Issue writing preprocessed cube for CESM2-WACCM dataset #3738
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@valeriupredoi - can you please look into what I might be doing wrong when you get a chance? Thanks! |
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@rswamina could you please post the entire trace or the debug file, please? Not much I can gauge from that bit of output 😁 |
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Yes, of course..will try to attache the whole main_log_debug.txt file attached above. Let me know if you cannot access it. |
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If all preprocessor functions are lazy, the The timestamps in the attached debug log do not match those in the top post. |
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I reran it to generate a fresh debug file. Please consider only the timestamps in the file. I waited around 30 minutes and then killed the job. How long should I wait for? |
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I should add that I tried this several times wondering if there was an issue with JASMIN. The longest I waited (not sure if it was this particular run) was 30 minutes. |
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I tried running the recipe on my laptop with just the first dataset It completes in about 6 seconds and uses 2GB of RAM with ESMValCore v2.11.0 and 9 seconds / 4GB of RAM with v2.10.0. Maybe it is something specific to Jasmin indeed. Can you access the files that are listed in the top post, e.g. with |
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I had a similar problem with other data that originated from using dask distributed with the |
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From the debug log it looks like @rswamina is using the default scheduler (so no distributed). |
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I am using the default scheduler. On JASMIN, SSP245 has just the r1 ensemble member's data. It seems to hang for both historical and ssp245 experiments. I tried an |
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Am travelling back to the UK today, will have a look tommz or on Thu, before I fo that though - Ranjini, could you pls confirm there is enough room on the disk you writing to, and what iris and esmvalcore you using? Cheers 🍺 |
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Thanks @valeriupredoi. I have enough space on disk. I am using the I am not sure how to check the iris version though. |
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Thanks Ranjini! I know how to do that 😁 Speaking of, I should install 2.11 rather sooner than later |
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Hi @valeriupredoi - can you let me know if you diagnosed the problem? If this might take time, I will exclude the data set for now. Thanks! |
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on it, will have a look today, apols for the delay, too many emails to check after holidays 🤣 |
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hi Ranjini, am currently running that recipe, a few points:
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@valeriupredoi - Thanks..I am outputting to Are writes to scratch slower or as you indicate is this still a processing delay. I wonder why that is, it is not very much data. |
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My guess is it's not data but rather, those region selections are intensive. Have left my run on overnight, see how long it takes 🍺 |
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I am curious as to why. This worked quite quickly for @bouweandela on a different machine and the same preprocessing worked quickly again for other model data sets (same time period but perhaps different resolutions). I have successfully run this preprocessor on JASMIN before for the same data set but I can't remember if I just let it run overnight. |
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so my job is still running, it hasn't outputted any actual preprocessed data, and it looks like it's going nowhere - this is on sci2, and the load on the node is pretty decent, it's not running out of memory, and it should definitely run a little faster 😁 (note: |
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OK, starting to make sense of this: the save is indeed waiting on a fairly large number of still running tasks (see the wait statement in |
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In fact, after a fair while, the |
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So, what does this mean? |
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found it! This codeblock trips it: for cube in cubes:
logger.debug("Saving cube:\n%s\nwith %s data to %s", cube,
"lazy" if cube.has_lazy_data() else "realized", filename)Unbelievably sneaky! |
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@bouweandela have a look at this - simplifying for debugging that code block above (from for cube in cubes:
if cube.has_lazy_data():
data_state = "lazy"
else:
data_state = "realized"
logger.debug("Saving cube: %s with %s data to %s", cube, data_state, filename)the whole run hangs; commenting out the debug logger line: for cube in cubes:
if cube.has_lazy_data():
data_state = "lazy"
else:
data_state = "realized"
# logger.debug("Saving cube: %s with %s data to %s", cube, data_state, filename)run goes through at light speed! Something is really wonky at JASMIN with debug stringIO |
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@rswamina you can now run the recipe no problem, I've taken out the offending bit - it is the issue with |
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@valeriupredoi - many thanks for this!!! I will let you know if I have further issues. |
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The |
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So why does this not happen for other data sets? |
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that is a one million dollar question! Here is a model code that mimicks our logging mechanism: import logging
import logging.config
import esmvalcore
import iris
import time
import yaml
from pathlib import Path
logger = logging.getLogger(__name__)
def _update_stream_level(cfg: dict, level=None):
"""Update the log level for the stream handlers."""
handlers = cfg['handlers']
for handler in handlers.values():
if level is not None and 'stream' in handler:
if handler['stream'] in ('ext://sys.stdout', 'ext://sys.stderr'):
handler['level'] = level.upper()
def configure_logging(cfg_file: str = None,
output_dir: str = None,
console_log_level: str = None) -> list:
if cfg_file is None:
cfg_loc = Path(esmvalcore.__file__ + "esmvalcore")
cfg_file = cfg_loc.parents[0] / 'config' / 'config-logging.yml'
cfg_file = Path(cfg_file).absolute()
with open(cfg_file) as file_handler:
cfg = yaml.safe_load(file_handler)
if output_dir is None:
_purge_file_handlers(cfg)
_update_stream_level(cfg, level=console_log_level)
logging.config.dictConfig(cfg)
logging.Formatter.converter = time.gmtime
logging.captureWarnings(True)
def loaddebug():
# configure logger
run_dir = "."
log_files = configure_logging(output_dir="testdebuglog",
console_log_level="debug")
c = iris.load_cube("testRS.nc")
logger.debug("crap")
logger.debug("cube %s", c)
return c
if __name__ == "__main__":
loaddebug()maybe you can make some sense with it - I'll just open a PR and plop a |
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I suspect this issue may be related to the (un)availability of parallel writes on most Jasmin filesystems (see here). In particular, I would recommend choosing a storage location that supports parallel writes for the esmvaltool Could you try using e.g. |
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that would be interesting to experiment with! But I don't think that's the case here, since if we don't include the |
@bouweandela I just reintroduced the original debug logger with |
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Apologies..that was a typo. I used |
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so this particular hang is due to that logger issue with |
ESMValTool seems to have trouble writing a preprocessed cube after extracting IPCC regions for the CEMS2-WACCM dataset. I don't know if the program hangs or simply is taking too long but the log message stops at a point where the cube is being saved under the preproc directory. I am using the
esmvaltoolmodule installed on JASMIN. As far as I can tell there are no typos!Here is the recipe:
Here are the final lines of the error message. After the last line shown, the program just waits and I don't know why it hangs there. This recipe works for other models.:
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