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Error when running beat sample Laquila --hypers #20

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hvasbath opened this issue Nov 26, 2018 · 12 comments
Closed

Error when running beat sample Laquila --hypers #20

hvasbath opened this issue Nov 26, 2018 · 12 comments

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@hvasbath
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User issue:
Hi, when I running "beat sample Laquila --hypers" following Scenario I, I meet a error said
"AttributeError: Can't get attribute 'Quadtree' on <module 'beat.heart' from '/usr/local/lib/python3.4/dist-packages/beat-1.0rc1-py3.4-linux-x86_64.egg/beat/heart.py'>".
Can you help me solve this problem?
@hvasbath
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First of all please make sure you use python3.5. On python3.4 it is not tested at all and likely you will run into troubles.

@vic-chou
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Thanks! I used python 3.4. Maybe that's the problem.

@hvasbath
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The error you got here is unrelated to the python version. I hope it is fixed now. Please update beat and copy the geodetic_data.pkl from the beat/data/examples/Rectangular directory to your project directory.

@vic-chou
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Hi, we used python 3.5, but this error is still there. I have updata beat and copy the geodetic_data.pkl from the beat/data/examples/Rectangular directory to my project directory. But it does not work. So I want ask if I should modify the config_geometry.yaml file?
"geodetic_config: !beat.GeodeticConfig
datadir: /home/vasyurhm/BEATS/RectangularStatic/insar
names: [Laquila_dscxn, Laquila_ascxn]",
I noticed the dataset is not offered in the example data. Is it a problem here?

@vic-chou
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Hi, I have solve this problem based on your suggestion. I re-update the beat and re-copy the geodetic_data.pkl. And it works. But I meet a new problems. When I start to calculate the seismic GF function, I use the Crust2.0 earthquake model, it jump out a error
"STOP Error: earth radius smaller than pre-defined!".
I want ask that how can I use the Crust2.0 correctly?
image

image

@vic-chou
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When I run " beat sample Laquila --hypers", I stll meet a problem said that
"pyrocko.gf.store.StoreError: EMPTY_RECORD in store /home/vasyurhm/BEATS/GF/TSUM_ak135_0.500Hz_0"

@hvasbath
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Hi again! Meaning that your Greens Function calculation was not successful. Please paste only full error trace-backs otherwise I wont be able to help you.

@vic-chou
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Hi, the Greens Function calculation is successful. But I meet the error, when I run "beat sample Laquila --hypers", it appears "
root@matrix-VirtualBox:/home/matrix/test_beat# beat sample Laquila --hypers
config - INFO All parameter-priors ok!
config - INFO All hyper-parameters ok!
config - INFO All hierarchical-parameters ok!
models - INFO ... Initialising Geometry Optimizer ...

models - INFO Analysing problem ...
models - INFO ---------------------

/usr/local/lib/python3.5/dist-packages/scipy-1.1.0-py3.5-linux-x86_64.egg/scipy/signal/signaltools.py:1341: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
out_full[ind] += zi
/usr/local/lib/python3.5/dist-packages/scipy-1.1.0-py3.5-linux-x86_64.egg/scipy/signal/signaltools.py:1344: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
out = out_full[ind]
/usr/local/lib/python3.5/dist-packages/scipy-1.1.0-py3.5-linux-x86_64.egg/scipy/signal/signaltools.py:1350: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.
zf = out_full[ind]
heart - INFO Consistent number of datasets and targets in any_P_0 wavemap!
heart - INFO Number of seismic datasets for wavemap: any_P_0: 35
geodetic - INFO Number of geodetic datasets: 2
geodetic - INFO Number of geodetic data points: 419
geodetic - WARNING Covariance estimation not implemented (yet)! Using imported covariances!
geodetic - INFO Fit residual ramp selected!
models - INFO ... Building Hyper model ...

geodetic - INFO Estimating ramp for each dataset...
geodetic - INFO Initialized 4 hierarchical parameters (ramps).
models - INFO Optimization for 3 hyperparameters in total!
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/pyrocko/gf/store.py", line 856, in _sum
int(itmin), int(nsamples)))
pyrocko.gf.store_ext.StoreExtError: EMPTY_RECORD

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/bin/beat", line 11, in
load_entry_point('beat==1.0rc1', 'console_scripts', 'beat')()
File "/usr/local/lib/python3.5/dist-packages/beat-1.0rc1-py3.5-linux-x86_64.egg/beat/apps/beat.py", line 1588, in main
globals()'command_' + command
File "/usr/local/lib/python3.5/dist-packages/beat-1.0rc1-py3.5-linux-x86_64.egg/beat/apps/beat.py", line 748, in command_sample
project_dir, options.mode, options.hypers)
File "/usr/local/lib/python3.5/dist-packages/beat-1.0rc1-py3.5-linux-x86_64.egg/beat/models/problems.py", line 831, in load_model
problem.built_hyper_model()
File "/usr/local/lib/python3.5/dist-packages/beat-1.0rc1-py3.5-linux-x86_64.egg/beat/models/problems.py", line 266, in built_hyper_model
composite.analyse_noise(point)
File "/usr/local/lib/python3.5/dist-packages/beat-1.0rc1-py3.5-linux-x86_64.egg/beat/models/seismic.py", line 111, in analyse_noise
tpoint, order='wmap', chop_bounds=['b', 'c'])
File "/usr/local/lib/python3.5/dist-packages/beat-1.0rc1-py3.5-linux-x86_64.egg/beat/models/seismic.py", line 254, in assemble_results
chop_bounds=chop_bounds, order='wmap')
File "/usr/local/lib/python3.5/dist-packages/beat-1.0rc1-py3.5-linux-x86_64.egg/beat/models/seismic.py", line 533, in get_synthetics
**kwargs)
File "/usr/local/lib/python3.5/dist-packages/beat-1.0rc1-py3.5-linux-x86_64.egg/beat/heart.py", line 2574, in seis_synthetics
targets=targets, nprocs=nprocs)
File "/usr/local/lib/python3.5/dist-packages/pyrocko/gf/seismosizer.py", line 3146, in process
nthreads=nthreads):
File "/usr/local/lib/python3.5/dist-packages/pyrocko/gf/seismosizer.py", line 2692, in process_dynamic
source, target, components, dsource_cache, nthreads)
File "/usr/local/lib/python3.5/dist-packages/pyrocko/gf/seismosizer.py", line 2989, in base_seismogram
nthreads=nthreads)
File "/usr/local/lib/python3.5/dist-packages/pyrocko/gf/store.py", line 1907, in seismogram
'c', optimization)
File "/usr/local/lib/python3.5/dist-packages/pyrocko/gf/store.py", line 861, in _sum
raise StoreError(str(e) + ' in store %s' % self.store_dir)
pyrocko.gf.store.StoreError: EMPTY_RECORD in store /home/vasyurhm/BEATS/GF/TSUM_ak135_0.500Hz_0"
There are no GF function for the TSUM, but the Greens Function calculation is successful.

Here is the running log of calculation GF function
2018-11-27 11:26:23,079 - config - INFO - All parameter-priors ok!
2018-11-27 11:26:23,079 - config - INFO - All hyper-parameters ok!
2018-11-27 11:26:23,080 - config - INFO - All hierarchical-parameters ok!
2018-11-27 11:26:23,080 - beat - INFO - Creating Green's Function stores individually for each station!
2018-11-27 11:26:23,138 - heart - INFO - Using global model ...
2018-11-27 11:26:23,172 - heart - INFO - Station TSUM
2018-11-27 11:26:23,172 - heart - INFO - ---------------------
2018-11-27 11:26:23,183 - heart - INFO - Store /home/vasyurhm/BEATS/GF/TSUM_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,201 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,201 - heart - INFO - Station RCBR
2018-11-27 11:26:23,201 - heart - INFO - ---------------------
2018-11-27 11:26:23,202 - heart - INFO - Store /home/vasyurhm/BEATS/GF/RCBR_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,202 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,202 - heart - INFO - Station RES
2018-11-27 11:26:23,202 - heart - INFO - ---------------------
2018-11-27 11:26:23,203 - heart - INFO - Store /home/vasyurhm/BEATS/GF/RES_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,204 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,204 - heart - INFO - Station KMI
2018-11-27 11:26:23,204 - heart - INFO - ---------------------
2018-11-27 11:26:23,204 - heart - INFO - Store /home/vasyurhm/BEATS/GF/KMI_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,208 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,208 - heart - INFO - Station SSPA
2018-11-27 11:26:23,208 - heart - INFO - ---------------------
2018-11-27 11:26:23,209 - heart - INFO - Store /home/vasyurhm/BEATS/GF/SSPA_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,209 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,209 - heart - INFO - Station BTDF
2018-11-27 11:26:23,210 - heart - INFO - ---------------------
2018-11-27 11:26:23,210 - heart - INFO - Store /home/vasyurhm/BEATS/GF/BTDF_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,228 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,229 - heart - INFO - Station ANWB
2018-11-27 11:26:23,229 - heart - INFO - ---------------------
2018-11-27 11:26:23,229 - heart - INFO - Store /home/vasyurhm/BEATS/GF/ANWB_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,230 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,230 - heart - INFO - Station MBO
2018-11-27 11:26:23,230 - heart - INFO - ---------------------
2018-11-27 11:26:23,231 - heart - INFO - Store /home/vasyurhm/BEATS/GF/MBO_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,232 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,232 - heart - INFO - Station TEIG
2018-11-27 11:26:23,232 - heart - INFO - ---------------------
2018-11-27 11:26:23,233 - heart - INFO - Store /home/vasyurhm/BEATS/GF/TEIG_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,234 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,234 - heart - INFO - Station KBL
2018-11-27 11:26:23,234 - heart - INFO - ---------------------
2018-11-27 11:26:23,235 - heart - INFO - Store /home/vasyurhm/BEATS/GF/KBL_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,236 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,237 - heart - INFO - Station MSEY
2018-11-27 11:26:23,237 - heart - INFO - ---------------------
2018-11-27 11:26:23,251 - heart - INFO - Store /home/vasyurhm/BEATS/GF/MSEY_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,252 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,252 - heart - INFO - Station DBIC
2018-11-27 11:26:23,252 - heart - INFO - ---------------------
2018-11-27 11:26:23,253 - heart - INFO - Store /home/vasyurhm/BEATS/GF/DBIC_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,257 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,258 - heart - INFO - Station HIA
2018-11-27 11:26:23,258 - heart - INFO - ---------------------
2018-11-27 11:26:23,259 - heart - INFO - Store /home/vasyurhm/BEATS/GF/HIA_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,260 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,260 - heart - INFO - Station YAK
2018-11-27 11:26:23,260 - heart - INFO - ---------------------
2018-11-27 11:26:23,261 - heart - INFO - Store /home/vasyurhm/BEATS/GF/YAK_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,261 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,261 - heart - INFO - Station QIZ
2018-11-27 11:26:23,261 - heart - INFO - ---------------------
2018-11-27 11:26:23,262 - heart - INFO - Store /home/vasyurhm/BEATS/GF/QIZ_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,262 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,263 - heart - INFO - Station KBS
2018-11-27 11:26:23,263 - heart - INFO - ---------------------
2018-11-27 11:26:23,263 - heart - INFO - Store /home/vasyurhm/BEATS/GF/KBS_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,264 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,264 - heart - INFO - Station LSZ
2018-11-27 11:26:23,264 - heart - INFO - ---------------------
2018-11-27 11:26:23,264 - heart - INFO - Store /home/vasyurhm/BEATS/GF/LSZ_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,265 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,265 - heart - INFO - Station TLY
2018-11-27 11:26:23,265 - heart - INFO - ---------------------
2018-11-27 11:26:23,266 - heart - INFO - Store /home/vasyurhm/BEATS/GF/TLY_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,267 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,267 - heart - INFO - Station INCN
2018-11-27 11:26:23,268 - heart - INFO - ---------------------
2018-11-27 11:26:23,269 - heart - INFO - Store /home/vasyurhm/BEATS/GF/INCN_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,269 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,270 - heart - INFO - Station DWPF
2018-11-27 11:26:23,270 - heart - INFO - ---------------------
2018-11-27 11:26:23,274 - heart - INFO - Store /home/vasyurhm/BEATS/GF/DWPF_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,288 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,289 - heart - INFO - Station WMQ
2018-11-27 11:26:23,289 - heart - INFO - ---------------------
2018-11-27 11:26:23,289 - heart - INFO - Store /home/vasyurhm/BEATS/GF/WMQ_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,290 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,290 - heart - INFO - Station AAK
2018-11-27 11:26:23,290 - heart - INFO - ---------------------
2018-11-27 11:26:23,290 - heart - INFO - Store /home/vasyurhm/BEATS/GF/AAK_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,291 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,291 - heart - INFO - Station XAN
2018-11-27 11:26:23,291 - heart - INFO - ---------------------
2018-11-27 11:26:23,291 - heart - INFO - Store /home/vasyurhm/BEATS/GF/XAN_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,292 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,292 - heart - INFO - Station KMBO
2018-11-27 11:26:23,292 - heart - INFO - ---------------------
2018-11-27 11:26:23,292 - heart - INFO - Store /home/vasyurhm/BEATS/GF/KMBO_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,293 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,293 - heart - INFO - Station KURK
2018-11-27 11:26:23,293 - heart - INFO - ---------------------
2018-11-27 11:26:23,293 - heart - INFO - Store /home/vasyurhm/BEATS/GF/KURK_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,294 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,294 - heart - INFO - Station ADYE
2018-11-27 11:26:23,294 - heart - INFO - ---------------------
2018-11-27 11:26:23,294 - heart - INFO - Store /home/vasyurhm/BEATS/GF/ADYE_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,295 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,295 - heart - INFO - Station SDV
2018-11-27 11:26:23,295 - heart - INFO - ---------------------
2018-11-27 11:26:23,295 - heart - INFO - Store /home/vasyurhm/BEATS/GF/SDV_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,296 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,296 - heart - INFO - Station ARU
2018-11-27 11:26:23,296 - heart - INFO - ---------------------
2018-11-27 11:26:23,298 - heart - INFO - Store /home/vasyurhm/BEATS/GF/ARU_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,298 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,299 - heart - INFO - Station SAML
2018-11-27 11:26:23,299 - heart - INFO - ---------------------
2018-11-27 11:26:23,299 - heart - INFO - Store /home/vasyurhm/BEATS/GF/SAML_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,300 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,300 - heart - INFO - Station ALE
2018-11-27 11:26:23,300 - heart - INFO - ---------------------
2018-11-27 11:26:23,300 - heart - INFO - Store /home/vasyurhm/BEATS/GF/ALE_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,301 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,301 - heart - INFO - Station OTAV
2018-11-27 11:26:23,302 - heart - INFO - ---------------------
2018-11-27 11:26:23,302 - heart - INFO - Store /home/vasyurhm/BEATS/GF/OTAV_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,303 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,303 - heart - INFO - Station ABKT
2018-11-27 11:26:23,304 - heart - INFO - ---------------------
2018-11-27 11:26:23,304 - heart - INFO - Store /home/vasyurhm/BEATS/GF/ABKT_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,308 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,308 - heart - INFO - Station AKTO
2018-11-27 11:26:23,308 - heart - INFO - ---------------------
2018-11-27 11:26:23,309 - heart - INFO - Store /home/vasyurhm/BEATS/GF/AKTO_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,312 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,312 - heart - INFO - Station BJT
2018-11-27 11:26:23,312 - heart - INFO - ---------------------
2018-11-27 11:26:23,313 - heart - INFO - Store /home/vasyurhm/BEATS/GF/BJT_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,313 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,313 - heart - INFO - Station SSE
2018-11-27 11:26:23,313 - heart - INFO - ---------------------
2018-11-27 11:26:23,314 - heart - INFO - Store /home/vasyurhm/BEATS/GF/SSE_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,314 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,314 - heart - INFO - Station CHTO
2018-11-27 11:26:23,315 - heart - INFO - ---------------------
2018-11-27 11:26:23,315 - heart - INFO - Store /home/vasyurhm/BEATS/GF/CHTO_ak135_0.500Hz_0 exists! Use force=True to overwrite!
2018-11-27 11:26:23,322 - heart - INFO - Traces exist use force=True to overwrite!
2018-11-27 11:26:23,322 - beat - INFO - seismic GF calculations successful!

@braunfuss
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So either your config files points to a non successfully build gf_store or I could imagine that is connected to running the building of the greens functions a couple of times on the same folder. Running the building of the greens functions store building several times will at some point overcome inital error messages and return a positive build, even when errors are persistent. Resolving that would include deleting the ak135_0.500Hz_0 folder and re-run only the build gfs command once and lookout for potential errors in that log.

@hvasbath
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Can you please run:
beat check Laquila --what=stores

This will return you the store names that contain empty grid-points.
Can you please write here what it returns?

If it is not empty:
You will have to rerun the calculation of these stores with:
beat build_gfs Laquila --datatypes=seismic --force --execute

I will update the tutorial regarding that ...

@vic-chou
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Thanks for your reply. I have solved this problem based on your suggestions.

@hvasbath
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Great! If you face any other issue please open a new topic!

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@hvasbath @braunfuss @vic-chou