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workflow status stuck in Running occasionally (no repro) #13238

Open
3 of 4 tasks
heidongxianhua opened this issue Jun 24, 2024 · 11 comments
Open
3 of 4 tasks

workflow status stuck in Running occasionally (no repro) #13238

heidongxianhua opened this issue Jun 24, 2024 · 11 comments
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area/controller Controller issues, panics P3 Low priority type/bug

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@heidongxianhua
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heidongxianhua commented Jun 24, 2024

Pre-requisites

  • I have double-checked my configuration
  • I have tested with the :latest image tag (i.e. quay.io/argoproj/workflow-controller:latest) and can confirm the issue still exists on :latest. If not, I have explained why, in detail, in my description below.
  • I have searched existing issues and could not find a match for this bug
  • I'd like to contribute the fix myself (see contributing guide)

What happened/what did you expect to happen?

when I check the workflow, the pod of last step of this workflow has completed, but the wf status is pending.
image

and the pod status:
image

and according the pod logs, this pod finished just need 1 min, and there are 1700 running workflow total. And according the logs from controller, it is maybe caused by the max parallelism limit, and the parallelism value is 6000 in configmap.
image

Version

latest

Paste a small workflow that reproduces the issue. We must be able to run the workflow; don't enter a workflows that uses private images.

none, cannot reproduce stably.

Logs from the workflow controller

time="2024-06-24T02:29:55.215Z" level=info msg="Processing workflow" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:29:55.220Z" level=info msg="Task-result reconciliation" namespace=bytevs numObjs=0 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:29:55.220Z" level=warning msg="workflow uses legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:29:55.220Z" level=info msg="node unchanged" namespace=bytevs nodeID=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:29:55.223Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:29:55.227Z" level=info msg="Workflow step group node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-254110657 not yet completed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:29:55.227Z" level=info msg="TaskSet Reconciliation" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:29:55.227Z" level=info msg=reconcileAgentPod namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.850Z" level=info msg="Processing workflow" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.854Z" level=info msg="Task-result reconciliation" namespace=bytevs numObjs=0 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.854Z" level=warning msg="workflow uses legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.854Z" level=warning msg="workflow uses legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.854Z" level=info msg="node changed" namespace=bytevs new.message= new.phase=Succeeded new.progress=0/1 nodeID=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766 old.message= old.phase=Running old.progress=0/1 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.854Z" level=info msg="setting workflow.outputs.parameters.step-vina-docking: 'posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockvinadocking-k92s7-7f1z5-1142978766'" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.855Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.858Z" level=info msg="Step group node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-254110657 successful" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.858Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-254110657 phase Running -> Succeeded" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.858Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-254110657 finished: 2024-06-24 02:32:34.85803606 +0000 UTC" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.858Z" level=info msg="StepGroup node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 initialized Running" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.858Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.858Z" level=warning msg="Node was nil, will be initialized as type Skipped" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:34.860Z" level=info msg="Pod node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354 initialized Pending" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:35.203Z" level=info msg="Created pod: posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l[2].step-ligand-prepare (posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockligandprepare-bxj9c-2i67o-4106583354)" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:35.203Z" level=info msg="Workflow step group node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 not yet completed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:35.203Z" level=info msg="TaskSet Reconciliation" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:35.203Z" level=info msg=reconcileAgentPod namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:35.256Z" level=info msg="Workflow update successful" namespace=bytevs phase=Running resourceVersion=1339611002 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:35.262Z" level=info msg="cleaning up pod" action=labelPodCompleted key=bytevs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockvinadocking-k92s7-7f1z5-1142978766/labelPodCompleted
time="2024-06-24T02:32:44.953Z" level=info msg="Processing workflow" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:44.956Z" level=info msg="Task-result reconciliation" namespace=bytevs numObjs=0 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:44.956Z" level=warning msg="workflow uses legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:44.957Z" level=info msg="node changed" namespace=bytevs new.message= new.phase=Running new.progress=0/1 nodeID=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354 old.message= old.phase=Pending old.progress=0/1 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:44.958Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:44.958Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:44.959Z" level=info msg="Workflow step group node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 not yet completed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:44.960Z" level=info msg="TaskSet Reconciliation" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:44.960Z" level=info msg=reconcileAgentPod namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:32:45.322Z" level=info msg="Workflow update successful" namespace=bytevs phase=Running resourceVersion=1339612836 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.805Z" level=info msg="Processing workflow" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.808Z" level=info msg="Task-result reconciliation" namespace=bytevs numObjs=0 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.809Z" level=warning msg="workflow uses legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.809Z" level=warning msg="workflow uses legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.809Z" level=info msg="node changed" namespace=bytevs new.message= new.phase=Succeeded new.progress=0/1 nodeID=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354 old.message= old.phase=Running old.progress=0/1 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.809Z" level=info msg="setting workflow.outputs.parameters.step-ligand-prepare: 'posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockligandprepare-bxj9c-2i67o-4106583354'" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.810Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.810Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.812Z" level=info msg="Step group node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 successful" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.812Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 phase Running -> Succeeded" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.812Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 finished: 2024-06-24 02:33:30.812188663 +0000 UTC" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.812Z" level=info msg="StepGroup node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1260370439 initialized Running" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.812Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.812Z" level=warning msg="Node was nil, will be initialized as type Skipped" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:30.814Z" level=info msg="Pod node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4148759088 initialized Pending" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:31.016Z" level=info msg="Created pod: posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l[3].step-minimize-cpp (posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockminimize-v8w7l-ot9ur-4148759088)" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:31.017Z" level=info msg="Workflow step group node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1260370439 not yet completed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:31.017Z" level=info msg="TaskSet Reconciliation" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:31.017Z" level=info msg=reconcileAgentPod namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:31.125Z" level=info msg="Workflow update successful" namespace=bytevs phase=Running resourceVersion=1339623623 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:31.132Z" level=info msg="cleaning up pod" action=labelPodCompleted key=bytevs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockligandprepare-bxj9c-2i67o-4106583354/labelPodCompleted
time="2024-06-24T02:33:41.106Z" level=info msg="Processing workflow" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.109Z" level=info msg="Task-result reconciliation" namespace=bytevs numObjs=0 workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.110Z" level=error msg="was unable to obtain node for posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4148759088" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.110Z" level=info msg="Workflow pod is missing" namespace=bytevs nodeName="posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l[2].step-ligand-prepare" nodePhase=Running recentlyStarted=false workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.110Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354 phase Running -> Error" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.110Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354 message: pod deleted" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.110Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354 finished: 2024-06-24 02:33:41.110077329 +0000 UTC" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.111Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-3406984913]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.111Z" level=info msg="SG Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766 are [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1142978766]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="Step group node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 deemed failed: child 'posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354' failed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 phase Running -> Failed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 message: child 'posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354' failed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 finished: 2024-06-24 02:33:41.113189699 +0000 UTC" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="step group posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1327628010 was unsuccessful: child 'posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354' failed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354 is [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="Outbound nodes of posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l is [posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354]" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l phase Running -> Failed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l message: child 'posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354' failed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l finished: 2024-06-24 02:33:41.113258001 +0000 UTC" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="TaskSet Reconciliation" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg=reconcileAgentPod namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="Updated phase Running -> Failed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="Updated message  -> child 'posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354' failed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="Marking workflow completed" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.113Z" level=info msg="Marking workflow as pending archiving" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.119Z" level=info msg="cleaning up pod" action=deletePod key=bytevs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-1340600742-agent/deletePod
time="2024-06-24T02:33:41.218Z" level=warning msg="Error updating workflow: Operation cannot be fulfilled on workflows.argoproj.io \"posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l\": the object has been modified; please apply your changes to the latest version and try again Conflict" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.218Z" level=info msg="Re-applying updates on latest version and retrying update" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:41.321Z" level=info msg="Failed to re-apply update" error="must never update completed node posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354" namespace=bytevs workflow=posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:33:51.245Z" level=info msg="Workflow processing has been postponed due to max parallelism limit" key=bytevs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T02:34:26.603Z" level=info msg="Workflow processing has been postponed due to max parallelism limit" key=bytevs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
E0624 02:35:30.103821       1 event.go:267] Server rejected event '&v1.Event{TypeMeta:v1.TypeMeta{Kind:"", APIVersion:""}, ObjectMeta:v1.ObjectMeta{Name:"posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l.17dbd0094b9528a1", GenerateName:"", Namespace:"bytevs", SelfLink:"", UID:"", ResourceVersion:"", Generation:0, CreationTimestamp:time.Date(1, time.January, 1, 0, 0, 0, 0, time.UTC), DeletionTimestamp:<nil>, DeletionGracePeriodSeconds:(*int64)(nil), Labels:map[string]string(nil), Annotations:map[string]string(nil), OwnerReferences:[]v1.OwnerReference(nil), Finalizers:[]string(nil), ZZZ_DeprecatedClusterName:"", ManagedFields:[]v1.ManagedFieldsEntry(nil)}, InvolvedObject:v1.ObjectReference{Kind:"Workflow", Namespace:"bytevs", Name:"posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l", UID:"8f6dff64-4724-42b8-bff1-095313c50b02", APIVersion:"argoproj.io/v1alpha1", ResourceVersion:"1339612836", FieldPath:""}, Reason:"WorkflowFailed", Message:"child 'posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354' failed", Source:v1.EventSource{Component:"workflow-controller", Host:""}, FirstTimestamp:time.Date(2024, time.June, 24, 2, 33, 41, 113325729, time.Local), LastTimestamp:time.Date(2024, time.June, 24, 2, 33, 41, 113325729, time.Local), Count:1, Type:"Warning", EventTime:time.Date(1, time.January, 1, 0, 0, 0, 0, time.UTC), Series:(*v1.EventSeries)(nil), Action:"", Related:(*v1.ObjectReference)(nil), ReportingController:"", ReportingInstance:""}': 'Too many requests: limit reached on type User for key system:serviceaccount:argo:argo' (will not retry!)
time="2024-06-24T02:54:26.604Z" level=info msg="Workflow processing has been postponed due to max parallelism limit" key=bytevs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T03:14:26.606Z" level=info msg="Workflow processing has been postponed due to max parallelism limit" key=bytevs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l
time="2024-06-24T03:34:26.607Z" level=info msg="Workflow processing has been postponed due to max parallelism limit" key=bytevs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l

Logs from in your workflow's wait container

time="2024-06-24T02:32:24.768Z" level=info msg="Successfully saved file: /tmp/argo/outputs/artifacts/serverless_output"
time="2024-06-24T02:32:24.768Z" level=info msg="S3 Save path: /tmp/argo/outputs/logs/main.log, key: argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockvinadocking-k92s7-7f1z5-1142978766/main.log"
time="2024-06-24T02:32:24.768Z" level=info msg="Creating minio client using static credentials" endpoint=tos-s3-cn-beijing-inner.ivolces.com
time="2024-06-24T02:32:24.770Z" level=info msg="Saving file to s3" bucket=ai4s endpoint=tos-s3-cn-beijing-inner.ivolces.com key=argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockvinadocking-k92s7-7f1z5-1142978766/main.log path=/tmp/argo/outputs/logs/main.log
time="2024-06-24T02:32:24.780Z" level=info msg="Save artifact" artifactName=main-logs duration=12.087666ms error="<nil>" key=argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockvinadocking-k92s7-7f1z5-1142978766/main.log
time="2024-06-24T02:32:24.780Z" level=info msg="not deleting local artifact" localArtPath=/tmp/argo/outputs/logs/main.log
time="2024-06-24T02:32:24.780Z" level=info msg="Successfully saved file: /tmp/argo/outputs/logs/main.log"
time="2024-06-24T02:32:24.786Z" level=warning msg="failed to patch task set, falling back to legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" error="workflowtaskresults.argoproj.io is forbidden: User \"system:serviceaccount:bytevs:default\" cannot create resource \"workflowtaskresults\" in API group \"argoproj.io\" in the namespace \"bytevs\""
time="2024-06-24T02:32:24.814Z" level=info msg="Alloc=11694 TotalAlloc=25513 Sys=50045 NumGC=7 Goroutines=12"
time="2024-06-24T02:32:24.814Z" level=info msg="Deadline monitor stopped"
time="2024-06-24T02:33:20.939Z" level=info msg="Successfully saved file: /tmp/argo/outputs/artifacts/serverless_output"
time="2024-06-24T02:33:20.939Z" level=info msg="S3 Save path: /tmp/argo/outputs/logs/main.log, key: argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockligandprepare-bxj9c-2i67o-4106583354/main.log"
time="2024-06-24T02:33:20.939Z" level=info msg="Creating minio client using static credentials" endpoint=tos-s3-cn-beijing-inner.ivolces.com
time="2024-06-24T02:33:20.941Z" level=info msg="Saving file to s3" bucket=ai4s endpoint=tos-s3-cn-beijing-inner.ivolces.com key=argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockligandprepare-bxj9c-2i67o-4106583354/main.log path=/tmp/argo/outputs/logs/main.log
time="2024-06-24T02:33:20.951Z" level=info msg="Save artifact" artifactName=main-logs duration=12.236806ms error="<nil>" key=argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockligandprepare-bxj9c-2i67o-4106583354/main.log
time="2024-06-24T02:33:20.951Z" level=info msg="not deleting local artifact" localArtPath=/tmp/argo/outputs/logs/main.log
time="2024-06-24T02:33:20.951Z" level=info msg="Successfully saved file: /tmp/argo/outputs/logs/main.log"
time="2024-06-24T02:33:20.958Z" level=warning msg="failed to patch task set, falling back to legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" error="workflowtaskresults.argoproj.io is forbidden: User \"system:serviceaccount:bytevs:default\" cannot create resource \"workflowtaskresults\" in API group \"argoproj.io\" in the namespace \"bytevs\""
time="2024-06-24T02:33:20.983Z" level=info msg="Alloc=13746 TotalAlloc=25184 Sys=44925 NumGC=5 Goroutines=12"
time="2024-06-24T02:33:20.983Z" level=info msg="Deadline monitor stopped"
time="2024-06-24T02:34:16.615Z" level=info msg="Successfully saved file: /tmp/argo/outputs/artifacts/serverless_output"
time="2024-06-24T02:34:16.615Z" level=info msg="S3 Save path: /tmp/argo/outputs/logs/main.log, key: argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockminimize-v8w7l-ot9ur-4148759088/main.log"
time="2024-06-24T02:34:16.615Z" level=info msg="Creating minio client using static credentials" endpoint=tos-s3-cn-beijing-inner.ivolces.com
time="2024-06-24T02:34:16.617Z" level=info msg="Saving file to s3" bucket=ai4s endpoint=tos-s3-cn-beijing-inner.ivolces.com key=argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockminimize-v8w7l-ot9ur-4148759088/main.log path=/tmp/argo/outputs/logs/main.log
time="2024-06-24T02:34:16.631Z" level=info msg="Save artifact" artifactName=main-logs duration=16.214241ms error="<nil>" key=argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockminimize-v8w7l-ot9ur-4148759088/main.log
time="2024-06-24T02:34:16.631Z" level=info msg="not deleting local artifact" localArtPath=/tmp/argo/outputs/logs/main.log
time="2024-06-24T02:34:16.631Z" level=info msg="Successfully saved file: /tmp/argo/outputs/logs/main.log"
time="2024-06-24T02:34:16.639Z" level=warning msg="failed to patch task set, falling back to legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" error="workflowtaskresults.argoproj.io is forbidden: User \"system:serviceaccount:bytevs:default\" cannot create resource \"workflowtaskresults\" in API group \"argoproj.io\" in the namespace \"bytevs\""
time="2024-06-24T02:34:16.666Z" level=info msg="Alloc=18266 TotalAlloc=25319 Sys=54653 NumGC=5 Goroutines=12"
time="2024-06-24T02:34:16.666Z" level=info msg="Deadline monitor stopped"
time="2024-06-24T02:27:25.435Z" level=info msg="S3 Save path: /tmp/argo/outputs/logs/main.log, key: argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockpreparereceptor-fn1xk-sb2u4-3406984913/main.log"
time="2024-06-24T02:27:25.435Z" level=info msg="Creating minio client using static credentials" endpoint=tos-s3-cn-beijing-inner.ivolces.com
time="2024-06-24T02:27:25.443Z" level=info msg="Saving file to s3" bucket=ai4s endpoint=tos-s3-cn-beijing-inner.ivolces.com key=argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockpreparereceptor-fn1xk-sb2u4-3406984913/main.log path=/tmp/argo/outputs/logs/main.log
time="2024-06-24T02:27:25.457Z" level=info msg="Save artifact" artifactName=main-logs duration=21.851559ms error="<nil>" key=argo_logs/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l/posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-bytedockpreparereceptor-fn1xk-sb2u4-3406984913/main.log
time="2024-06-24T02:27:25.457Z" level=info msg="not deleting local artifact" localArtPath=/tmp/argo/outputs/logs/main.log
time="2024-06-24T02:27:25.457Z" level=info msg="Successfully saved file: /tmp/argo/outputs/logs/main.log"
time="2024-06-24T02:27:25.464Z" level=warning msg="failed to patch task set, falling back to legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" error="workflowtaskresults.argoproj.io is forbidden: User \"system:serviceaccount:bytevs:default\" cannot create resource \"workflowtaskresults\" in API group \"argoproj.io\" in the namespace \"bytevs\""
time="2024-06-24T02:27:25.489Z" level=info msg="Alloc=10582 TotalAlloc=19252 Sys=45181 NumGC=5 Goroutines=10"
time="2024-06-24T02:27:25.489Z" level=info msg="Deadline monitor stopped"
time="2024-06-24T02:27:25.489Z" level=info msg="stopping progress monitor (context done)" error="context canceled"
@agilgur5 agilgur5 changed the title workflow status updated not timely workflow status not updated timely Jun 24, 2024
@agilgur5 agilgur5 added area/controller Controller issues, panics P3 Low priority labels Jun 24, 2024
@agilgur5
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workflow status not updated timely

and according the pod logs, this pod finished just need 1 min,

By "not timely", do you mean it was delayed by 1 min?

I don't think that's a very long delay, especially if you have high load.

E0624 02:35:30.103821       1 event.go:267] Server rejected event '&v1.Event{TypeMeta:v1.TypeMeta{Kind:"", APIVersion:""}, ObjectMeta:v1.ObjectMeta{Name:"posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l.17dbd0094b9528a1", GenerateName:"", Namespace:"bytevs", SelfLink:"", UID:"", ResourceVersion:"", Generation:0, CreationTimestamp:time.Date(1, time.January, 1, 0, 0, 0, 0, time.UTC), DeletionTimestamp:<nil>, DeletionGracePeriodSeconds:(*int64)(nil), Labels:map[string]string(nil), Annotations:map[string]string(nil), OwnerReferences:[]v1.OwnerReference(nil), Finalizers:[]string(nil), ZZZ_DeprecatedClusterName:"", ManagedFields:[]v1.ManagedFieldsEntry(nil)}, InvolvedObject:v1.ObjectReference{Kind:"Workflow", Namespace:"bytevs", Name:"posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l", UID:"8f6dff64-4724-42b8-bff1-095313c50b02", APIVersion:"argoproj.io/v1alpha1", ResourceVersion:"1339612836", FieldPath:""}, Reason:"WorkflowFailed", Message:"child 'posebuster-bytedock-cpp-eval-7mmh-zjy-bmv8l-4106583354' failed", Source:v1.EventSource{Component:"workflow-controller", Host:""}, FirstTimestamp:time.Date(2024, time.June, 24, 2, 33, 41, 113325729, time.Local), LastTimestamp:time.Date(2024, time.June, 24, 2, 33, 41, 113325729, time.Local), Count:1, Type:"Warning", EventTime:time.Date(1, time.January, 1, 0, 0, 0, 0, time.UTC), Series:(*v1.EventSeries)(nil), Action:"", Related:(*v1.ObjectReference)(nil), ReportingController:"", ReportingInstance:""}': 'Too many requests: limit reached on type User for key system:serviceaccount:argo:argo' (will not retry!)

And this error in your logs also suggests you're getting rate-limited (see also nodeEvents in the ConfigMap), which I'm not sure there's anything Argo can do for you if you are.

You also have an Executor deprecation warning:

time="2024-06-24T02:32:24.786Z" level=warning msg="failed to patch task set, falling back to legacy/insecure pod patch, see https://argoproj.github.io/argo-workflows/workflow-rbac/" error="workflowtaskresults.argoproj.io is forbidden: User \"system:serviceaccount:bytevs:default\" cannot create resource \"workflowtaskresults\" in API group \"argoproj.io\" in the namespace \"bytevs\""

Which you should really fix by following the Workflow RBAC page. The fallback will be removed in 3.6: #13100

and the pod status:

the parallelism value is 6000 in configmap.

Also, please use text instead of images when listing logs, configurations, or code, as text is much more accessible than images

@agilgur5 agilgur5 added the problem/more information needed Not enough information has been provide to diagnose this issue. label Jun 30, 2024
@heidongxianhua
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heidongxianhua commented Jul 1, 2024

yeah, but from the image of UI, this step has running 1h10min with pending status. The pod is completed, but the workflow is in pending status.
image

@agilgur5
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agilgur5 commented Jul 1, 2024

Is the Workflow stuck in Running despite all Pods being Completed? Or does the Workflow eventually become Succeeded?

Those are two very different things. I have a feeling you meant the former, but you wrote the latter

Paste a small workflow that reproduces the issue. We must be able to run the workflow; don't enter a workflows that uses private images.

none, cannot reproduce stably.

Also without a Workflow, nor even a specific version, this issue is not really actionable -- there is nothing to investigate.

Please provide the Workflow that is Pending. If you can provide its full status and the Completed Pod, that could be helpful as well.

Given that you're using deprecated pod patch permissions though, you have no WorkflowTaskResults, and we wouldn't fix a bug with pod patch -- you should use the appropriate Workflow RBAC as I already linked.

@heidongxianhua
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heidongxianhua commented Jul 2, 2024

yeah, I can not give a workflow to reproduce this bug stably, and today I got this bug again.

argo get posebuster-bytedock-cpp-eval-8slg-g5a-gdn68 -n bytevs
Name:                posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
Namespace:           bytevs
ServiceAccount:      unset (will run with the default ServiceAccount)
Status:              Running
Conditions:
 PodRunning          False
Created:             Tue Jul 02 10:54:04 +0800 (3 hours ago)
Started:             Tue Jul 02 10:54:04 +0800 (3 hours ago)
Duration:            3 hours 30 minutes
Progress:            2/3
ResourcesDuration:   5m4s*(1 cpu),53m8s*(100Mi memory)
Output Parameters:
  step-receptor-prepare: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockpreparereceptor-kjzln-oxn6f-1049446578
  step-vina-docking: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockvinadocking-zsxd5-myk9u-2932115425

STEP                                            TEMPLATE                                     PODNAME                                                                                     DURATION  MESSAGE
 ● posebuster-bytedock-cpp-eval-8slg-g5a-gdn68  posebuster-bytedock-cpp-eval-8slg-g5a-steps
 ├───✔ step-receptor-prepare                    bytedockpreparereceptor-kjzln-oxn6f          posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockpreparereceptor-kjzln-oxn6f-1049446578  30s
 ├───✔ step-vina-docking                        bytedockvinadocking-zsxd5-myk9u              posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockvinadocking-zsxd5-myk9u-2932115425      2m
 └───◷ step-ligand-prepare                      bytedockligandprepare-86wtx-jrgik            posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockligandprepare-86wtx-jrgik-2269680813    3h
kubectl get pod posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockligandprepare-86wtx-jrgik-2269680813 -n bytevs
NAME                                                                                       READY   STATUS      RESTARTS   AGE
posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockligandprepare-86wtx-jrgik-2269680813   0/2     Completed   0          3h30m

we can get that the pod of step-ligand-prepare has finished 3h30m ago, but the workflow status is always pending.

@agilgur5
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agilgur5 commented Jul 2, 2024

By "not timely", do you mean it was delayed by 1 min?

Is the Workflow stuck in Running despite all Pods being Completed? Or does the Workflow eventually become Succeeded?

@heidongxianhua could you answer the above questions?

Please provide the Workflow that is Pending. If you can provide its full status and the Completed Pod, that could be helpful as well.

To clarify, by this I meant the output of kubectl get wf <my-wf> -o yaml and kubectl get pod <my-pod> -o yaml.

plain get does not include the full status, only a summary

@heidongxianhua
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heidongxianhua commented Jul 2, 2024

yeah, this pending status step block the workflow, and the workflow is always in running status, can not reach finished status.

wf yaml
apiVersion: argoproj.io/v1alpha1
kind: Workflow
metadata:
  annotations:
    workflows.argoproj.io/pod-name-format: v2
  creationTimestamp: "2024-07-02T02:54:04Z"
  generateName: posebuster-bytedock-cpp-eval-8slg-g5a-
  generation: 6
  labels:
    workflows.argoproj.io/creator: system-serviceaccount-argo-argo-server
    workflows.argoproj.io/phase: Running
  name: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
  namespace: bytevs
  resourceVersion: "1379931806"
  uid: e11ff5c4-d430-449e-87d8-ea40e3139aab
spec:
  arguments: {}
  entrypoint: posebuster-bytedock-cpp-eval-8slg-g5a-steps
  nodeSelector:
    node-tag: bytevs
  podGC: {}
  podPriorityClassName: critical
  templates:
  - inputs:
      artifacts:
      - name: flow_bigpar_serverless_input
        path: /tmp/inputs/parameters/serverless_input
      - name: flow_python_packages
        path: /tmp/inputs/artifacts/flow_python_packages
      parameters:
      - description: '{"type": "<class ''str''>"}'
        name: receptor_pdb
        value: ""
      - description: '{"type": "<class ''str''>"}'
        name: receptor_prepared_dir_tos
        value: ""
      - description: '{"type": "<class ''str''>"}'
        name: reference_tos
        value: ""
      - description: '{"type": "<class ''dict''>"}'
        name: flow_info
        value: '{"flow_throughput": 0, "cpu_cost": 0, "gpu_cost": 0, "invt_id": -1,
          "gpu_info": {}, "resource_platform": "", "class_name": ""}'
      - description: '{"type": "<class ''str''>"}'
        name: flow_lock
        value: ""
      - name: flow_key
        value: ""
    metadata:
      annotations:
        workflows.argoproj.io/progress: 0/1
    name: bytedockpreparereceptor-kjzln-oxn6f
    outputs:
      parameters:
      - description: '{"type": "<class ''str''>"}'
        name: receptor_info_tos
        valueFrom:
          default: ""
          path: /tmp/outputs/parameters/receptor_info_tos
      - description: '{"type": "<class ''dict''>"}'
        name: flow_info
        valueFrom:
          default: '{"flow_throughput": 0, "cpu_cost": 0, "gpu_cost": 0, "invt_id":
            -1, "gpu_info": {}, "resource_platform": "", "class_name": ""}'
          path: /tmp/outputs/parameters/flow_info
      - description: '{"type": "<class ''str''>"}'
        name: flow_lock
        valueFrom:
          default: ""
          path: /tmp/outputs/parameters/flow_lock
      - globalName: '{{inputs.parameters.flow_key}}'
        name: flow_global
        value: '{{pod.name}}'
    script:
      command:
      - python3
      image: test:6f2c8db77a010c813e0125bf35023d1b
      name: ""
      resources:
        limits:
          cpu: "96"
          memory: 96Gi
        requests:
          cpu: "1"
          memory: 2Gi
      source: ""
  - inputs:
      artifacts:
      - name: flow_bigpar_serverless_input
        path: /tmp/inputs/parameters/serverless_input
      - name: flow_python_packages
        path: /tmp/inputs/artifacts/flow_python_packages
      parameters:
      - description: '{"type": "<class ''str''>"}'
        name: receptor_info_tos
        value: ""
      - description: '{"type": "<class ''bool''>"}'
        name: load_results_if_exist
        value: "false"
      - description: '{"type": "<class ''bool''>"}'
        name: run_vina_local
        value: "false"
      - description: '{"type": "<class ''int''>"}'
        name: vina_cpu
        value: "16"
      - description: '{"type": "<class ''int''>"}'
        name: vina_n_poses
        value: "50"
      - description: '{"type": "<class ''int''>"}'
        name: vina_seed
        value: "12345"
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        name: vina_energy_range
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    metadata:
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        workflows.argoproj.io/progress: 0/1
    name: bytedockvinadocking-zsxd5-myk9u
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        name: flow_bigpar_serverless_output
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      parameters:
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      - description: '{"type": "<class ''str''>"}'
        name: flow_lock
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          path: /tmp/outputs/parameters/flow_lock
      - globalName: '{{inputs.parameters.flow_key}}'
        name: flow_global
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      command:
      - python3
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      resources:
        limits:
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          memory: 96Gi
        requests:
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          memory: 2Gi
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  - inputs:
      artifacts:
      - name: flow_bigpar_serverless_input
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      - name: flow_python_packages
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      parameters:
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        name: load_results_if_exist
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      - description: '{"type": "<class ''bool''>"}'
        name: write_csv_per_row
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      - name: flow_key
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    metadata:
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        workflows.argoproj.io/progress: 0/1
    name: bytedockligandprepare-86wtx-jrgik
    outputs:
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          none: {}
        name: flow_bigpar_serverless_output
        path: /tmp/outputs/parameters/serverless_output
      parameters:
      - description: '{"type": "<class ''dict''>"}'
        name: flow_info
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          default: '{"flow_throughput": 0, "cpu_cost": 0, "gpu_cost": 0, "invt_id":
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          path: /tmp/outputs/parameters/flow_info
      - description: '{"type": "<class ''str''>"}'
        name: flow_lock
        valueFrom:
          default: ""
          path: /tmp/outputs/parameters/flow_lock
      - globalName: '{{inputs.parameters.flow_key}}'
        name: flow_global
        value: '{{pod.name}}'
    script:
      command:
      - python3
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      name: ""
      resources:
        limits:
          cpu: "96"
          memory: 96Gi
        requests:
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          memory: 2Gi
      source: ""
  - inputs:
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        name: receptor_info_tos
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        name: ligand_variable
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        name: granularity
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        name: output_dir_tos
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      - description: '{"type": "<class ''dict''>"}'
        name: kwargs
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        name: eval_type
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      - description: '{"type": "<class ''str''>"}'
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      - name: flow_key
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    metadata:
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    name: bytedockminimize-lhgtu-vax30
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      parameters:
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          path: /tmp/outputs/parameters/flow_lock
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      command:
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        requests:
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  - inputs: {}
    metadata: {}
    name: posebuster-bytedock-cpp-eval-8slg-g5a-steps
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            s3:
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          - name: flow_python_packages
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            s3:
              key: bytevs/workflow/upload/72bc1f56-6e6f-406a-92a1-a8068debb522/tmp8bhkqwnn.tgz
          parameters:
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            name: receptor_pdb
            value: 8SLG_G5A_protein_prepared_noHETATM
          - description: '{"type": "<class ''str''>"}'
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          - description: '{"type": "<class ''str''>"}'
            name: reference_tos
            value: bytedock/data_redock/raw/posebuster/reference_sdf/8SLG_G5A_ligand_prepared.sdf
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            name: flow_info
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          - description: '{"type": "<class ''str''>"}'
            name: flow_lock
            value: ""
          - name: flow_key
            value: step-receptor-prepare
        continueOn: {}
        name: step-receptor-prepare
        template: bytedockpreparereceptor-kjzln-oxn6f
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            s3:
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          - name: flow_python_packages
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            s3:
              key: bytevs/workflow/upload/72bc1f56-6e6f-406a-92a1-a8068debb522/tmp8bhkqwnn.tgz
          parameters:
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            name: receptor_info_tos
            value: '{{=steps[''step-receptor-prepare''].outputs.parameters[''receptor_info_tos'']}}'
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          - description: '{"type": "<class ''int''>"}'
            name: vina_exhaustiveness
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          - description: '{"type": "<class ''int''>"}'
            name: vina_search_depth
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          - description: '{"type": "<class ''float''>"}'
            name: vina_energy_range
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          - description: '{"type": "<class ''str''>"}'
            name: output_dir_tos
            value: bytedock_cpp/data_redock/reference_todock_sdf_seed12345_allfix_fp64/posebuster/8SLG_G5A
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            name: flow_info
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          - description: '{"type": "<class ''str''>"}'
            name: flow_lock
            value: ""
          - name: flow_key
            value: step-vina-docking
        continueOn: {}
        name: step-vina-docking
        template: bytedockvinadocking-zsxd5-myk9u
    - - arguments:
          artifacts:
          - from: '{{steps.step-vina-docking.outputs.artifacts.flow_bigpar_serverless_output}}'
            name: flow_bigpar_serverless_input
            path: /tmp/inputs/parameters/serverless_input
          - name: flow_python_packages
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            s3:
              key: bytevs/workflow/upload/72bc1f56-6e6f-406a-92a1-a8068debb522/tmp8bhkqwnn.tgz
          parameters:
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            name: load_results_if_exist
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            name: write_csv_per_row
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          - description: '{"type": "<class ''str''>"}'
            name: output_dir_tos
            value: bytedock_cpp/data_redock/reference_todock_sdf_seed12345_allfix_fp64/posebuster/8SLG_G5A
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            name: kwargs
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            name: flow_info
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          - description: '{"type": "<class ''str''>"}'
            name: flow_lock
            value: ""
          - name: flow_key
            value: step-ligand-prepare
        continueOn: {}
        name: step-ligand-prepare
        template: bytedockligandprepare-86wtx-jrgik
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          artifacts:
          - from: '{{steps.step-ligand-prepare.outputs.artifacts.flow_bigpar_serverless_output}}'
            name: flow_bigpar_serverless_input
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          - name: flow_python_packages
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            s3:
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          parameters:
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            name: receptor_info_tos
            value: '{{=steps[''step-receptor-prepare''].outputs.parameters[''receptor_info_tos'']}}'
          - description: '{"type": "<class ''str''>"}'
            name: receptor_variable
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            name: ligand_variable
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            name: reference_tos
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            name: kwargs
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          - description: '{"type": "<class ''str''>"}'
            name: eval_type
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          - description: '{"type": "<class ''str''>"}'
            name: flow_lock
            value: ""
          - name: flow_key
            value: step-minimize-cpp
        continueOn: {}
        name: step-minimize-cpp
        template: bytedockminimize-lhgtu-vax30
      - arguments:
          artifacts:
          - from: '{{steps.step-ligand-prepare.outputs.artifacts.flow_bigpar_serverless_output}}'
            name: flow_bigpar_serverless_input
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          - name: flow_python_packages
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            s3:
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          parameters:
          - description: '{"type": "<class ''str''>"}'
            name: receptor_info_tos
            value: '{{=steps[''step-receptor-prepare''].outputs.parameters[''receptor_info_tos'']}}'
          - description: '{"type": "<class ''str''>"}'
            name: receptor_variable
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          - description: '{"type": "<class ''str''>"}'
            name: ligand_variable
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            name: check_rmsd
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            name: use_map
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          - description: '{"type": "<class ''float''>"}'
            name: granularity
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            name: penalty_coeff
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          - description: '{"type": "<class ''str''>"}'
            name: maps_tos
            value: ""
          - description: '{"type": "<class ''str''>"}'
            name: reference_tos
            value: bytedock/data_redock/raw/posebuster/reference_sdf/8SLG_G5A_ligand_prepared.sdf
          - description: '{"type": "<class ''str''>"}'
            name: output_dir_tos
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          - description: '{"type": "<class ''dict''>"}'
            name: kwargs
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              true}'
          - description: '{"type": "<class ''str''>"}'
            name: eval_type
            value: py
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            name: flow_info
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          - description: '{"type": "<class ''str''>"}'
            name: flow_lock
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          - name: flow_key
            value: step-minimize-py
        continueOn: {}
        name: step-minimize-py
        template: bytedockminimize-lhgtu-vax30
  tolerations:
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    key: node-tag
    operator: Equal
    value: bytevs
  ttlStrategy:
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status:
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  artifactRepositoryRef:
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        keyFormat: argo_logs/{{workflow.name}}/{{pod.name}}
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        secretKeySecret:
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    configMap: artifact-repositories
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  conditions:
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      startedAt: "2024-07-02T02:54:04Z"
      templateName: posebuster-bytedock-cpp-eval-8slg-g5a-steps
      templateScope: local/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      type: Steps
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      templateScope: local/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
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      hostNodeName: 10.249.83.145
      id: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-1049446578
      inputs:
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        parameters:
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          name: receptor_pdb
          value: 8SLG_G5A_protein_prepared_noHETATM
        - description: '{"type": "<class ''str''>"}'
          name: receptor_prepared_dir_tos
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          name: reference_tos
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        - name: flow_key
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        parameters:
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        - description: '{"type": "<class ''str''>"}'
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          valueFrom:
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      phase: Succeeded
      progress: 1/1
      resourcesDuration:
        cpu: 51
        memory: 528
      startedAt: "2024-07-02T02:54:04Z"
      templateName: bytedockpreparereceptor-kjzln-oxn6f
      templateScope: local/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      type: Pod
    posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-1897784327:
      boundaryID: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      children:
      - posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-1049446578
      displayName: '[0]'
      finishedAt: "2024-07-02T02:54:44Z"
      id: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-1897784327
      name: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68[0]
      phase: Succeeded
      progress: 2/3
      resourcesDuration:
        cpu: 304
        memory: 3188
      startedAt: "2024-07-02T02:54:04Z"
      templateScope: local/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      type: StepGroup
    posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-1965041898:
      boundaryID: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      children:
      - posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-2932115425
      displayName: '[1]'
      finishedAt: "2024-07-02T02:57:01Z"
      id: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-1965041898
      name: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68[1]
      phase: Succeeded
      progress: 1/2
      resourcesDuration:
        cpu: 253
        memory: 2660
      startedAt: "2024-07-02T02:54:44Z"
      templateScope: local/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      type: StepGroup
    posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-2269680813:
      boundaryID: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      displayName: step-ligand-prepare
      finishedAt: null
      id: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-2269680813
      inputs:
        artifacts:
        - archive:
            none: {}
          name: flow_bigpar_serverless_input
          path: /tmp/inputs/parameters/serverless_input
          s3:
            key: argo_logs/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockvinadocking-zsxd5-myk9u-2932115425/serverless_output
        - name: flow_python_packages
          path: /tmp/inputs/artifacts/flow_python_packages
          s3:
            key: bytevs/workflow/upload/72bc1f56-6e6f-406a-92a1-a8068debb522/tmp8bhkqwnn.tgz
        parameters:
        - description: '{"type": "<class ''bool''>"}'
          name: load_results_if_exist
          value: "true"
        - description: '{"type": "<class ''bool''>"}'
          name: write_csv_per_row
          value: "false"
        - description: '{"type": "<class ''str''>"}'
          name: output_dir_tos
          value: bytedock_cpp/data_redock/reference_todock_sdf_seed12345_allfix_fp64/posebuster/8SLG_G5A
        - description: '{"type": "<class ''dict''>"}'
          name: kwargs
          value: '{"pose_batch_size": 1, "write_to_sdf": true, "select_best_pose":
            true}'
        - description: '{"type": "<class ''dict''>"}'
          name: flow_info
          value: '{"flow_throughput": 0, "cpu_cost": 0, "gpu_cost": 0, "invt_id":
            2186, "gpu_info": {}, "resource_platform": "", "class_name": ""}'
        - description: '{"type": "<class ''str''>"}'
          name: flow_lock
          value: ""
        - name: flow_key
          value: step-ligand-prepare
      name: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68[2].step-ligand-prepare
      phase: Pending
      progress: 0/1
      startedAt: "2024-07-02T02:57:01Z"
      templateName: bytedockligandprepare-86wtx-jrgik
      templateScope: local/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      type: Pod
    posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-2932115425:
      boundaryID: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      children:
      - posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-891524545
      displayName: step-vina-docking
      finishedAt: "2024-07-02T02:56:51Z"
      hostNodeName: 10.249.83.197
      id: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-2932115425
      inputs:
        artifacts:
        - name: flow_bigpar_serverless_input
          path: /tmp/inputs/parameters/serverless_input
          s3:
            key: bytevs/workflow/upload/5c00e12d-09f4-44b9-819a-1d65c383c381/serverless_input
        - name: flow_python_packages
          path: /tmp/inputs/artifacts/flow_python_packages
          s3:
            key: bytevs/workflow/upload/72bc1f56-6e6f-406a-92a1-a8068debb522/tmp8bhkqwnn.tgz
        parameters:
        - description: '{"type": "<class ''str''>"}'
          name: receptor_info_tos
          value: bytedock/data_redock/raw/posebuster/prepared_receptor/8SLG_G5A/8SLG_G5A_protein_prepared_noHETATM_cpp.yaml
        - description: '{"type": "<class ''bool''>"}'
          name: load_results_if_exist
          value: "true"
        - description: '{"type": "<class ''bool''>"}'
          name: run_vina_local
          value: "false"
        - description: '{"type": "<class ''int''>"}'
          name: vina_cpu
          value: "8"
        - description: '{"type": "<class ''int''>"}'
          name: vina_n_poses
          value: "50"
        - description: '{"type": "<class ''int''>"}'
          name: vina_seed
          value: "12345"
        - description: '{"type": "<class ''int''>"}'
          name: vina_exhaustiveness
          value: "32"
        - description: '{"type": "<class ''int''>"}'
          name: vina_search_depth
          value: "0"
        - description: '{"type": "<class ''float''>"}'
          name: vina_energy_range
          value: "1000"
        - description: '{"type": "<class ''str''>"}'
          name: output_dir_tos
          value: bytedock_cpp/data_redock/reference_todock_sdf_seed12345_allfix_fp64/posebuster/8SLG_G5A
        - description: '{"type": "<class ''dict''>"}'
          name: flow_info
          value: '{"flow_throughput": 0, "cpu_cost": 0, "gpu_cost": 0, "invt_id":
            2186, "gpu_info": {}, "resource_platform": "", "class_name": ""}'
        - description: '{"type": "<class ''str''>"}'
          name: flow_lock
          value: ""
        - name: flow_key
          value: step-vina-docking
      name: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68[1].step-vina-docking
      outputs:
        artifacts:
        - archive:
            none: {}
          name: flow_bigpar_serverless_output
          path: /tmp/outputs/parameters/serverless_output
          s3:
            key: argo_logs/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockvinadocking-zsxd5-myk9u-2932115425/serverless_output
        - name: main-logs
          s3:
            key: argo_logs/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockvinadocking-zsxd5-myk9u-2932115425/main.log
        exitCode: "0"
        parameters:
        - description: '{"type": "<class ''dict''>"}'
          name: flow_info
          value: '{"cpu_cost": 1711, "gpu_cost": 0, "gpu_info": {}, "resource_platform":
            "megatron", "class_name": "ByteDockVinaDocking", "invt_id": 2186, "flow_throughput":
            1}'
          valueFrom:
            default: '{"flow_throughput": 0, "cpu_cost": 0, "gpu_cost": 0, "invt_id":
              -1, "gpu_info": {}, "resource_platform": "", "class_name": ""}'
            path: /tmp/outputs/parameters/flow_info
        - description: '{"type": "<class ''str''>"}'
          name: flow_lock
          value: ""
          valueFrom:
            default: ""
            path: /tmp/outputs/parameters/flow_lock
        - globalName: step-vina-docking
          name: flow_global
          value: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockvinadocking-zsxd5-myk9u-2932115425
      phase: Succeeded
      progress: 1/1
      resourcesDuration:
        cpu: 253
        memory: 2660
      startedAt: "2024-07-02T02:54:44Z"
      templateName: bytedockvinadocking-zsxd5-myk9u
      templateScope: local/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
      type: Pod
  outputs:
    parameters:
    - name: step-receptor-prepare
      value: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockpreparereceptor-kjzln-oxn6f-1049446578
    - name: step-vina-docking
      value: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockvinadocking-zsxd5-myk9u-2932115425
  phase: Running
  progress: 2/3
  resourcesDuration:
    cpu: 304
    memory: 3188
  startedAt: "2024-07-02T02:54:04Z"

@heidongxianhua
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heidongxianhua commented Jul 2, 2024

pod yaml
apiVersion: v1
kind: Pod
metadata:
  annotations:
    kubectl.kubernetes.io/default-container: main
    workflows.argoproj.io/node-id: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-2269680813
    workflows.argoproj.io/node-name: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68[2].step-ligand-prepare
    workflows.argoproj.io/outputs: '{"parameters":[{"name":"flow_info","value":"{\"cpu_cost\":
      217, \"gpu_cost\": 0, \"gpu_info\": {}, \"resource_platform\": \"megatron\",
      \"class_name\": \"ByteDockLigandPrepare\", \"invt_id\": 2186, \"flow_throughput\":
      1}","valueFrom":{"path":"/tmp/outputs/parameters/flow_info","default":"{\"flow_throughput\":
      0, \"cpu_cost\": 0, \"gpu_cost\": 0, \"invt_id\": -1, \"gpu_info\": {}, \"resource_platform\":
      \"\", \"class_name\": \"\"}"},"description":"{\"type\": \"\u003cclass ''dict''\u003e\"}"},{"name":"flow_lock","value":"","valueFrom":{"path":"/tmp/outputs/parameters/flow_lock","default":""},"description":"{\"type\":
      \"\u003cclass ''str''\u003e\"}"},{"name":"flow_global","value":"posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockligandprepare-86wtx-jrgik-2269680813","globalName":"step-ligand-prepare"}],"artifacts":[{"name":"flow_bigpar_serverless_output","path":"/tmp/outputs/parameters/serverless_output","s3":{"key":"argo_logs/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockligandprepare-86wtx-jrgik-2269680813/serverless_output"},"archive":{"none":{}}},{"name":"main-logs","s3":{"key":"argo_logs/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68/posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockligandprepare-86wtx-jrgik-2269680813/main.log"}}]}'
    workflows.argoproj.io/progress: 0/1
  creationTimestamp: "2024-07-02T02:57:01Z"
  labels:
    workflows.argoproj.io/completed: "false"
    workflows.argoproj.io/workflow: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
  name: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-bytedockligandprepare-86wtx-jrgik-2269680813
  namespace: bytevs
  ownerReferences:
  - apiVersion: argoproj.io/v1alpha1
    blockOwnerDeletion: true
    controller: true
    kind: Workflow
    name: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
    uid: e11ff5c4-d430-449e-87d8-ea40e3139aab
  resourceVersion: "1379936854"
  uid: fad58c50-bf83-4632-ade6-5204b3068bfc
spec:
  containers:
  - command:
    - argoexec
    - wait
    - --loglevel
    - info
    - --log-format
    - text
    env:
    - name: ARGO_POD_NAME
      valueFrom:
        fieldRef:
          apiVersion: v1
          fieldPath: metadata.name
    - name: ARGO_POD_UID
      valueFrom:
        fieldRef:
          apiVersion: v1
          fieldPath: metadata.uid
    - name: GODEBUG
      value: x509ignoreCN=0
    - name: ARGO_WORKFLOW_NAME
      value: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
    - name: ARGO_CONTAINER_NAME
      value: wait
    - name: ARGO_TEMPLATE
      value: ''
    - name: ARGO_NODE_ID
      value: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-2269680813
    - name: ARGO_INCLUDE_SCRIPT_OUTPUT
      value: "false"
    - name: ARGO_DEADLINE
      value: "0001-01-01T00:00:00Z"
    - name: ARGO_PROGRESS_FILE
      value: /var/run/argo/progress
    - name: ARGO_PROGRESS_PATCH_TICK_DURATION
      value: 1m0s
    - name: ARGO_PROGRESS_FILE_TICK_DURATION
      value: 3s
    image: mlp-byted-cn-beijing.cr.volces.com/molecule/argoexec:v3.5.5-ai4s
    imagePullPolicy: Always
    name: wait
    resources:
      requests:
        cpu: 10m
        memory: 64Mi
    terminationMessagePath: /dev/termination-log
    terminationMessagePolicy: File
    volumeMounts:
    - mountPath: /argo/secret/tos-cred
      name: tos-cred
      readOnly: true
    - mountPath: /mainctrfs/tmp/inputs/parameters/serverless_input
      name: input-artifacts
      subPath: flow_bigpar_serverless_input
    - mountPath: /mainctrfs/tmp/inputs/artifacts/flow_python_packages
      name: input-artifacts
      subPath: flow_python_packages
    - mountPath: /mainctrfs/argo/staging
      name: argo-staging
    - mountPath: /tmp
      name: tmp-dir-argo
      subPath: "0"
    - mountPath: /var/run/argo
      name: var-run-argo
    - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
      name: default-token-r6ndr
      readOnly: true
  - args:
    - /argo/staging/script
    command:
    - /var/run/argo/argoexec
    - emissary
    - --loglevel
    - info
    - --log-format
    - text
    - --
    - python3
    env:
    - name: ARGO_CONTAINER_NAME
      value: main
    - name: ARGO_TEMPLATE
      value: ''
    - name: ARGO_NODE_ID
      value: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-2269680813
    - name: ARGO_INCLUDE_SCRIPT_OUTPUT
      value: "false"
    - name: ARGO_DEADLINE
      value: "0001-01-01T00:00:00Z"
    - name: ARGO_PROGRESS_FILE
      value: /var/run/argo/progress
    - name: ARGO_PROGRESS_PATCH_TICK_DURATION
      value: 1m0s
    - name: ARGO_PROGRESS_FILE_TICK_DURATION
      value: 3s
    image: test:6f2c8db77a010c813e0125bf35023d1b
    imagePullPolicy: Always
    name: main
    resources:
      limits:
        cpu: "96"
        memory: 96Gi
      requests:
        cpu: "1"
        memory: 2Gi
    terminationMessagePath: /dev/termination-log
    terminationMessagePolicy: File
    volumeMounts:
    - mountPath: /tmp/inputs/parameters/serverless_input
      name: input-artifacts
      subPath: flow_bigpar_serverless_input
    - mountPath: /tmp/inputs/artifacts/flow_python_packages
      name: input-artifacts
      subPath: flow_python_packages
    - mountPath: /argo/staging
      name: argo-staging
    - mountPath: /var/run/argo
      name: var-run-argo
    - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
      name: default-token-r6ndr
      readOnly: true
  dnsPolicy: ClusterFirst
  enableServiceLinks: true
  imagePullSecrets:
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  - name: cr-mlp-byted-cn-beijing
  - name: hub-byted-org
  initContainers:
  - command:
    - argoexec
    - init
    - --loglevel
    - info
    - --log-format
    - text
    env:
    - name: ARGO_POD_NAME
      valueFrom:
        fieldRef:
          apiVersion: v1
          fieldPath: metadata.name
    - name: ARGO_POD_UID
      valueFrom:
        fieldRef:
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          fieldPath: metadata.uid
    - name: GODEBUG
      value: x509ignoreCN=0
    - name: ARGO_WORKFLOW_NAME
      value: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68
    - name: ARGO_CONTAINER_NAME
      value: init
    - name: ARGO_TEMPLATE
      value: ''
    - name: ARGO_NODE_ID
      value: posebuster-bytedock-cpp-eval-8slg-g5a-gdn68-2269680813
    - name: ARGO_INCLUDE_SCRIPT_OUTPUT
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    - name: ARGO_DEADLINE
      value: "0001-01-01T00:00:00Z"
    - name: ARGO_PROGRESS_FILE
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    - name: ARGO_PROGRESS_PATCH_TICK_DURATION
      value: 1m0s
    - name: ARGO_PROGRESS_FILE_TICK_DURATION
      value: 3s
    image: mlp-byted-cn-beijing.cr.volces.com/molecule/argoexec:v3.5.5-ai4s
    imagePullPolicy: Always
    name: init
    resources:
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        memory: 64Mi
    terminationMessagePath: /dev/termination-log
    terminationMessagePolicy: File
    volumeMounts:
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      readOnly: true
    - mountPath: /argo/inputs/artifacts
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    - mountPath: /argo/staging
      name: argo-staging
    - mountPath: /var/run/argo
      name: var-run-argo
    - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
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      readOnly: true
  nodeName: 10.249.82.186
  nodeSelector:
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  priorityClassName: critical
  restartPolicy: Never
  schedulerName: default-scheduler
  securityContext: {}
  serviceAccount: default
  serviceAccountName: default
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    key: node-tag
    operator: Equal
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    tolerationSeconds: 300
  - effect: NoExecute
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    operator: Exists
    tolerationSeconds: 300
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    name: var-run-argo
  - emptyDir: {}
    name: tmp-dir-argo
  - name: tos-cred
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      - key: secretkey
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      secretName: tos-cred
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status:
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    lastTransitionTime: "2024-07-02T02:57:03Z"
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    lastTransitionTime: "2024-07-02T02:57:29Z"
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    lastTransitionTime: "2024-07-02T02:57:29Z"
    reason: PodCompleted
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    lastTransitionTime: "2024-07-02T02:57:01Z"
    status: "True"
    type: PodScheduled
  containerStatuses:
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    lastState: {}
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    restartCount: 0
    started: false
    state:
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        exitCode: 0
        finishedAt: "2024-07-02T02:57:29Z"
        reason: Completed
        startedAt: "2024-07-02T02:57:04Z"
  - containerID: containerd://f4a55a4ea01a18d56dcf3dcbae62ffcf2224b792b91497201e0df9d66e4e739b
    image: mlp-byted-cn-beijing.cr.volces.com/molecule/argoexec:v3.5.5-ai4s
    imageID: mlp-byted-cn-beijing.cr.volces.com/molecule/argoexec@sha256:1d783cadfaf49f348346aa31cb7df0114d56c42206151590bd93135a70a9f34a
    lastState: {}
    name: wait
    ready: false
    restartCount: 0
    started: false
    state:
      terminated:
        containerID: containerd://f4a55a4ea01a18d56dcf3dcbae62ffcf2224b792b91497201e0df9d66e4e739b
        exitCode: 0
        finishedAt: "2024-07-02T02:57:29Z"
        reason: Completed
        startedAt: "2024-07-02T02:57:03Z"
  hostIP: 10.249.82.186
  initContainerStatuses:
  - containerID: containerd://e985f5e4f86fdf3bc3b1b38cac9244ce28982ed63f0e443df908b731a838e52c
    image: mlp-byted-cn-beijing.cr.volces.com/molecule/argoexec:v3.5.5-ai4s
    imageID: mlp-byted-cn-beijing.cr.volces.com/molecule/argoexec@sha256:1d783cadfaf49f348346aa31cb7df0114d56c42206151590bd93135a70a9f34a
    lastState: {}
    name: init
    ready: true
    restartCount: 0
    state:
      terminated:
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        exitCode: 0
        finishedAt: "2024-07-02T02:57:02Z"
        reason: Completed
        startedAt: "2024-07-02T02:57:02Z"
  phase: Succeeded
  podIP: 192.168.155.104
  podIPs:
  - ip: 192.168.155.104
  qosClass: Burstable
  startTime: "2024-07-02T02:57:01Z"

@heidongxianhua
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and until now, the workflow is in running status with the step is pending.
image

image

This comment was marked as resolved.

@github-actions github-actions bot added the problem/stale This has not had a response in some time label Jul 17, 2024
@agilgur5 agilgur5 changed the title workflow status not updated timely workflow status stuck in Running Jul 20, 2024
@agilgur5
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agilgur5 commented Jul 20, 2024

yeah, this pending status step block the workflow, and the workflow is always in running status, can not reach finished status.

and until now, the workflow is in running status with the step is pending.

Ok I've rewritten the title of your issue to reflect this. There are a few other existing issues of this nature as well.

I also added syntax highlighting to your \```yaml and minimized them by default with a <details> tag (see my edits to the comments).

I still need to take a look at them, however, they are very large -- a minimal repro would really help.

@agilgur5 agilgur5 removed problem/stale This has not had a response in some time problem/more information needed Not enough information has been provide to diagnose this issue. labels Jul 20, 2024
@agilgur5 agilgur5 changed the title workflow status stuck in Running workflow status stuck in Running occasionally (no repro) Jul 20, 2024
@tooptoop4
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maybe related to #12103

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