[Swift-user] Channel Timeout on Beagle?

Matthew Shaxted Matthew.Shaxted at som.com
Fri May 29 13:19:04 CDT 2015 

Thanks Mike - running on local filesystem makes a lot of sense. Will give this a try as well.

MATTHEW SHAXTED
SKIDMORE, OWINGS & MERRILL LLP
224 SOUTH MICHIGAN AVENUE
CHICAGO, IL 60604
T  (312) 360-4368
MATTHEW.SHAXTED at SOM.COM<mailto:MATTHEW.SHAXTED at SOM.COM>

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The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited and may be unlawful. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

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From: Michael Wilde [mailto:wilde at anl.gov]
Sent: Friday, May 29, 2015 11:41 AM
To: Matthew Shaxted; Swift User
Subject: Re: [Swift-user] Channel Timeout on Beagle?

Matthew,

You should consider using Swift 0.96.0, and to the extent possible use local filesystems instead of the shared filesystem, which is often under excessive load.

We can discuss how to do this in subsequent followup as needed.  Basically, try provider-staging, and put both the input data on the login node's local filesystem, and the site workdirectory under /dev/shm or /tmp. (You may need to probe the compute node as to which of these is writable and has sufficient space).

- Mike
On 5/29/15 10:39 AM, Matthew Shaxted wrote:
It looks like the timeout problem is not solved actually. For some reason I am having much difficulty running on Beagle, and I have an feeling it is due to slow read/write.

For example, I finished ~1,200 / 12,000 runs before failure (see below paragraph) and moving these results (of not very large result files) to the public_html is taking an hour or so. I'm hoping to scale up to 100-300k runs or so, thus this will become a significant bottleneck. I have emailed beagle-support about this issue just now.

In all test environments my Swift workflow is working well, but when submitting jobs to Beagle queue, it completes some number of simulations before the timeout error occurs and all jobs stop. I'm using Swift-0.95-RC7 (and am in process of updating to 0.95 latest), but think these errors may also be due to this slow read/write.

Any suggestions?

Below is the error I see and the job completely stops:

Host: cluster
Directory: epsweep-run004/jobs/a/RunEP-ai2mic9m  exception @ swift-int-staging.k, line: 181
Caused by: exception @ swift-int-staging.k, line: 177
Caused by: Block task failed: Connection to worker lost
org.globus.cog.coaster.TimeoutException: Channel timed out. lastTime=150526-142313.128,
50526-142514.107, channel=TCPChannel [type: server, contact: 0526-0802460-000014-000456
at org.globus.cog.coaster.channels.AbstractCoasterChannel.checkTimeouts(AbstractCoasterChannel.java:133)
        at org.globus.cog.coaster.channels.AbstractCoasterChannel$1.run(AbstractCoasterChannel.java:124)
        at java.util.TimerThread.mainLoop(Timer.java:566)
        at java.util.TimerThread.run(Timer.java:516)


MATTHEW SHAXTED
SKIDMORE, OWINGS & MERRILL LLP
224 SOUTH MICHIGAN AVENUE
CHICAGO, IL 60604
T  (312) 360-4368
MATTHEW.SHAXTED at SOM.COM<mailto:MATTHEW.SHAXTED at SOM.COM>

[cid:image003.png at 01D09A12.0897A870]<http://www.som.com/>
The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited and may be unlawful. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

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From: Matthew Shaxted
Sent: Wednesday, May 27, 2015 2:04 PM
To: 'Swift User'
Subject: RE: Channel Timeout on Beagle?

Hi All: I was able to get the runs working successfully by changing the maxtime flag in the sites file.

Thanks


From: Matthew Shaxted
Sent: Wednesday, May 27, 2015 9:50 AM
To: Swift User
Subject: Channel Timeout on Beagle?

Hi Swift Users:

I am running some studies on Beagle using Swift, and experiencing a strange error. The Swift scripts run great on cloud and on the Beagle login node, but seems to be timing out for some reason.

Does anyone have insight into the cause of this? Thanks for any help.

Below is the error I am getting:

Host: cluster
Directory: epsweep-run004/jobs/a/RunEP-ai2mic9m  exception @ swift-int-staging.k, line: 181
Caused by: exception @ swift-int-staging.k, line: 177
Caused by: Block task failed: Connection to worker lost
org.globus.cog.coaster.TimeoutException: Channel timed out. lastTime=150526-142313.128,
50526-142514.107, channel=TCPChannel [type: server, contact: 0526-0802460-000014-000456
at org.globus.cog.coaster.channels.AbstractCoasterChannel.checkTimeouts(AbstractCoasterChannel.java:133)
        at org.globus.cog.coaster.channels.AbstractCoasterChannel$1.run(AbstractCoasterChannel.java:124)
        at java.util.TimerThread.mainLoop(Timer.java:566)
        at java.util.TimerThread.run(Timer.java:516)

Below is my sites.xml file:

<pool handle="cluster">
    <execution provider="coaster" jobmanager="local:pbs" />
    <profile namespace="globus" key="project">CI-SES000178</profile>
    <profile namespace="globus" key="jobsPerNode">24</profile>
    <profile namespace="globus" key="lowOverAllocation">100</profile>
    <profile namespace="globus" key="highOverAllocation">100</profile>
    <profile namespace="globus" key="providerAttributes">pbs.aprun;pbs.mpp;depth=24</profile>
    <profile namespace="globus" key="maxtime">10800</profile>
    <profile namespace="globus" key="maxWalltime">01:25:00</profile>
    <profile namespace="globus" key="userHomeOverride">/lustre/beagle2/mattshax/epsweep/swifthome</profile>
    <profile namespace="globus" key="slots">20</profile>
    <profile namespace="globus" key="maxnodes">600</profile>
    <profile namespace="globus" key="nodeGranularity">1</profile>
    <profile namespace="karajan" key="jobThrottle">180</profile>
    <profile namespace="karajan" key="initialScore">10000</profile>
    <!-- <profile namespace="karajan" key="workerLoggingLevel">trace</profile> -->
    <workdirectory>/dev/shm/mattshax/swiftapp</workdirectory>
  </pool>


MATTHEW SHAXTED
SKIDMORE, OWINGS & MERRILL LLP
224 SOUTH MICHIGAN AVENUE
CHICAGO, IL 60604
T  (312) 360-4368
MATTHEW.SHAXTED at SOM.COM<mailto:MATTHEW.SHAXTED at SOM.COM>

[cid:image003.png at 01D09A12.0897A870]<http://www.som.com/>
The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited and may be unlawful. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

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--

Michael Wilde

Mathematics and Computer Science          Computation Institute

Argonne National Laboratory               The University of Chicago
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