Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-08-17T23:39:07ZEcoinformatics Redmine
Redmine Bug #5686 (New): datasets produced by archiveDataturbineDataToMetacat workflow show samples 'slid...https://projects.ecoinformatics.org/ecoinfo/issues/56862012-08-17T23:39:07ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Data sample times slowly increase, e.g. second by second, over time, instead of staying on expected markers. This makes for irregular, messy datasets. I would guess the problem lies with SPAN.</p>
<p>A dataset available here shows examples of this:<br /><a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&sessionid=&docid=doc.1345243176506661893.1&displaymodule=entity&entitytype=dataTable&entityindex=1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&sessionid=&docid=doc.1345243176506661893.1&displaymodule=entity&entitytype=dataTable&entityindex=1</a></p>
<p>Some example problematic changes found within:</p>
<p>timestamps data<br />2012-08-16 00:10:09 13.302116394<br />2012-08-16 00:10:39 13.302242279<br />[SNIP]<br />2012-08-16 02:46:09 13.295635223<br />2012-08-16 02:46:39 13.295513153<br />2012-08-16 02:47:10 13.295863152 # <== slip<br />2012-08-16 02:47:40 13.296142578<br />[SNIP]<br />2012-08-16 08:09:10 13.290791512<br />2012-08-16 08:09:40 13.290988922<br />2012-08-16 08:10:11 13.290698051 # <== slip<br />2012-08-16 08:10:41 13.290913582<br />...</p> Bug #5685 (New): data isn't always chunked properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/56852012-08-17T23:29:49ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Jing ran the workflow in Windows XP today, and it produced at least one datapackage with data from different sampling rates. See:<br /><a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&sessionid=&docid=doc.1345243176506661893.1&displaymodule=entity&entitytype=dataTable&entityindex=1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&sessionid=&docid=doc.1345243176506661893.1&displaymodule=entity&entitytype=dataTable&entityindex=1</a></p>
<p>Example change section from data from above link:</p>
<p>2012-08-16 22:18:14 13.28463459<br />2012-08-16 22:18:44 13.284519196<br />2012-08-16 22:19:14 13.284427643<br />2012-08-16 22:19:44 13.284352303<br />2012-08-16 22:20:19 13.284294128<br />2012-08-16 22:38:14 13.28584671<br />2012-08-16 22:38:15 13.28584671<br />2012-08-16 22:38:16 13.291329384</p>
<p>These were the results Jing got from the workflow for this particular sensor:</p>
<p>Sensor Name: gpp-data/CR800_Batt_Volt<br />Document URL: <a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243176506661893.1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243176506661893.1</a><br />Time Range: 2012-08-16 00:10:09 ~ 2012-08-16 22:38:32<br />Number of Records: 2680<br />Sensor Name: gpp-data/CR800_Batt_Volt<br />Document URL: <a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243308947314582.1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243308947314582.1</a><br />Time Range: 2012-08-16 22:38:34 ~ 2012-08-16 22:39:54<br />Number of Records: 75<br />Sensor Name: gpp-data/CR800_Batt_Volt<br />Document URL: <a class="external" href="http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243447776683166.1">http://dev2.nceas.ucsb.edu/knb/metacat?action=read&qformat=default&docid=doc.1345243447776683166.1</a><br />Time Range: 2012-08-16 22:39:55 ~ 2012-08-17 22:37:21<br />Number of Records: 8186</p> Bug #5684 (Resolved): Add warning to archiving workflow that it must be run on one machine to not...https://projects.ecoinformatics.org/ecoinfo/issues/56842012-08-17T23:23:20ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>See <a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5401">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5401</a></p> Bug #5683 (Resolved): archiveDataturbineDataToMetacat.kar can fail with an IOException on win7 an...https://projects.ecoinformatics.org/ecoinfo/issues/56832012-08-17T21:11:12ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>When trying to run the archival workflow on win7, I got this error. Jing got it today in XP.</p>
<p>ptolemy.kernel.util.IllegalActionException: Error: java.io.IOException: The filename, directory name, or volume label syntax is incorrect<br />in .archiveDataturbineDataToMetacat.GenerateEMLAndDataFile.CreateDataSets<br /> at org.kepler.actors.CreateDataSets.createFile(CreateDataSets.java:325)<br /> at org.kepler.actors.CreateDataSets.fire(CreateDataSets.java:234)<br /> at ptolemy.actor.process.ProcessThread.run(ProcessThread.java:229)</p> Bug #5681 (Resolved): Tracking bug for sensor-view-0.9.0 release testinghttps://projects.ecoinformatics.org/ecoinfo/issues/56812012-08-16T21:36:47ZDerik Barseghianbarseghian@nceas.ucsb.edu
I've already gone through a few rounds of testing on Mac 10.8 and Win7.<br />During the last round Jianwu, Dan, and Jing did some testing on linux. <br />Today I cut a new sensor-view-0.9.0 to fix workflow issues. In this current round I've done the usual sensor-view testing, and run all sensor-view and demo workflows successfully except:
<ul>
<li>Matlab workflows (Matlab's giving me license errors under 10.8: <a class="external" href="http://www.mathworks.com/support/solutions/en/data/1-17RCK/index.html?s_cid=pl_LME9_r2012a">http://www.mathworks.com/support/solutions/en/data/1-17RCK/index.html?s_cid=pl_LME9_r2012a</a>)</li>
<li>the web service and REST demos, which use a webservice that is 'temporarily' down.</li>
<li>those in the 'unsupported' dir.</li>
</ul>
<p>I'm going to test on Win7 and Ubuntu 10.04, and hope to release as is soon.</p>
<p>The last thing I think that needs doing is, if we don't want people working off trunk for these webapps, for Jing to tag a 'release' of the workflow runengine and scheduler, and update any docs to refer to those tags.</p> Bug #5679 (In Progress): the workflows in sensor-view should be resaved beneath sensor-view-0.9.0...https://projects.ecoinformatics.org/ecoinfo/issues/56792012-08-16T01:28:36ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Now that sensor-view-0.9.0's suite list is finalized, the sensor-view demo workflows should be saved beneath it instead of trunk. Verify dataturbine addresses used therein.</p>
<p>Move the archive workflow into demos too. Check if any documentation refers to its current path.</p> Bug #5678 (New): growingDegreeDays workflow at kepler repository has type resolve errorhttps://projects.ecoinformatics.org/ecoinfo/issues/56782012-08-15T23:27:54Zjianwu jianwujianwu@sdsc.edu
<p>After talking to Derik, reconfiguring the DT actor to use nibbler.nceas.ucsb.edu works for me. Derik said maybe more workflows in kepler repository need to be updated.</p> Bug #5675 (New): new ProgressMeter demo workflows give errors when opening in sensor-view-0.9.0https://projects.ecoinformatics.org/ecoinfo/issues/56752012-08-11T02:03:33ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>There are a few errors when opening these xml workflows beneath sensor-view-0.9.0, despite working in trunk, e.g.:</p>
<p>ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "init" into a container that already contains an object with that name.</p>
<p>Even though the workflow only contains one "init" PortParameter.</p>
<p>After a kepler restart, I was able to save a copy of this workflow from beneath sensor-view-0.9.0, and can then re-open this copy without error.</p>
<p>I don't know the cause. Maybe these momls will have to be resaved using sensor-view-0.9.0, and the outreach test-patch release recreated.</p> Bug #5583 (New): Sensor Simulator controllable through Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/55832012-03-30T03:32:16ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>To start the sensor simulator you must currently use ant to compile some classes and start it. This means a user would have to download source to use the simulator.</p>
<p>I propose creating a SensorSimulator actor that invokes the SpanSim (sensor simulator). I've tried this locally, and can get the simulator to start up from within Kepler using this actor. Stopping isn't working, and parameters (the usual simulator cmd line params) and actor documentation would have to be done too, but this seems like it could be a fairly easy solution.</p> Bug #5582 (New): DataTurbine server crashing the JREhttps://projects.ecoinformatics.org/ecoinfo/issues/55822012-03-29T03:19:05ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I don't think this is a Kepler bug but I want to record my notes somewhere:</p>
<p>I was able to get the DataTurbine server to crash the JRE around 10 times today. Sometimes the JRE would leave a log file, I submitted one to Sun. I was using DT 3.2b5 but moved to 3.2b6, but this didn't seem to help. Likewise I moved the client (Kepler DT actor) from 3.2b5 to 3.2b6, to no avail. I was able to crash the server using both Ubuntu w/ java 1.6.0_26-b03 and osX 10.6 w/ java 1.6.0_29-b11-402-10M3527. I'm in the process of doing some cleanup on the DT actor, but I verified these crashes would occur with none of the new changes. Generally the procedure was I'd run the growingDegreeDays workflow requesting 1 day of data. After about 6-10 iterations of this workflow in succession the server would crash.</p>
<p>This hasn't been well vetted but what seems to have "fixed" it is starting the server with a larger archiveSize -- I bumped from 500000 to 1000000. Recently I loaded a lot more data to the reap02 channels, so perhaps that's why this has only recently cropped up. I've now run the GDD workflow requesting <strong>100</strong> days of data 10 times, and no crash w/ the 3.2b6 DT server on my mac. I'm going to run a long stress test over night and see what happens.</p> Bug #5377 (New): DataTurbine actor fetch time outs (blockTimeout param not used?)https://projects.ecoinformatics.org/ecoinfo/issues/53772011-04-11T19:45:15ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Sometimes when attempting to connect to my gumstix DT server w/ the DT actor, I get a fetch timeout message, and no channels (i.e. no data output ports):</p>
<p>MC 12:33:02,094: [WARN]: WARNING: fetch timed out. Try increasing the blockTimeOut value [org.kepler.data.datasource.datasource.dataturbine.DataTurbine]<br />MC 12:33:02,095: [ERROR]: DataTurbine actor Error: only 0 channels were returned [org.kepler.data.datasource.datasource.dataturbine.DataTurbine]</p>
<p>The server does have channels and RDV 2.2.1 is sometimes able to show them in just 2-3 seconds. Increasing the blockTimeout actor parameter from 15s to higher doesn't seem to change anything - it still takes 15s before it times out. Either the actor is not using the parameter, or 15s is a max somewhere.</p> Bug #5363 (New): spanTodt performancehttps://projects.ecoinformatics.org/ecoinfo/issues/53632011-04-01T23:30:14ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>The spanTodt process is often hovering around 90% cpu usage on my gumstix (i'm currently sampling batt_volt every 5s, 2 other sensors every 30s, and we're still doing periodic (every 60s) metadata writes for each channel). I made logging pretty verbose, which probably isn't helping performance.<br />Would be good to improve this.</p> Bug #5341 (New): Belkin f5u409 usb=>serial dongle periodically stops workinghttps://projects.ecoinformatics.org/ecoinfo/issues/53412011-03-05T02:35:09ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Sometimes the Belkin dongle gets in a state where all 3 of its LEDs stay off. This corresponds with being unable to run cr1k_d over it. I'm not sure if this is the sole reason for bug#5332, or if that sometimes happens even when the lights are on.</p>
<p>When this state occurs, and you try to use cr1k_d, dmesg starts showing errors like:</p>
<p>usb 1-1: cr1k_d timed out on ep0out len=0/1<br />usb 1-1: Set MODEM CTRL 0xb failed (error = -110)<br />usb 1-1: cr1k_d timed out on ep0out len=0/1<br />usb 1-1: Set LINE CTRL 0x3 failed (error = -110)<br />usb 1-1: cr1k_d timed out on ep0in len=0/1<br />usb 1-1: Get MODEM STATus failed (error = -110)<br />usb 1-1: cr1k_d timed out on ep0out len=0/1</p>
<p>I've tried this procedure to see if I could get the dongle working again, but it didn't work:<br />lsmod | grep -i usb<br />sudo rmmod mct_u232; <br />lsmod | grep -i usb; <br />sudo modprobe mct_u232</p>
<p>Rebooting consistently makes it work again.</p>
<p>Nick recommends trying a Keyspan dongle, and updating from ubuntu 9.04 to 10.04 (new kernel, possible hardware fixes). <br />I'll try the dongle he recommends when I get a chance.</p> Bug #5210 (New): Focus stolen from user trying to drag components around during executionhttps://projects.ecoinformatics.org/ecoinfo/issues/52102010-10-19T20:42:35ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>When trying to drag around a component during a sensor site workflow execution, focus on the component is lost. This makes it nearly impossible to rearrange a workflow with sensors with high sampling rates.</p>
<p>Maybe this is related to how sensor actors update in the gui to show their last data points.</p> Bug #5202 (In Progress): update existing site layout with span changeshttps://projects.ecoinformatics.org/ecoinfo/issues/52022010-10-15T22:16:54ZDaniel Crawldanielcrawl@gmail.com
<p>An existing site layout should be updated with any changes performed on the SPAN server when the workflow is run. This makes sure the site layout always has the latest information about a site.</p>