arv:UsePreemptible:
usePreemptible: true
+
+ arv:OutOfMemoryRetry:
+ memoryRetryMultipler: 2
+ memoryErrorRegex: "custom memory error"
{% endcodeblock %}
h2(#RunInSingleContainer). arv:RunInSingleContainer
|_. Field |_. Type |_. Description |
|usePreemptible|boolean|Required, true to opt-in to using preemptible instances, false to opt-out.|
+
+h2(#OutOfMemoryRetry). arv:OutOfMemoryRetry
+
+Specify that when a workflow step appears to have failed because it did not request enough RAM, it should be re-submitted with more RAM. Out of memory conditions are detected either by the container being unexpectedly killed (exit code 137) or by matching a pattern in the container's output (see @memoryErrorRegex@). Retrying will increase the base RAM request by the value of @memoryRetryMultipler@. For example, if the original RAM request was 10 GiB and the multiplier is 1.5, then it will re-submit with 15 GiB.
+
+Containers are only re-submitted once. If it fails a second time after increasing RAM, then the worklow step will still fail.
+
+Also note that expressions that use @$(runtime.ram)@ (such as dynamic command line parameters) are not reevaluated when the container is resubmitted.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|memoryRetryMultipler|float|Required, the retry will multiply the base memory request by this factor to get the retry memory request.|
+|memoryErrorRegex|string|Optional, a custom regex that, if found in the stdout, stderr or crunch-run logging of a program, will trigger a retry with greater RAM. If not provided, the default pattern matches "out of memory" (with or without spaces), "memory error" (with or without spaces), "bad_alloc" and "container using over 90% of memory".|
+
h2. arv:dockerCollectionPDH
This is an optional extension field appearing on the standard @DockerRequirement@. It specifies the portable data hash of the Arvados collection containing the Docker image. If present, it takes precedence over @dockerPull@ or @dockerImageId@.
"http://arvados.org/cwl#UsePreemptible",
"http://arvados.org/cwl#OutputCollectionProperties",
"http://arvados.org/cwl#KeepCacheTypeRequirement",
+ "http://arvados.org/cwl#OutOfMemoryRetry",
])
def exit_signal_handler(sigcode, frame):
only or written to disk and memory-mapped. The disk cache
leverages the kernel's virtual memory system so "hot" data will
generally still be kept in RAM.
+
+- name: OutOfMemoryRetry
+ type: record
+ extends: cwl:ProcessRequirement
+ inVocab: false
+ doc: |
+ Detect when a failed tool run may have run out of memory, and
+ re-submit the container with more RAM.
+ fields:
+ - name: class
+ type: string
+ doc: "'arv:OutOfMemoryRetry"
+ jsonldPredicate:
+ _id: "@type"
+ _type: "@vocab"
+ - name: memoryErrorRegex
+ type: string?
+ doc: |
+ A regular expression that will be used on the text of stdout
+ and stderr produced by the tool to determine if a failed job
+ should be retried with more RAM. By default, searches for the
+ substrings 'bad_alloc' and 'OutOfMemory'.
+ - name: memoryRetryMultipler
+ type: float
+ doc: |
+ If the container failed on its first run, re-submit the
+ container with the RAM request multiplied by this factor.
only or written to disk and memory-mapped. The disk cache
leverages the kernel's virtual memory system so "hot" data will
generally still be kept in RAM.
+
+- name: OutOfMemoryRetry
+ type: record
+ extends: cwl:ProcessRequirement
+ inVocab: false
+ doc: |
+ Detect when a failed tool run may have run out of memory, and
+ re-submit the container with more RAM.
+ fields:
+ - name: class
+ type: string
+ doc: "'arv:OutOfMemoryRetry"
+ jsonldPredicate:
+ _id: "@type"
+ _type: "@vocab"
+ - name: memoryErrorRegex
+ type: string?
+ doc: |
+ A regular expression that will be used on the text of stdout
+ and stderr produced by the tool to determine if a failed job
+ should be retried with more RAM. By default, searches for the
+ substrings 'bad_alloc' and 'OutOfMemory'.
+ - name: memoryRetryMultipler
+ type: float
+ doc: |
+ If the container failed on its first run, re-submit the
+ container with the RAM request multiplied by this factor.
only or written to disk and memory-mapped. The disk cache
leverages the kernel's virtual memory system so "hot" data will
generally still be kept in RAM.
+
+
+- name: OutOfMemoryRetry
+ type: record
+ extends: cwl:ProcessRequirement
+ inVocab: false
+ doc: |
+ Detect when a failed tool run may have run out of memory, and
+ re-submit the container with more RAM.
+ fields:
+ - name: class
+ type: string
+ doc: "'arv:OutOfMemoryRetry"
+ jsonldPredicate:
+ _id: "@type"
+ _type: "@vocab"
+ - name: memoryErrorRegex
+ type: string?
+ doc: |
+ A regular expression that will be used on the text of stdout
+ and stderr produced by the tool to determine if a failed job
+ should be retried with more RAM. By default, searches for the
+ substrings 'bad_alloc' and 'OutOfMemory'.
+ - name: memoryRetryMultipler
+ type: float
+ doc: |
+ If the container failed on its first run, re-submit the
+ container with the RAM request multiplied by this factor.
import ciso8601
import uuid
import math
+import re
import arvados_cwl.util
import ruamel.yaml
self.job_runtime = job_runtime
self.running = False
self.uuid = None
+ self.attempt_count = 0
def update_pipeline_component(self, r):
pass
container_request["output_path"] = self.outdir
container_request["cwd"] = self.outdir
container_request["priority"] = runtimeContext.priority
- container_request["state"] = "Committed"
+ container_request["state"] = "Uncommitted"
container_request.setdefault("properties", {})
container_request["properties"]["cwl_input"] = self.joborder
logger.warning("%s API revision is %s, revision %s is required to support setting properties on output collections.",
self.arvrunner.label(self), self.arvrunner.api._rootDesc["revision"], "20220510")
+ ram_multiplier = [1]
+
+ oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry")
+ if oom_retry_req and oom_retry_req.get('memoryRetryMultipler'):
+ ram_multiplier.append(oom_retry_req.get('memoryRetryMultipler'))
+
if runtimeContext.runnerjob.startswith("arvwf:"):
wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
container_request["name"] = wfrecord["name"]
container_request["properties"]["template_uuid"] = wfuuid
- self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
+ if self.attempt_count == 0:
+ self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
try:
- if runtimeContext.submit_request_uuid:
- response = self.arvrunner.api.container_requests().update(
- uuid=runtimeContext.submit_request_uuid,
- body=container_request,
- **extra_submit_params
- ).execute(num_retries=self.arvrunner.num_retries)
- else:
- response = self.arvrunner.api.container_requests().create(
- body=container_request,
- **extra_submit_params
- ).execute(num_retries=self.arvrunner.num_retries)
+ ram = runtime_constraints["ram"]
+
+ self.uuid = runtimeContext.submit_request_uuid
+
+ for i in ram_multiplier:
+ runtime_constraints["ram"] = ram * i
+
+ if self.uuid:
+ response = self.arvrunner.api.container_requests().update(
+ uuid=self.uuid,
+ body=container_request,
+ **extra_submit_params
+ ).execute(num_retries=self.arvrunner.num_retries)
+ else:
+ response = self.arvrunner.api.container_requests().create(
+ body=container_request,
+ **extra_submit_params
+ ).execute(num_retries=self.arvrunner.num_retries)
+ self.uuid = response["uuid"]
+
+ if response["container_uuid"] is not None:
+ break
+
+ if response["container_uuid"] is None:
+ runtime_constraints["ram"] = ram * ram_multiplier[self.attempt_count]
+
+ container_request["state"] = "Committed"
+ response = self.arvrunner.api.container_requests().update(
+ uuid=self.uuid,
+ body=container_request,
+ **extra_submit_params
+ ).execute(num_retries=self.arvrunner.num_retries)
- self.uuid = response["uuid"]
self.arvrunner.process_submitted(self)
+ self.attempt_count += 1
if response["state"] == "Final":
logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
logger.debug("Container request was %s", container_request)
self.output_callback({}, "permanentFail")
+ def out_of_memory_retry(self, record, container):
+ oom_retry_req, _ = self.get_requirement("http://arvados.org/cwl#OutOfMemoryRetry")
+ if oom_retry_req is None:
+ return False
+
+ # Sometimes it gets killed with no warning
+ if container["exit_code"] == 137:
+ return True
+
+ logc = arvados.collection.CollectionReader(record["log_uuid"],
+ api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries)
+
+ loglines = [""]
+ def callback(v1, v2, v3):
+ loglines[0] = v3
+
+ done.logtail(logc, callback, "", maxlen=1000)
+
+ # Check allocation failure
+ oom_matches = oom_retry_req.get('memoryErrorRegex') or r'(bad_alloc|out ?of ?memory|memory ?error|container using over 9.% of memory)'
+ if re.search(oom_matches, loglines[0], re.IGNORECASE | re.MULTILINE):
+ return True
+
+ return False
+
def done(self, record):
outputs = {}
+ retried = False
try:
container = self.arvrunner.api.containers().get(
uuid=record["container_uuid"]
else:
processStatus = "permanentFail"
+ if processStatus == "permanentFail" and self.attempt_count == 1 and self.out_of_memory_retry(record, container):
+ logger.warning("%s Container failed with out of memory error, retrying with more RAM.",
+ self.arvrunner.label(self))
+ self.job_runtime.submit_request_uuid = None
+ self.uuid = None
+ self.run(None)
+ retried = True
+ return
+
if rcode == 137:
- logger.warning("%s Container may have been killed for using too much RAM. Try resubmitting with a higher 'ramMin'.",
+ logger.warning("%s Container may have been killed for using too much RAM. Try resubmitting with a higher 'ramMin' or use the arv:OutOfMemoryRetry feature.",
self.arvrunner.label(self))
else:
processStatus = "permanentFail"
logger.exception("%s while getting output object:", self.arvrunner.label(self))
processStatus = "permanentFail"
finally:
- self.output_callback(outputs, processStatus)
+ if not retried:
+ self.output_callback(outputs, processStatus)
class RunnerContainer(Runner):
}
tool: 19678-name-id.cwl
doc: "Test issue 19678 - non-string type input parameter called 'name'"
+
+- job: oom/fakeoom.yml
+ output: {}
+ tool: oom/19975-oom.cwl
+ doc: "Test feature 19975 - retry on exit 137"
+
+- job: oom/fakeoom2.yml
+ output: {}
+ tool: oom/19975-oom.cwl
+ doc: "Test feature 19975 - retry on memory error"
+
+- job: oom/fakeoom3.yml
+ output: {}
+ tool: oom/19975-oom3.cwl
+ doc: "Test feature 19975 - retry on custom error"
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.2
+class: CommandLineTool
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+hints:
+ arv:OutOfMemoryRetry:
+ memoryRetryMultipler: 2
+ ResourceRequirement:
+ ramMin: 256
+ arv:APIRequirement: {}
+inputs:
+ fakeoom: File
+outputs: []
+arguments: [python3, $(inputs.fakeoom)]
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.2
+class: CommandLineTool
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+hints:
+ arv:OutOfMemoryRetry:
+ memoryRetryMultipler: 2
+ memoryErrorRegex: Whoops
+ ResourceRequirement:
+ ramMin: 256
+ arv:APIRequirement: {}
+inputs:
+ fakeoom: File
+outputs: []
+arguments: [python3, $(inputs.fakeoom)]
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+import sys
+import time
+import arvados
+
+api = arvados.api()
+current_container = api.containers().current().execute()
+
+if current_container["runtime_constraints"]["ram"] < (512*1024*1024):
+ sys.exit(137)
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+fakeoom:
+ class: File
+ location: fakeoom.py
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+import sys
+import time
+import arvados
+
+api = arvados.api()
+current_container = api.containers().current().execute()
+
+if current_container["runtime_constraints"]["ram"] < (512*1024*1024):
+ raise MemoryError()
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+fakeoom:
+ class: File
+ location: fakeoom2.py
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+import sys
+import time
+import arvados
+
+api = arvados.api()
+current_container = api.containers().current().execute()
+
+if current_container["runtime_constraints"]["ram"] < (512*1024*1024):
+ print("Whoops")
+ sys.exit(1)
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+fakeoom:
+ class: File
+ location: fakeoom3.py
projects / arvados.git / commitdiff