equal to 7 decimals
E ACTUAL: 1.3016674437258846
E DESIRED: 1.301670132868937
/Users/yanghaote2/Documents/code/LASIF_2.0/lasif/tests/components/test_adjoint_sources_component.py:57: AssertionError
------------------------------------------- Captured stdout call --------------------------------------------
===========================================================
Starting adjoint source calculation for event 1 of 2...
===========================================================
Writing adjoint sources...
1 Adjoint sources are in your file.
Finalizing adjoint sources...
===========================================================
Starting adjoint source calculation for event 2 of 2...
===========================================================
Writing adjoint sources...
1 Adjoint sources are in your file.
Finalizing adjoint sources...
------------------------------------------- Captured stderr call --------------------------------------------
100%|██████████| 4/4 [00:00<00:00, 43.20it/s]
100%|██████████| 4/4 [00:00<00:00, 17.19it/s]
______________________________________ test_calculate_adjoint_sources _______________________________________
comm = <lasif.components.communicator.Communicator object at 0x1383f58d0>
def test_calculate_adjoint_sources(comm):
events = lasif.api.list_events(comm, output=True)
file = (
comm.project.paths["adjoint_sources"]
/ "ITERATION_1"
/ events[0]
/ "auxiliary_adjoint.npy"
)
should_be = np.load(file)
lasif.api.calculate_adjoint_sources_multiprocessing(comm, "1", "A", weight_set="sw_1")
output = (
comm.project.paths["adjoint_sources"]
/ "ITERATION_1"
/ events[0]
/ "adjoint_source_auxiliary.h5"
)
with pyasdf.ASDFDataSet(output) as ds:
adj = ds.auxiliary_data.AdjointSources.HT_ALN.Channel__HHZ.data[()]
> np.testing.assert_array_almost_equal(should_be, adj)
E AssertionError:
E Arrays are not almost equal to 6 decimals
E
E (shapes (30002,), (30001,) mismatch)
E x: array([0., 0., 0., ..., 0., 0., 0.])
E y: array([0., 0., 0., ..., 0., 0., 0.])
/Users/yanghaote2/Documents/code/LASIF_2.0/lasif/tests/components/test_adjoint_sources_component.py:103: AssertionError
------------------------------------------- Captured stdout call --------------------------------------------
===========================================================
Starting adjoint source calculation for event 1 of 2...
===========================================================
Writing adjoint sources...
1 Adjoint sources are in your file.
Finalizing adjoint sources...
===========================================================
Starting adjoint source calculation for event 2 of 2...
===========================================================
Writing adjoint sources...
1 Adjoint sources are in your file.
Finalizing adjoint sources...
------------------------------------------- Captured stderr call --------------------------------------------
100%|██████████| 4/4 [00:00<00:00, 47.66it/s]
100%|██████████| 4/4 [00:00<00:00, 17.33it/s]
___________________________________ test_config_file_creation_and_parsing ___________________________________
tmpdir = local('/private/var/folders/_4/17zvg8wd3vbf51txxcqystc00000gq/T/pytest-of-yanghaote2/pytest-3/test_config_file_creation_and_0')
def test_config_file_creation_and_parsing(tmpdir):
"""
Tests the creation of a default config file and the reading of the file.
"""
# Create a new project.
pr = Project(
project_root_path=pathlib.Path(str(tmpdir)).absolute(),
init_project="TestProject",
)
del pr
# Init it once again.
pr = Project(pathlib.Path(str(tmpdir)).absolute())
# Assert the config file will test the creation of the default file and the
# reading.
assert pr.lasif_config["project_name"] == "TestProject"
assert pr.lasif_config["description"] == ""
assert pr.lasif_config["download_settings"]["channel_priorities"] == [
"BH?",
"LH[Z,N,E]",
"HH[Z,N,E]",
"EH[Z,N,E]",
"MH[Z,N,E]",
]
assert pr.lasif_config["download_settings"]["location_priorities"] == [
"",
"00",
"10",
"20",
"01",
"02",
]
assert pr.lasif_config["download_settings"]["networks"] == "None"
assert (
pr.lasif_config["download_settings"]["interstation_distance_in_m"]
== 1000.0
)
assert (
pr.lasif_config["download_settings"]["seconds_after_event"] == 3600.0
)
assert (
pr.lasif_config["download_settings"]["seconds_before_event"] == 300.0
)
> assert not pr.salvus_settings["attenuation"]
E assert not True
/Users/yanghaote2/Documents/code/LASIF_2.0/lasif/tests/components/test_project_component.py:80: AssertionError
========================================== short test summary info ==========================================
FAILED lasif/tests/components/test_adjoint_sources_component.py::test_get_misfit_for_event - AssertionError:
FAILED lasif/tests/components/test_adjoint_sources_component.py::test_calculate_adjoint_sources - AssertionError:
FAILED lasif/tests/components/test_project_component.py::test_config_file_creation_and_parsing - assert not True
================================ 3 failed, 190 passed, 14 skipped in 24.60s =================================Have the plots for the time frequency adjoint source fancier. A bit more like they used to be. I'm submitting this as an issue just so I won't forget :)
In a recent commit the absorbing_boundaries_in_km was refactored from salvus_settings into simulation_settings. This was reflected in the following line change of the create_salvus_forward_simulation method in the salvus_utils module.
LASIF_2.0/lasif/salvus_utils.py
Line 103 in 66b7051
However, a few lines further, this variable is used again, and taken from the old dictionary:
LASIF_2.0/lasif/salvus_utils.py
Lines 107 to 109 in 66b7051
This raises an exception when the used mesh is not global. Simple refactor would be sufficient, but I'll put that burden on the original muppet who introduced the bug, @solvithrastar .
Generating input files for event 1 of 116 -- 2410946_2007test
Segmentation fault (core dumped)
hey cool guys, here I confronted with segmentation fault running the lasif generate_input_files ..., have you any ideas about that? Thanks!
Hi,
when trying to install LASIF 2.0 based on your github instructions I get the following error (in a fresh environment):
ImportError: .../miniconda3/envs/TEST/lib/python3.6/site-packages/mpi4py/MPI.cpython-36m-x86_64-linux-gnu.so: undefined symbol: MPI_Type_create_f90_integer
when carrying out
python -c "import pyasdf; pyasdf.print_sys_info()"
and/or
py.test
based on the following installation lines:
$ pip install mpi4py
$ conda install -c spectraldns h5py-parallel
It was working fine several weeks ago - were there some changes or may it interfere with the integrated Salvus MPI I installed later on (in a separate env though)?
Cheers,
Debby
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