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Strange start/end time issue with quick-running dependent jobs #324

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sb10 opened this issue Jul 1, 2020 · 0 comments
Open

Strange start/end time issue with quick-running dependent jobs #324

sb10 opened this issue Jul 1, 2020 · 0 comments
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@sb10
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sb10 commented Jul 1, 2020

The following 2 jobs claim they started and ended in the same millisecond, and their output files had the same timestamp (but only to second accuracy). wr notes that the jobs took over 0.3s walltime, so clearly the reported start and end time are bogus. The concern is, did they actually run sequentially according to the dependency (1 is dependent on the other)?

[
  {
    "Key": "e248a45513c553563647f88a4490150f",
    "RepGroup": "28204-run_archival_in_progress",
    "DepGroups": [
      "run_archival_in_progress-28204-3489770802"
    ],
    "Dependencies": [
      "pipeline_start-28204-3486915445"
    ],
    "Cmd": "( npg_status2file --id_run 28204 --status \"archival in progress\" --dir_out /redacted ) 2>&1 | tee -a \"/redacted\"",
    "State": "complete",
    "Cwd": "/wr_cwd/e/2/4/8a45513c553563647f88a4490150f994389581/cwd",
    "CwdBase": "/tmp",
    "HomeChanged": false,
    "Behaviours": "{\"on_exit\":[{\"cleanup\":true}]}",
    "Mounts": "",
    "MonitorDocker": "",
    "ExpectedRAM": 2000,
    "ExpectedTime": 3600,
    "RequestedDisk": 0,
    "OtherRequests": [
      "rtimeout:1"
    ],
    "Cores": 0,
    "PeakRAM": 58,
    "PeakDisk": 0,
    "Exited": true,
    "Exitcode": 0,
    "FailReason": "",
    "Pid": 17523,
    "Host": "esa-analysis-20190114-server-ra6hafsqyxln",
    "HostID": "",
    "HostIP": "192.168.0.107",
    "Walltime": 0.384074345,
    "CPUtime": 0.366763,
    "Started": 1550143766,
    "Ended": 1550143766,
    "StdErr": "",
    "StdOut": "",
    "Env": null,
    "Attempts": 1,
    "Similar": 0
  },
  {
    "Key": "0921d0c35f7a38f4b61225c2aa2056cc",
    "RepGroup": "28204-run_qc_complete",
    "DepGroups": [
      "run_qc_complete-28204-3678272585"
    ],
    "Dependencies": [
      "run_run_archived-28204-3232308204"
    ],
    "Cmd": "( npg_status2file --id_run 28204 --status \"qc complete\" --dir_out /redacted ) 2>&1 | tee -a \"/redacted\"",
    "State": "complete",
    "Cwd": "/wr_cwd/0/9/2/1d0c35f7a38f4b61225c2aa2056cc159060972/cwd",
    "CwdBase": "/tmp",
    "HomeChanged": false,
    "Behaviours": "{\"on_exit\":[{\"cleanup\":true}]}",
    "Mounts": "",
    "MonitorDocker": "",
    "ExpectedRAM": 2000,
    "ExpectedTime": 3600,
    "RequestedDisk": 0,
    "OtherRequests": [
      "rtimeout:1"
    ],
    "Cores": 0,
    "PeakRAM": 59,
    "PeakDisk": 0,
    "Exited": true,
    "Exitcode": 0,
    "FailReason": "",
    "Pid": 13251,
    "Host": "esa-analysis-20190114-server-ra6hafsqyxln",
    "HostID": "",
    "HostIP": "192.168.0.107",
    "Walltime": 0.363033561,
    "CPUtime": 0.361349,
    "Started": 1550169077,
    "Ended": 1550169077,
    "StdErr": "",
    "StdOut": "",
    "Env": null,
    "Attempts": 1,
    "Similar": 0
  },
  {
    "Key": "851165b3bd805bfa2785dea1084affa5",
    "RepGroup": "28204-run_run_archived",
    "DepGroups": [
      "run_run_archived-28204-3232308204"
    ],
    "Dependencies": [
      "upload_fastqcheck_to_qc_database-28204-2674049854",
      "update_ml_warehouse-28204-1565627731"
    ],
    "Cmd": "( npg_status2file --id_run 28204 --status \"run archived\" --dir_out /redacted ) 2>&1 | tee -a \"/redacted\"",
    "State": "complete",
    "Cwd": "/wr_cwd/8/5/1/165b3bd805bfa2785dea1084affa5712177281/cwd",
    "CwdBase": "/tmp",
    "HomeChanged": false,
    "Behaviours": "{\"on_exit\":[{\"cleanup\":true}]}",
    "Mounts": "",
    "MonitorDocker": "",
    "ExpectedRAM": 2000,
    "ExpectedTime": 3600,
    "RequestedDisk": 0,
    "OtherRequests": [
      "rtimeout:1"
    ],
    "Cores": 0,
    "PeakRAM": 58,
    "PeakDisk": 0,
    "Exited": true,
    "Exitcode": 0,
    "FailReason": "",
    "Pid": 13245,
    "Host": "esa-analysis-20190114-server-ra6hafsqyxln",
    "HostID": "",
    "HostIP": "192.168.0.107",
    "Walltime": 0.393142191,
    "CPUtime": 0.363732,
    "Started": 1550169077,
    "Ended": 1550169077,
    "StdErr": "",
    "StdOut": "",
    "Env": null,
    "Attempts": 1,
    "Similar": 0
  }
]
@sb10 sb10 added the bug label Jul 1, 2020
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