Document issues at scale #20
Comments
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Over the course of a day, here are a few problems I discovered when trying to ramp up to ~20 nodes in a cluster to run jobs. This including deleting and creating clusters serveral times throughout the day. It isn't clear to me which of these are definitely due to the larger cluster and which are just spurious. I'll log them in case they continue to occur.
Normally the cluster is immediately accessible after a resize.
Full Trace2020-10-21 14:06:27,368 | __main__ | INFO | Filter summary:
Traceback (most recent call last):
File "scripts/gwas_dev.py", line 300, in
# logger.info("Done")
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/fire/core.py", line 138, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/fire/core.py", line 463, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/fire/core.py", line 672, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "scripts/gwas_dev.py", line 232, in run_qc_1
logger.info('Applying QC filters')
File "scripts/gwas_dev.py", line 112, in apply_filters
v = v.compute()
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/xarray/core/dataarray.py", line 834, in compute
return new.load(**kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/xarray/core/dataarray.py", line 808, in load
ds = self._to_temp_dataset().load(**kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/xarray/core/dataset.py", line 654, in load
evaluated_data = da.compute(*lazy_data.values(), **kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/dask/base.py", line 452, in compute
results = schedule(dsk, keys, **kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 2725, in get
results = self.gather(packed, asynchronous=asynchronous, direct=direct)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 1986, in gather
return self.sync(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 832, in sync
return sync(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/utils.py", line 340, in sync
raise exc.with_traceback(tb)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/utils.py", line 324, in f
result[0] = yield future
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 1851, in _gather
raise exception.with_traceback(traceback)
File "/opt/conda/lib/python3.8/site-packages/dask/array/core.py", line 102, in getter
File "/opt/conda/lib/python3.8/site-packages/numpy/core/_asarray.py", line 85, in asarray
File "/opt/conda/lib/python3.8/site-packages/xarray/core/indexing.py", line 495, in __array__
File "/opt/conda/lib/python3.8/site-packages/numpy/core/_asarray.py", line 85, in asarray
File "/opt/conda/lib/python3.8/site-packages/xarray/core/indexing.py", line 560, in __array__
File "/opt/conda/lib/python3.8/site-packages/numpy/core/_asarray.py", line 85, in asarray
File "/opt/conda/lib/python3.8/site-packages/xarray/coding/variables.py", line 70, in __array__
File "/opt/conda/lib/python3.8/site-packages/xarray/coding/variables.py", line 218, in _scale_offset_decoding
File "/opt/conda/lib/python3.8/site-packages/xarray/coding/variables.py", line 70, in __array__
File "/opt/conda/lib/python3.8/site-packages/xarray/coding/variables.py", line 138, in _apply_mask
File "/opt/conda/lib/python3.8/site-packages/numpy/core/_asarray.py", line 85, in asarray
File "/opt/conda/lib/python3.8/site-packages/xarray/core/indexing.py", line 560, in __array__
File "/opt/conda/lib/python3.8/site-packages/xarray/backends/zarr.py", line 54, in __getitem__
File "/opt/conda/lib/python3.8/site-packages/xarray/backends/zarr.py", line 51, in get_array
File "/opt/conda/lib/python3.8/site-packages/zarr/hierarchy.py", line 338, in __getitem__
File "/opt/conda/lib/python3.8/site-packages/zarr/core.py", line 124, in __init__
File "/opt/conda/lib/python3.8/site-packages/zarr/core.py", line 141, in _load_metadata
File "/opt/conda/lib/python3.8/site-packages/zarr/core.py", line 150, in _load_metadata_nosync
File "/opt/conda/lib/python3.8/site-packages/fsspec/mapping.py", line 133, in __getitem__
AttributeError: 'FSMap' object has no attribute 'missing_exceptions'
Full Log(gwas-dev) eczech@ukb-experiments:~/repos/ukb-gwas-pipeline-nealelab$ python scripts/gwas_dev.py run_qc_1 --input-path=rs-ukb/prep/gt-imputation/ukb_chr21.zarr --output-path=rs-ukb/prep/gt-imputation-qc/ukb_chr21.zarr
2020-10-21 15:46:30,108 | __main__ | INFO | Initialized script with dask client:
2020-10-21 15:46:30,109 | __main__ | INFO | Running stage 1 QC
2020-10-21 15:46:43,305 | __main__ | INFO | Loaded dataset:
Dimensions: (alleles: 2, genotypes: 3, samples: 487409, variants: 1261158)
Dimensions without coordinates: alleles, genotypes, samples, variants
Data variables:
call_genotype_probability_mask (variants, samples, genotypes) bool dask.array
sample_id (samples) int32 dask.array
sample_sex (samples) uint8 dask.array
variant_allele (variants, alleles) |S101 dask.array
variant_contig (variants) int64 dask.array
variant_contig_name (variants) |S2 dask.array
variant_id (variants) |S115 dask.array
variant_info (variants) float32 dask.array
variant_maf (variants) float32 dask.array
variant_minor_allele (variants) |S101 dask.array
variant_position (variants) int32 dask.array
variant_rsid (variants) |S115 dask.array
call_genotype_probability (variants, samples, genotypes) float16 dask.array
call_dosage (variants, samples) float16 dask.array
call_dosage_mask (variants, samples) bool dask.array
Attributes:
contig_index: 20
contig_name: 21
contigs: ['21']
2020-10-21 15:46:43,305 | __main__ | INFO | Applying QC filters
2020-10-21 15:46:43,384 | __main__ | INFO | Filter summary:
2020-10-21 15:46:43,911 | __main__ | INFO | high_info: {False: 896362, True: 364796}
2020-10-21 15:46:44,550 | __main__ | INFO | Filter summary:
2020-10-21 16:05:33,221 | __main__ | INFO | nonzero_stddev: {True: 364796}
2020-10-21 16:05:34,199 | __main__ | INFO | Saving dataset to rs-ukb/prep/gt-imputation-qc/ukb_chr21.zarr:
Dimensions: (alleles: 2, genotypes: 3, samples: 487409, variants: 364796)
Dimensions without coordinates: alleles, genotypes, samples, variants
Data variables:
call_genotype_probability_mask (variants, samples, genotypes) bool dask.array
sample_id (samples) int32 dask.array
sample_sex (samples) uint8 dask.array
variant_allele (variants, alleles) |S101 dask.array
variant_contig (variants) int64 dask.array
variant_contig_name (variants) |S2 dask.array
variant_id (variants) |S115 dask.array
variant_info (variants) float32 dask.array
variant_maf (variants) float32 dask.array
variant_minor_allele (variants) |S101 dask.array
variant_position (variants) int32 dask.array
variant_rsid (variants) |S115 dask.array
call_genotype_probability (variants, samples, genotypes) float16 dask.array
call_dosage (variants, samples) float16 dask.array
call_dosage_mask (variants, samples) bool dask.array
variant_dosage_std (variants) float32 dask.array
Attributes:
contig_index: 20
contig_name: 21
contigs: ['21']
Traceback (most recent call last):
File "scripts/gwas_dev.py", line 304, in
fire.Fire()
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/fire/core.py", line 138, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/fire/core.py", line 463, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/fire/core.py", line 672, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "scripts/gwas_dev.py", line 227, in run_qc_1
save_dataset(ds, output_path)
File "scripts/gwas_dev.py", line 65, in save_dataset
ds.to_zarr(store, mode="w", consolidated=True)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/xarray/core/dataset.py", line 1652, in to_zarr
return to_zarr(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/xarray/backends/api.py", line 1369, in to_zarr
writes = writer.sync(compute=compute)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/xarray/backends/common.py", line 155, in sync
delayed_store = da.store(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/dask/array/core.py", line 981, in store
result.compute(**kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/dask/base.py", line 167, in compute
(result,) = compute(self, traverse=False, **kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/dask/base.py", line 452, in compute
results = schedule(dsk, keys, **kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 2725, in get
results = self.gather(packed, asynchronous=asynchronous, direct=direct)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 1986, in gather
return self.sync(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 832, in sync
return sync(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/utils.py", line 340, in sync
raise exc.with_traceback(tb)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/utils.py", line 324, in f
result[0] = yield future
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 1851, in _gather
raise exception.with_traceback(traceback)
File "/opt/conda/lib/python3.8/site-packages/distributed/protocol/pickle.py", line 75, in loads
pass
File "/opt/conda/lib/python3.8/site-packages/zarr/core.py", line 1946, in __setstate__
File "/opt/conda/lib/python3.8/site-packages/zarr/core.py", line 124, in __init__
File "/opt/conda/lib/python3.8/site-packages/zarr/core.py", line 141, in _load_metadata
File "/opt/conda/lib/python3.8/site-packages/zarr/core.py", line 150, in _load_metadata_nosync
File "/opt/conda/lib/python3.8/site-packages/fsspec/mapping.py", line 132, in __getitem__
File "/opt/conda/lib/python3.8/site-packages/fsspec/asyn.py", line 227, in cat
File "/opt/conda/lib/python3.8/site-packages/gcsfs/core.py", line 826, in _cat_file
File "/opt/conda/lib/python3.8/site-packages/gcsfs/core.py", line 487, in _call
File "/opt/conda/lib/python3.8/site-packages/aiohttp/client.py", line 1012, in __aenter__
File "/opt/conda/lib/python3.8/site-packages/aiohttp/client.py", line 504, in _request
File "/opt/conda/lib/python3.8/site-packages/aiohttp/client_reqrep.py", line 847, in start
File "/opt/conda/lib/python3.8/site-packages/aiohttp/streams.py", line 591, in read
aiohttp.client_exceptions.ServerDisconnectedError
Full Log2020-10-21 21:39:06,490 | __main__ | INFO | Initialized script with dask client:
2020-10-21 21:39:06,490 | __main__ | INFO | Running stage 1 QC (input_path=rs-ukb/prep/gt-imputation-qc/ukb_chr22.zarr, output_path=rs-ukb/pipe/nealelab-gwas-uni-ancestry-v3/input/gt-imputation/ukb_chr22.zarr)
2020-10-21 21:39:06,748 | __main__ | INFO | Loaded dataset:
Dimensions: (alleles: 2, genotypes: 3, samples: 487409, variants: 365260)
Dimensions without coordinates: alleles, genotypes, samples, variants
Data variables:
call_dosage (variants, samples) float16 dask.array
call_dosage_mask (variants, samples) bool dask.array
call_genotype_probability (variants, samples, genotypes) float16 dask.array
call_genotype_probability_mask (variants, samples, genotypes) bool dask.array
sample_id (samples) int32 dask.array
sample_sex (samples) uint8 dask.array
variant_allele (variants, alleles) |S414 dask.array
variant_contig (variants) int64 dask.array
variant_contig_name (variants) |S2 dask.array
variant_dosage_std (variants) float32 dask.array
variant_id (variants) |S428 dask.array
variant_info (variants) float32 dask.array
variant_maf (variants) float32 dask.array
variant_minor_allele (variants) |S414 dask.array
variant_position (variants) int32 dask.array
variant_rsid (variants) |S304 dask.array
Attributes:
contig_index: 21
contig_name: 22
contigs: ['22']
2020-10-21 21:39:06,748 | __main__ | INFO | Applying variant QC filters
2020-10-21 21:39:08,630 | __main__ | INFO | Filter summary (True ==> kept):
2020-10-21 21:39:09,108 | __main__ | INFO | high_maf: {True: 213203, False: 152057}
2020-10-21 21:39:09,435 | __main__ | INFO | Filter summary (True ==> kept):
2020-10-21 21:45:10,070 | __main__ | INFO | in_hwe: {True: 142510, False: 70693}
2020-10-21 21:45:10,326 | __main__ | INFO | Applying sample QC filters (sample_qc_path=rs-ukb/prep/main/ukb_sample_qc.zarr)
2020-10-21 21:45:10,905 | __main__ | INFO | Filter summary (True ==> kept):
2020-10-21 21:45:11,098 | __main__ | INFO | no_aneuploidy: {True: 501854, False: 651}
2020-10-21 21:45:11,220 | __main__ | INFO | in_pca: {True: 407127, False: 95378}
2020-10-21 21:45:11,305 | __main__ | INFO | in_ethnic_groups: {True: 455793, False: 46712}
2020-10-21 21:45:11,322 | __main__ | INFO | overall: {True: 365941, False: 136564}
2020-10-21 21:45:15,710 | __main__ | INFO | Saving dataset to rs-ukb/pipe/nealelab-gwas-uni-ancestry-v3/input/gt-imputation/ukb_chr22.zarr:
Dimensions: (alleles: 2, genotypes: 3, principal_components: 40, samples: 365941, variants: 142510)
Dimensions without coordinates: alleles, genotypes, principal_components, samples, variants
Data variables:
variant_hwe_p_value (variants) float64 dask.array
call_dosage (variants, samples) float16 dask.array
call_dosage_mask (variants, samples) bool dask.array
call_genotype_probability (variants, samples, genotypes) float16 dask.array
call_genotype_probability_mask (variants, samples, genotypes) bool dask.array
sample_id (samples) int32 dask.array
sample_sex (samples) uint8 dask.array
variant_allele (variants, alleles) |S414 dask.array
variant_contig (variants) int64 dask.array
variant_contig_name (variants) |S2 dask.array
variant_dosage_std (variants) float32 dask.array
variant_id (variants) |S428 dask.array
variant_info (variants) float32 dask.array
variant_maf (variants) float32 dask.array
variant_minor_allele (variants) |S414 dask.array
variant_position (variants) int32 dask.array
variant_rsid (variants) |S304 dask.array
variant_genotype_counts (variants, genotypes) int32 dask.array
sample_qc_sex (samples) float64 dask.array
sample_genetic_sex (samples) float64 dask.array
sample_age_at_recruitment (samples) float64 dask.array
sample_principal_component (samples, principal_components) float64 dask.array
sample_ethnic_background (samples) float64 dask.array
sample_genotype_measurement_batch (samples) float64 dask.array
sample_genotype_measurement_plate (samples) |S13 dask.array
sample_genotype_measurement_well (samples) |S3 dask.array
Traceback (most recent call last):
File "scripts/gwas_dev.py", line 304, in
# logger.info(f"Saving p-values to {output_path}")
File "/home/eczech/repos/ukb-gwas-pipeline-nealelab/.snakemake/conda/0522a0a1/lib/python3.8/site-packages/fire/core.py", line 138, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/home/eczech/repos/ukb-gwas-pipeline-nealelab/.snakemake/conda/0522a0a1/lib/python3.8/site-packages/fire/core.py", line 463, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/home/eczech/repos/ukb-gwas-pipeline-nealelab/.snakemake/conda/0522a0a1/lib/python3.8/site-packages/fire/core.py", line 672, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "scripts/gwas_dev.py", line 247, in run_qc_2
Full TraceTraceback (most recent call last):
File "scripts/gwas_dev.py", line 304, in
fire.Fire()
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/fire/core.py", line 138, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/fire/core.py", line 463, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/fire/core.py", line 672, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "scripts/gwas_dev.py", line 227, in run_qc_1
save_dataset(ds, output_path)
File "scripts/gwas_dev.py", line 65, in save_dataset
ds.to_zarr(store, mode="w", consolidated=True)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/xarray/core/dataset.py", line 1652, in to_zarr
return to_zarr(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/xarray/backends/api.py", line 1369, in to_zarr
writes = writer.sync(compute=compute)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/xarray/backends/common.py", line 155, in sync
delayed_store = da.store(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/dask/array/core.py", line 981, in store
result.compute(**kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/dask/base.py", line 167, in compute
(result,) = compute(self, traverse=False, **kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/dask/base.py", line 452, in compute
results = schedule(dsk, keys, **kwargs)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 2725, in get
results = self.gather(packed, asynchronous=asynchronous, direct=direct)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 1986, in gather
return self.sync(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 832, in sync
return sync(
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/utils.py", line 340, in sync
raise exc.with_traceback(tb)
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/utils.py", line 324, in f
result[0] = yield future
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/home/eczech/miniconda3/envs/gwas-dev/lib/python3.8/site-packages/distributed/client.py", line 1851, in _gather
raise exception.with_traceback(traceback)
File "/opt/conda/lib/python3.8/site-packages/distributed/protocol/pickle.py", line 75, in loads
pass
ModuleNotFoundError: No module named 'gcsfs'
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On several occasions when all work seems to bottleneck at a single node, I see an Info page like this:
Clicking on that individual worker with all the pending tasks results in "500: Internal Server Error". This workload (running GWAS regressions) eventually failed and it appears that all the workers reset, or at least the "logs" link above shows output as if they were all restarted after the failure. I'll see if the individual VMs have logs retained somewhere. |
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Nope, looks like all worker logs get cleared for some reason. |
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For some reason this step failed on chr22 but not chr21 today. The error was consistent with OOM yet this step does nothing but filter and rechunk. It is probably the rechunking that is problematic -- why it is not consistently problematic is odd (the datasets for chr 21 and 22 are very similar, they have same number of samples and ~365k variants +/- 1k). |
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Allowing fsspec to overwrite zarr archives is a very bad idea. On more than one occasion, I have been puzzled as to why a client script appears to be idling with little to no cpu usage for ~15 minutes only to find that it is deleting a previously written zarr archive very slowly. These should always be deleted first with "gsutil -m" instead of relying on Perhaps fsspec is deleting files synchronously instead of in parallel like gsutil does. |
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Today I tried to run more rechunking operations, but had an issue I have not seen before. I tried to run a GKE cluster with 5 64 vCPU (262144 MB RAM, 200G disk) nodes and a rechunking process on each one, for different contigs, but all jobs continuously failed with an error like "Exit code 255":
I believe this is somehow being thrown from the Python process run as part of the snakemake CLI command. There is no information in the logs though, e.g.:
This is the first time an error has occurred (other than OOM) without any useful logging, and in all cases it happens right after the bgen file is downloaded and before the conda environment is activated for the rechunking code. So far I have failed to reproduce this by running the same jobs, on the same VMs, and in the same cluster using smaller bgen files (chr XY runs as usual). I also tried running a job for a larger contig (e.g. 18) on a local Debian buster system (in the same conda env) but that also worked as expected. Changes in use for this work: c7318b5 UPDATE I tried this again on a cluster of 32 vCPUs instead. I still see the same failure for chromosome 19 and 20 (or presumably anything larger) but not 21 or 22. The problem likely has something to do with the file size. I'm not sure what code snakemake is using to do the file download, but the next logical step is probably to get onto a k8s cluster node, run the docker image manually, and then try to run the same command that snakemake issues. This might produce a system message or something else that is easier to catch in a terminal before digging into the code. Command used to run snakemake script: Note: I updated snakemake from 5.22 to 5.30 and google-cloud-sdk from 315.0 to 319.0 for these runs (the latest versions available). UPDATE See #25. The issue was disk space though it is still unclear why snakemake appears to be duplicating files on download. |
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In the last couple days while rechunking bgen files, I encountered two jobs that failed for these reasons (after running for ~6 hrs): |
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I have seen the first checksum error at least 4 or 5 times now, and it looks like it is a snakemake bug. I logged it at snakemake/snakemake#785. The second error was logged at fsspec/gcsfs#315. |
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And here is another error that came out of nowhere today: Filed as fsspec/gcsfs#316. |
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This is a broad issue that I'll use to document some of the problems that have come up when scaling out the UKB pipeline.
For convenience, here is a list of issues that have been filed as a result of these problems:
Some of these are discussed more below. Others were filed directly in upstream repos.
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