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<p class="MsoPlainText">Mihael, I ran a few more experiments where I ran a workflow on a single cluster node while monitoring its memory use but I didn't see any issues with it running out of memory since at all times /proc/meminfo reported 22GB out of 24GB
free. I've now begun a more focused analysis where I have a simple script that captures the high-level structure of my real script. It first generates a bunch of files, producing additional temporary files and the directories along with the main output file.
These files are then reduced using a reduction tree based on the example you sent me. I have not yet gotten the simple script to fail in the same way as the main script but I've noticed a few oddities.
<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">First, although my sites file has <profile namespace="swift" key="stagingMethod">file</profile> and my cf file has use.provider.staging=true, I see that all the intermediate files produced by my tasks are written to the global file system
specified in the sites file as <workdirectory>/p/lscratche/bronevet/swift_work</workdirectory>. How do I force Swift to use node-local storage for this data?<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Second, when I run as many processes on the one node as there are cores, the script runs but it keeps stalling. As you can see below, it processes tasks in batches of 12. However, after a few batches the job is aborted (~6 mins into
a 30 min allocation) even though the node appears healthy and does not run out of memory and Swift submits a new job into the batch queue. Why does this happen?<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Swift 0.94.1 swift-r7114 cog-r3803<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">RunID: 20140528-1504-1ndui8r0<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:04:36 -0700<o:p></o:p></p>
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<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:04:45 -0700 Selecting site:4408 Submitting:3<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:05:06 -0700 Selecting site:4010 Submitted:401<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">...<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:15:06 -0700 Selecting site:4010 Submitted:401<o:p></o:p></p>
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<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:15:21 -0700 Selecting site:4010 Stage in:9 Submitted:392<o:p></o:p></p>
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<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:15:36 -0700 Selecting site:4010 Submitted:389 Active:12<o:p></o:p></p>
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<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:20:06 -0700 Selecting site:3998 Submitted:389 Active:12 Finished successfully:12<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:20:18 -0700 Selecting site:3998 Submitted:389 Active:11 Stage out:1 Finished successfully:12<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:20:19 -0700 Selecting site:3998 Submitted:389 Active:7 Stage out:5 Finished successfully:12<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:20:21 -0700 Selecting site:3998 Submitted:389 Stage out:11 Finished successfully:13<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:20:36 -0700 Selecting site:3986 Submitted:401 Finished successfully:24<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:21:06 -0700 Selecting site:3986 Submitted:401 Finished successfully:24<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:21:36 -0700 Selecting site:3986 Submitted:401 Finished successfully:24<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in"><b><span style="color:#C00000">… Batch allocation released, new request submitted …<o:p></o:p></span></b></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:22:06 -0700 Selecting site:3986 Submitted:401 Finished successfully:24<o:p></o:p></p>
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<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:25:16 -0700 Selecting site:3986 Submitted:389 Active:11 Stage out:1 Finished successfully:24<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:25:26 -0700 Selecting site:3986 Submitted:389 Active:7 Stage out:5 Finished successfully:24<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:25:27 -0700 Selecting site:3986 Submitted:389 Stage out:12 Finished successfully:24<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:25:29 -0700 Selecting site:3975 Stage in:2 Submitted:398 Stage out:1 Finished successfully:35<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:25:32 -0700 Selecting site:3975 Stage in:3 Submitted:397 Stage out:1 Finished successfully:35<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:25:34 -0700 Selecting site:3975 Stage in:4 Submitted:396 Stage out:1 Finished successfully:35<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:25:35 -0700 Selecting site:3974 Stage in:1 Submitting:1 Submitted:389 Active:10 Finished successfully:36<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:25:36 -0700 Selecting site:3974 Submitted:389 Active:12 Finished successfully:36<o:p></o:p></p>
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<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:29:01 -0700 Selecting site:3962 Submitted:389 Active:8 Stage out:4 Finished successfully:48<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:29:02 -0700 Selecting site:3955 Submitting:1 Submitted:395 Finished successfully:60<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:29:06 -0700 Selecting site:3950 Submitted:401 Finished successfully:60<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:29:36 -0700 Selecting site:3950 Submitted:401 Finished successfully:60<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:30:06 -0700 Selecting site:3950 Submitted:401 Finished successfully:60<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:30:36 -0700 Selecting site:3950 Submitted:401 Finished successfully:60<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in"><b><span style="color:#C00000">… Batch allocation released, new request submitted …<o:p></o:p></span></b></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:31:06 -0700 Selecting site:3950 Submitted:401 Finished successfully:60<o:p></o:p></p>
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<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:33:31 -0700 Selecting site:3938 Stage in:1 Submitted:400 Finished successfully:72<o:p></o:p></p>
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<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:34:06 -0700 Selecting site:3938 Submitted:389 Active:12 Finished successfully:72<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:34:36 -0700 Selecting site:3938 Submitted:389 Active:12 Finished successfully:72<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Progress: time: Wed, 28 May 2014 15:35:06 -0700 Selecting site:3938 Submitted:389 Active:12 Finished successfully:72<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in"><b><span style="color:#C00000">… Batch allocation released, new request submitted …<o:p></o:p></span></b></p>
<p class="MsoPlainText" style="margin-left:.5in"><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Greg Bronevetsky<o:p></o:p></p>
<p class="MsoPlainText">Lawrence Livermore National Lab<o:p></o:p></p>
<p class="MsoPlainText">(925) 424-5756<o:p></o:p></p>
<p class="MsoPlainText">bronevetsky@llnl.gov<o:p></o:p></p>
<p class="MsoPlainText">http://greg.bronevetsky.com<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">swift -sites.file /g/g15/bronevet/apps/swift-0.94.1/etc/sites.pbatch.sierra.tmp.xml -tc.file ~/code/tmp/sight/apps/linsolve/iml/tc.data -config /g/g15/bronevet/apps/swift-0.94.1/etc/cf.tmp -lazy.errors false ~/code/tmp/sight/apps/linsolve/iml/psuadeExperiments.swift
-precond=diag -matrix=nasa1824 -modelType=singleModel -resume psuadeExperiments-20140528-0007-gx1v1o8g.0.rlog<o:p></o:p></p>
<p class="MsoPlainText">Swift 0.94.1 swift-r7114 cog-r3803<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">RunID: 20140528-1001-vnifrjtf<o:p></o:p></p>
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<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:03:54 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:04:24 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:04:54 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:05:24 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:05:54 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:06:24 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:06:54 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:07:24 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:07:54 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:08:24 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:08:54 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:09:24 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:09:54 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:10:24 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:10:54 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:11:24 -0700 Selecting site:15348 Submitted:389 Active:12 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:11:27 -0700 Selecting site:15348 Submitted:388 Active:13 Finished in previous run:269<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:11:28 -0700 Selecting site:15324 Submitting:23 Submitted:366 Active:12 Finished in previous run:269 Failed but can retry:24<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:11:54 -0700 Selecting site:15324 Submitted:389 Active:12 Finished in previous run:269 Failed but can retry:24<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:12:12 -0700 Selecting site:15324 Submitted:388 Active:13 Finished in previous run:269 Failed but can retry:24<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:12:13 -0700 Selecting site:15300 Submitting:23 Submitted:366 Active:12 Finished in previous run:269 Failed but can retry:48<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:12:24 -0700 Selecting site:15300 Submitted:389 Active:12 Finished in previous run:269 Failed but can retry:48<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:12:54 -0700 Selecting site:15300 Submitted:389 Active:12 Finished in previous run:269 Failed but can retry:48<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:12:58 -0700 Selecting site:15300 Submitted:388 Active:13 Finished in previous run:269 Failed but can retry:48<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:12:59 -0700 Selecting site:15276 Submitting:23 Submitted:366 Active:12 Finished in previous run:269 Failed but can retry:72<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:13:24 -0700 Selecting site:15276 Submitted:389 Active:12 Finished in previous run:269 Failed but can retry:72<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:13:43 -0700 Selecting site:15276 Submitted:388 Active:13 Finished in previous run:269 Failed but can retry:72<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:13:44 -0700 Selecting site:15252 Submitting:23 Submitted:366 Active:12 Finished in previous run:269 Failed but can retry:96<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:13:54 -0700 Selecting site:15252 Submitted:389 Active:12 Finished in previous run:269 Failed but can retry:96<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:14:24 -0700 Selecting site:15252 Submitted:389 Active:12 Finished in previous run:269 Failed but can retry:96<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:14:28 -0700 Selecting site:15252 Submitted:388 Active:13 Finished in previous run:269 Failed but can retry:96<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:14:29 -0700 Selecting site:15228 Submitting:23 Submitted:366 Active:12 Finished in previous run:269 Failed but can retry:120<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:14:54 -0700 Selecting site:15228 Submitted:389 Active:12 Finished in previous run:269 Failed but can retry:120<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:15:14 -0700 Selecting site:15228 Submitted:388 Active:13 Finished in previous run:269 Failed but can retry:120<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:15:15 -0700 Selecting site:15204 Submitting:23 Submitted:366 Active:12 Finished in previous run:269 Failed but can retry:144<o:p></o:p></p>
<p class="MsoPlainText">Progress: time: Wed, 28 May 2014 10:15:24 -0700 Selecting site:15204 Submitted:389 Active:12 Finished in previous run:269 Failed but can retry:144<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">-----Original Message-----<br>
From: Mihael Hategan [mailto:hategan@mcs.anl.gov] <br>
Sent: Tuesday, May 27, 2014 4:46 PM<br>
To: Bronevetsky, Greg<br>
Cc: swift-user@ci.uchicago.edu<br>
Subject: Re: [Swift-user] Data transfer error</p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">On Tue, 2014-05-27 at 22:56 +0000, Bronevetsky, Greg wrote:<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">[...]<o:p></o:p></p>
<p class="MsoPlainText">> Progress: time: Tue, 27 May 2014 15:39:42 -0700 Selecting site:1268
<o:p></o:p></p>
<p class="MsoPlainText">> Stage in:30 Submitted:328 Active:31 Finished successfully:3 Failed
<o:p></o:p></p>
<p class="MsoPlainText">> but can retry:344<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">I would really suggest disabling lazy errors and execution retries until you get things to run.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">[...]<o:p></o:p></p>
<p class="MsoPlainText">> 2014/05/27 15:34:56.648 INFO 000000 1401230034461 Staging out /p/lscratche/bronevet/swift/work/psuadeExperiments-20140527-1533-6dt18a4b/jobs/1/runModel-1r0az8rl/wrapper.error (mode = 2).<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Right. It means something went wrong running the app on the compute node. That's a file that is used to send back the exact error.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">[...]<o:p></o:p></p>
<p class="MsoPlainText">> _swiftwrap.staging: line 45: echo: write error: No space left on
<o:p></o:p></p>
<p class="MsoPlainText">> device<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> However, I can’t see how this could be since each node has 16GB of RAM (available as RAM or ramdisk). Is there a way to look into this further?<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Swift doesn't have much in that direction. The wrapper logs should contain some diagnostic information for failing jobs, but if they fail due to lack of disk space, I can't see how the wrapper log can be written to.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">What I would suggest is wrapping your app in a script that looks into disk issues (df, ls), and running multiple apps on a single node and hopefully catching a glimpse of what the problem is before all scratch space is exhausted.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">I think it would be a nice idea to add some node status (mem/disk/cpu) monitors to the swift monitoring interfaces.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Mihael<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
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