Error running gisola with event and no waveform plot #30

vdionicio · 2022-02-23T20:15:37Z

vdionicio
Feb 23, 2022

I'm tring to run gisola with a particular event like this:

./gisola.py --event SGC2022dugzug -c ../test/config_sgc.yaml -l log_cron

the program is running well but at the end it gave me this error:

2022-02-23 19:49:48,261 INFO Function 'calculateInversions' executed 290.32 seconds
/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/site-packages/obspy/io/quakeml/core.py:1109: UserWarning: 'smi:org.gfz-potsdam.de/geofon/RMHP(10)>>BW(4,1,5)' is not a valid QuakeML URI. It will be in the final file but note that the file will not be a valid QuakeML file.
warnings.warn(msg % obj.id)
2022-02-23 19:49:51,872 INFO Function 'gatherResults' executed 3.61 seconds
2022-02-23 19:49:58,946 ERROR Fatal Error occurred
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/home/sgc-geo46333/Gisola-main/src/plot.py", line 943, in caller
func()
File "/home/sgc-geo46333/Gisola-main/src/plot.py", line 430, in streams
tr=config.st.select(station=sta, channel=cha)[0]
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/site-packages/obspy/core/stream.py", line 649, in getitem
return self.traces.getitem(index)
IndexError: list index out of range
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/sgc-geo46333/Gisola-main/src/./gisola.py", line 236, in
plot.allplots()
File "/home/sgc-geo46333/Gisola-main/src/config.py", line 181, in inner
func(*args, **kwargs)
File "/home/sgc-geo46333/Gisola-main/src/plot.py", line 958, in allplots
res=p.map(caller, functions)
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
IndexError: list index out of range
2022-02-23 19:49:58,947 INFO Moving to next event, if any

When I open the list_all.html and get into the solution, I can not see the the waveforms image

I hope you can give suggestions to solve the problem.

Thanks a lot.

Best wishes,

Viviana

nikosT · 2022-02-24T00:34:25Z

nikosT
Feb 24, 2022
Maintainer

Dear @vdionicio,

This looks quite strange!
From the error message, it seems that there is a kind of inconsistency in the list with stations.

Is there enough space in the machine that runs Gisola?
Does this happen with every event you tried?
Does the test event (included in repo) work?
Could you share the output folder (send me in private message, if you think that it should not be public), including the log file?
Could you also send me the config.yaml file (don't forget to remove hostname/usernames/passwords in terms of privacy)?

0 replies

vdionicio · 2022-02-25T22:40:29Z

vdionicio
Feb 25, 2022
Author

Dear @nikosT,

Thanks a lot for your answer, to clarify the error, I wanna answer your questions:

Is there enough space in the machine that runs Gisola?
Yes, I'm runing gisola in a machine with 100G, and it has 80G available, 16 cores xeon, and 32 Gb ram.
Does this happen with every event you tried?

with my events yes, I run anotherone like: ./gisola.py --event SGC2019zgudxj -c ../test/config_sgc.yaml -l log_mesetas

and I got this error:
2022-02-25 21:52:21,487 INFO Function 'calculateInversions' executed 102.62 seconds
2022-02-25 21:52:29,637 INFO Function 'gatherResults' executed 8.15 seconds
2022-02-25 21:52:47,539 ERROR Fatal Error occurred
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/home/sgc-geo46333/Gisola-main/src/plot.py", line 943, in caller
func()
File "/home/sgc-geo46333/Gisola-main/src/plot.py", line 430, in streams
tr=config.st.select(station=sta, channel=cha)[0]
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/site-packages/obspy/core/stream.py", line 649, in getitem
return self.traces.getitem(index)
IndexError: list index out of range
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/sgc-geo46333/Gisola-main/src/./gisola.py", line 236, in
plot.allplots()
File "/home/sgc-geo46333/Gisola-main/src/config.py", line 181, in inner
func(*args, **kwargs)
File "/home/sgc-geo46333/Gisola-main/src/plot.py", line 958, in allplots
res=p.map(caller, functions)
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
IndexError: list index out of range
2022-02-25 21:52:47,540 INFO Moving to next event, if any

And I can't see the waveforms neither.

Does the test event (included in repo) work?
Yes, I runit like: ./gisola.py -c ../test/config.yaml --event-xml ../test/benchmark/event.xml

and the results is:

2022-02-25 22:23:33,523 INFO Function 'calculateInversions' executed 427.14 seconds
/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/site-packages/obspy/io/quakeml/core.py:1109: UserWarning: 'smi:org.gfz-potsdam.de/geofon/RMHP(10)>>ITAPER(30)>>BW_BP(2,3.0,4)>>STALTA(1,30)' is not a valid QuakeML URI. It will be in the final file but note that the file will not be a valid QuakeML file.
warnings.warn(msg % obj.id)
/home/sgc-geo46333/anaconda3/envs/gisola/lib/python3.9/site-packages/obspy/io/quakeml/core.py:1109: UserWarning: 'smi:org.gfz-potsdam.de/geofon/RMHP(10)>>ITAPER(10)>>BW(2,3.0,4)>>STALTA(1,30)' is not a valid QuakeML URI. It will be in the final file but note that the file will not be a valid QuakeML file.
warnings.warn(msg % obj.id)
2022-02-25 22:23:37,612 INFO Function 'gatherResults' executed 4.09 seconds
2022-02-25 22:23:46,128 INFO Function 'allplots' executed 8.52 seconds

Could you share the output folder (send me in private message, if you think that it should not be public), including the log file?
I have sent an email with this information, including the two events that I'm trying for this request in a .tar file
Could you also send me the config.yaml file (don't forget to remove hostname/usernames/passwords in terms of privacy)?
I have sent an email with this information, including the two events that I'm trying for this requestin a .tar file. I'm attaching also the inventory file.

0 replies

nikosT · 2022-02-25T23:52:04Z

nikosT
Feb 25, 2022
Maintainer

Hi @vdionicio,

I see no e-mail. Could you send it here: ntriantafyl {@} cslab.ece.ntua.gr?

Also, just to be sure. Could you check that you have installed the suggested versions of the Python libraries as shown in environment.yml file?

0 replies

vdionicio · 2022-02-26T00:04:41Z

vdionicio
Feb 26, 2022
Author

Dear @nikos, I'm attaching the log and config,files, for the results folder and the inventory file, I could not attach the tar file, but I'm sending a link where you can download it, Let me know if you have any problems. https://owncloudrsnc.sgc.gov.co/index.php/s/2t6pQB94UcMPIkF Thanks a lot for your help, With best regards, Viviana El mié, 23 feb 2022 a la(s) 19:34, Nikolaos Triantafyllis ( ***@***.***) escribió:

…

Dear @vdionicio <https://github.com/vdionicio>, This looks quite strange! From the error message, it seems that there is a kind of inconsistency in the list with stations. 1. Is there enough space in the machine that runs Gisola? 2. Does this happen with every event you tried? 3. Does the test event (included in repo) work? 4. Could you share the output folder (send me in private message, if you think that it should not be public), including the log file? 5. Could you also send me the config.yaml file (don't forget to remove hostname/usernames/passwords in terms of privacy)? — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXWDN3ATFKZMNRWDYH2WTG3U4V4J3ANCNFSM5PFM6M6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Viviana Dionicio

0 replies

nikosT · 2022-02-26T00:18:46Z

nikosT
Feb 26, 2022
Maintainer

@vdionicio, could you please share it in another way? I have already 5 failed attempts to download the zip file. 4.9 GB seems a pretty large event anyway. Could you share just one, with me?

0 replies

vdionicio · 2022-02-26T02:29:12Z

vdionicio
Feb 26, 2022
Author

Dear @nikosT, Could you try to download the folder results_sgc_2 in the same link: https://owncloudrsnc.sgc.gov.co/index.php/s/2t6pQB94UcMPIkF There you can fins the results form the event of 2019 that I mentioned in my previous comment in the foro. Let me know if you succeeded, With best regards, Viviana El vie, 25 feb 2022 a la(s) 19:18, Nikolaos Triantafyllis ( ***@***.***) escribió:

…

@vdionicio <https://github.com/vdionicio>, could you please share it in another way? I have already 5 failed attempts. 4.9 GB seems a pretty large event anyway. Could you share just one, with me? — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXWDN3DG4VDVBAGUCDRDZ2TU5AL7FANCNFSM5PFM6M6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Viviana Dionicio

0 replies

nikosT · 2022-02-26T13:25:37Z

nikosT
Feb 26, 2022
Maintainer

@vdionicio, failed again. Try google drive

0 replies

vdionicio · 2022-02-26T15:12:21Z

vdionicio
Feb 26, 2022
Author

ok, let's try with google drive: https://drive.google.com/file/d/1iWHPxbhQZoA5wAsrvi1iTQVVegD-3xQE/view?usp=sharing Thanks again, Viviana El sáb, 26 feb 2022 a la(s) 08:25, Nikolaos Triantafyllis ( ***@***.***) escribió:

…

@vdionicio <https://github.com/vdionicio>, failed again. Try google drive — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXWDN3FVCAE2QTJJBET3C3LU5DIF7ANCNFSM5PFM6M6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Viviana Dionicio

0 replies

nikosT · 2022-02-26T16:29:29Z

nikosT
Feb 26, 2022
Maintainer

Hi @vdionicio,
I downloaded the dir successfully. I'm already looking at the error which seems very weird! Could you also send me the config.yaml file (without usernames/passwords)? Meanwhile, until I come back with a workaround, could you double-check that you are using the versions (especially obspy library) suggested at the https://github.com/nikosT/Gisola/wiki/Installation?

0 replies

vdionicio · 2022-02-26T16:51:55Z

vdionicio
Feb 26, 2022
Author

Good to hear the you could downloaded the file, I'm attaching the config file. About the versions, I have installed: - conda 4.11.0 - GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 - I don't have nvfortran - Gisola v1.0.1 - Docker version 20.10.12, build e91ed57 Thanks for trying, Viviana El sáb, 26 feb 2022 a la(s) 11:29, Nikolaos Triantafyllis ( ***@***.***) escribió:

…

Hi @vdionicio <https://github.com/vdionicio>, I downloaded the dir successfully. I'm already looking at the error which seems very weird! Could you also send me the config.yaml file (without usernames/passwords)? Meanwhile, until I come back with a workaround, could double-check that you are using the versions suggested at the https://github.com/nikosT/Gisola/wiki/Installation? — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXWDN3DTUA6KNCK77ELNCFTU5D5XHANCNFSM5PFM6M6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Viviana Dionicio

1 reply

nikosT Feb 26, 2022
Maintainer

Good to hear the you could downloaded the file, I'm attaching the config file. About the versions, I have installed: - conda 4.11.0 - GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 - I don't have nvfortran - Gisola v1.0.1 - Docker version 20.10.12, build e91ed57 Thanks for trying, Viviana El sáb, 26 feb 2022 a la(s) 11:29, Nikolaos Triantafyllis ( @.) escribió:
…
Hi @vdionicio https://github.com/vdionicio, I downloaded the dir successfully. I'm already looking at the error which seems very weird! Could you also send me the config.yaml file (without usernames/passwords)? Meanwhile, until I come back with a workaround, could double-check that you are using the versions suggested at the https://github.com/nikosT/Gisola/wiki/Installation? — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AXWDN3DTUA6KNCK77ELNCFTU5D5XHANCNFSM5PFM6M6A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.>
-- Viviana Dionicio

@vdionicio
I see no attachments. Could you paste a link?

vdionicio · 2022-02-26T17:15:59Z

vdionicio
Feb 26, 2022
Author

This is the link: https://drive.google.com/file/d/1Cv-M3IFJmb53PqaYSTJI57-rU4o3ZPH7/view?usp=sharing El sáb, 26 feb 2022 a la(s) 12:13, Nikolaos Triantafyllis ( ***@***.***) escribió:

…

Good to hear the you could downloaded the file, I'm attaching the config file. About the versions, I have installed: - conda 4.11.0 - GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 - I don't have nvfortran - Gisola v1.0.1 - Docker version 20.10.12, build e91ed57 Thanks for trying, Viviana El sáb, 26 feb 2022 a la(s) 11:29, Nikolaos Triantafyllis ( *@*. *) escribió: … <#m_-1524555309963475216_> Hi @vdionicio <https://github.com/vdionicio> https://github.com/vdionicio <https://github.com/vdionicio>, I downloaded the dir successfully. I'm already looking at the error which seems very weird! Could you also send me the config.yaml file (without usernames/passwords)? Meanwhile, until I come back with a workaround, could double-check that you are using the versions suggested at the https://github.com/nikosT/Gisola/wiki/Installation <https://github.com/nikosT/Gisola/wiki/Installation>? — Reply to this email directly, view it on GitHub <#30 (comment) <#30 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AXWDN3DTUA6KNCK77ELNCFTU5D5XHANCNFSM5PFM6M6A <https://github.com/notifications/unsubscribe-auth/AXWDN3DTUA6KNCK77ELNCFTU5D5XHANCNFSM5PFM6M6A> . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: @.*> -- Viviana Dionicio @vdionicio <https://github.com/vdionicio> I see no attachments. Could you paste a link? — Reply to this email directly, view it on GitHub <#30 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXWDN3APT3FFA52VG33CGGTU5EC4PANCNFSM5PFM6M6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Viviana Dionicio

0 replies

nikosT · 2022-02-26T18:20:15Z

nikosT
Feb 26, 2022
Maintainer

@vdionicio, I also reproduce the problem. I'll let you know when it is fixed, as soon as possible.

0 replies

vdionicio · 2022-02-26T18:33:47Z

vdionicio
Feb 26, 2022
Author

Thanks a lot!!! Viviana

…

--- Viviana Dionicio Coordinadora Grupo Evaluación y Monitoreo de la Actividad Sísmica Servicio Geológico Colombiano Red Sismológica Nacional de Colombia Ext: 2168 Diag. 53 N.° 34-53 Bogotá, Colombia (571) 2200 200 Ext. 2107 La información contenida en este mensaje y adjuntos es confidencial, para el uso exclusivo de la persona o entidad destinataria. Si usted ha recibido este mensaje por equivocación, se le notifica que no está autorizado para revisarlo, reenviarlo, imprimirlo, copiarlo o distribuirlo de forma parcial o total; por favor comunique el error a la persona que lo envía y elimínelo.

El 26/02/2022, a la(s) 1:20 p.m., Nikolaos Triantafyllis ***@***.***> escribió: @vdionicio, I also reproduce the problem. I'll let you know when it is fixed, as soon as possible. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you were mentioned.

0 replies

nikosT · 2022-02-26T23:07:39Z

nikosT
Feb 26, 2022
Maintainer

Dear @vdionicio,

The error has been fixed. Could you download and try the latest Gisola release v.1.1.0?

Please let me know if this solved the issue.

By the way, if you run Gisola experimentally or operationally for your institute, we could add it to the use cases at the readme (if you want to).

0 replies

vdionicio · 2022-02-27T02:10:33Z

vdionicio
Feb 27, 2022
Author

Thanks a lot for the help I’ll try with the new version and let you know. I work at the Colombian Geological Survey (Servicio Geológico Colombiano) and we manage the Colombian Seismological Network, I’m doing test to run the code in real time and if everything works well the idea is using it in daily-realtime operation. Of course you can include de the in the readme. Best Regards, Viviana

…

---

El 26/02/2022, a la(s) 6:07 p.m., Nikolaos Triantafyllis ***@***.***> escribió: Dear @vdionicio, The error has been fixed. Could you download and try the latest Gisola release v.1.1.0? Please let me know if this solved the issue. By the way, if you run Gisola experimentally or operationally for your institute, please we could add it to the use cases at the readme (if you want to): — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you were mentioned.

0 replies

vdionicio · 2022-02-28T15:29:30Z

vdionicio
Feb 28, 2022
Author

Dear @nikosT,

Now it's working for both events,

Thanks a lot,

Viviana

1 reply

nikosT Feb 28, 2022
Maintainer

@vdionicio, great!

We added the use case at README. In case you publish the page or you want to share a new screenshot with more events, please let us know. Thank you!

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Error running gisola with event and no waveform plot #30

vdionicio Feb 23, 2022

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