https://issues.jalview.org/activityActivity Streams+00002024-03-29T15:05:12.278ZsourceJalview Discourseurn:uuid:6d66ad10-ae2e-3e56-8e65-b8d85af2f004<a href="https://builds.jalview.org/browse/JB-GTC-141">Jalview Builds &rsaquo; Getdown TESTING Channel &rsaquo; #141</a> &rsaquo; <a href="https://builds.jalview.org/browse/JB-GTC-JOB1-141">Default Job</a> <span class="stream-build-summary stream-build-success">was successful</span> Scheduled build, build took 5 minutes, <span class="stream-build-status stream-tests-none">no tests found</span> Anonymous Useranonymoushttp://activitystrea.ms/schema/1.0/person2024-03-29T00:20:24.935Z2024-03-29T00:20:24.935Zcom.atlassian.bamboohttp://streams.atlassian.com/syndication/verbs/bamboo/passurn:uuid:6d66ad10-ae2e-3e56-8e65-b8d85af2f004Default Jobhttp://streams.atlassian.com/syndication/types/joburn:uuid:6d66ad10-ae2e-3e56-8e65-b8d85af2f004Jalview Builds &rsaquo; Getdown TESTING Channel &rsaquo; #141http://streams.atlassian.com/syndication/types/build+0000https://builds.jalview.org/activity?use-accept-lang=true&authOnly=true&local=true&maxResults=10Activity Stream for all projects+0000Activity for Bamboo2024-03-29T00:20:24.935Zurn:uuid:a221fa5b-0602-3e35-91f7-568ce6da3de0<a href="https://builds.jalview.org/browse/JB-GTC-140">Jalview Builds &rsaquo; Getdown TESTING Channel &rsaquo; #140</a> &rsaquo; <a href="https://builds.jalview.org/browse/JB-GTC-JOB1-140">Default Job</a> <span class="stream-build-summary stream-build-success">was successful</span> Scheduled build, build took 4 minutes, <span class="stream-build-status stream-tests-none">no tests found</span> Anonymous Useranonymoushttp://activitystrea.ms/schema/1.0/person2024-03-28T00:19:39.002Z2024-03-28T00:19:39.002Zcom.atlassian.bamboohttp://streams.atlassian.com/syndication/verbs/bamboo/passurn:uuid:a221fa5b-0602-3e35-91f7-568ce6da3de0Default Jobhttp://streams.atlassian.com/syndication/types/joburn:uuid:a221fa5b-0602-3e35-91f7-568ce6da3de0Jalview Builds &rsaquo; Getdown TESTING Channel &rsaquo; #140http://streams.atlassian.com/syndication/types/build+0000https://builds.jalview.org/activity?use-accept-lang=true&authOnly=true&local=true&maxResults=10Activity Stream for all projects+0000Activity for Bamboo2024-03-29T00:20:24.935Zurn:uuid:ea646ce4-5e52-3d73-aeb5-da6a2156e8e1<a href="https://issues.jalview.org/secure/ViewProfile.jspa?name=morellthomas" class="activity-item-user activity-item-author">Thomas Morell</a> changed the Priority to 'Major' on <a href="https://issues.jalview.org/browse/JAL-4390">JAL-4390 - PairwiseAlignPanel running out of heap space</a> Thomas Morellhttps://issues.jalview.org/secure/ViewProfile.jspa?name=morellthomasmorellthomashttp://activitystrea.ms/schema/1.0/person2024-03-26T13:11:50.483Z2024-03-26T13:11:50.483Zcom.atlassian.jirahttp://activitystrea.ms/schema/1.0/updateurn:uuid:03075130-6523-30ea-8820-e40c5559dcbaJAL-4390PairwiseAlignPanel running out of heap spacehttp://streams.atlassian.com/syndication/types/issue+0000urn:uuid:a5a7f045-2955-3c44-a61a-0c65288bc7ea<a href="https://issues.jalview.org/secure/ViewProfile.jspa?name=morellthomas" class="activity-item-user activity-item-author">Thomas Morell</a> updated 2 fields of <a href="https://issues.jalview.org/browse/JAL-4390">JAL-4390 - PairwiseAlignPanel running out of heap space</a> <ul class="updates activity-list"> <li>Changed the Priority to 'Minor' <li>Updated the Urgency </ul> Thomas Morellhttps://issues.jalview.org/secure/ViewProfile.jspa?name=morellthomasmorellthomashttp://activitystrea.ms/schema/1.0/person2024-03-26T13:11:40.001Z2024-03-26T13:11:40.001Zcom.atlassian.jirahttp://activitystrea.ms/schema/1.0/updateurn:uuid:03075130-6523-30ea-8820-e40c5559dcbaJAL-4390PairwiseAlignPanel running out of heap spacehttp://streams.atlassian.com/syndication/types/issue+0000urn:uuid:f6bf0464-a4e8-3702-9370-5be3268b509d<a href="https://builds.jalview.org/browse/JB-GPC518-1">Jalview Builds &rsaquo; Getdown Plan Channel &rsaquo; <span class="icon icon-branch"/> spike-JAL-4047-JAL-4048_columns_in_sequenceID &rsaquo; #1</a> &rsaquo; <a href="https://builds.jalview.org/browse/JB-GPC518-JOB1-1">Default Job</a> <span class="stream-build-summary stream-build-success">was successful</span> Manual build by <a class="activity-item-user activity-item-author" href="https://builds.jalview.org/browse/user/jprocter">James Procter</a>, build took 1 minute, <span class="stream-build-status stream-tests-none">no tests found</span> James Procterjprocter@dundee.ac.ukhttps://builds.jalview.org/browse/user/jprocterjprocterhttp://activitystrea.ms/schema/1.0/person2024-03-22T21:03:51.297Z2024-03-22T21:03:51.297Zcom.atlassian.bamboohttp://streams.atlassian.com/syndication/verbs/bamboo/passurn:uuid:f6bf0464-a4e8-3702-9370-5be3268b509dDefault Jobhttp://streams.atlassian.com/syndication/types/joburn:uuid:f6bf0464-a4e8-3702-9370-5be3268b509dJalview Builds &rsaquo; Getdown Plan Channel &rsaquo; <span class="icon icon-branch"/> spike-JAL-4047-JAL-4048_columns_in_sequenceID &rsaquo; #1http://streams.atlassian.com/syndication/types/build+0000https://builds.jalview.org/activity?use-accept-lang=true&authOnly=true&local=true&maxResults=10Activity Stream for all projects+0000Activity for Bamboo2024-03-29T00:20:24.935Zurn:uuid:5828adfd-1409-3eff-a44c-20c236cedd2a<a href="https://issues.jalview.org/secure/ViewProfile.jspa?name=jprocter" class="activity-item-user activity-item-author">James Procter</a> created a link from <a href="https://issues.jalview.org/browse/JAL-4047" class="issue-link">JAL-4047 - Pfaat-style interactive annotation and display capabilities</a> to <a href="https://builds.jalview.org/browse/JB-GPC518/latest" class="issue-link">Jalview Builds › Getdown Plan Channel › spike-JAL-4047-JAL-4048_columns_in_sequenceID</a> (Jalview Bamboo)James Procterhttps://issues.jalview.org/secure/ViewProfile.jspa?name=jprocterjprocterhttp://activitystrea.ms/schema/1.0/person2024-03-22T21:01:11.713Z2024-03-22T21:01:11.713Zcom.atlassian.jirahttp://activitystrea.ms/schema/1.0/updateurn:uuid:54e71349-68d8-3e06-82a1-7d084e0ce113JAL-4047Pfaat-style interactive annotation and display capabilitieshttp://streams.atlassian.com/syndication/types/issue+0000urn:uuid:5bb09671-634b-31f2-8200-0002e1a78d11<a href="https://issues.jalview.org/secure/ViewProfile.jspa?name=jprocter" class="activity-item-user activity-item-author">James Procter</a> closed <a href="https://issues.jalview.org/browse/JAL-4391"><span class='resolved-link'>JAL-4391</span> - Job details &amp; Memory</a> <blockquote> Hi Xiang Cai - we had some issues with our cluster, so Jalview's multiple alignment services were not working as expected.<br> <br> We think everything is back to normal now - let me know if there are still problems. </blockquote> James Procterhttps://issues.jalview.org/secure/ViewProfile.jspa?name=jprocterjprocterhttp://activitystrea.ms/schema/1.0/person2024-03-21T01:01:57.830Z2024-03-21T01:01:57.830Zcom.atlassian.jirahttp://activitystrea.ms/schema/1.0/updatehttp://streams.atlassian.com/syndication/verbs/jira/transitionhttp://streams.atlassian.com/syndication/verbs/jira/closeurn:uuid:76d636a9-de87-3a06-b764-5315b13846afJAL-4391Job details & Memoryhttp://streams.atlassian.com/syndication/types/issue+0000urn:uuid:76d636a9-de87-3a06-b764-5315b13846af<a href="https://issues.jalview.org/secure/ViewProfile.jspa?name=xiangcai" class="activity-item-user activity-item-author">xiangcai</a> created <a href="https://issues.jalview.org/browse/JAL-4391"><span class='resolved-link'>JAL-4391</span> - Job details &amp; Memory</a> <div class="user-content"> Hello, The process of using jalview has been very smooth and pleasant lately. However, today when I tried to do a comparison, the software kept prompting me with this error:<br> Job details<br> Failed to submit sequences for alignment.<br> It is most likely that <a class="content-more" href="https://issues.jalview.org/browse/JAL-4391">Read more</a></div> <div class="user-content"> Hello, The process of using jalview has been very smooth and pleasant lately. However, today when I tried to do a comparison, the software kept prompting me with this error:<br> Job details<br> Failed to submit sequences for alignment.<br> It is most likely that there is a problem with the server.<br> Just close the window<br> After checking past Q&amp;A's on the forum, I'm guessing this might be a server memory issue with your company (I'm not very knowledgeable about these things), so I'm hoping you can solve my problem, thank you!<br> Your software has been a very big help to me, again my thanks! </div> xiangcaihttps://issues.jalview.org/secure/ViewProfile.jspa?name=xiangcaixiangcaihttp://activitystrea.ms/schema/1.0/person2024-03-20T10:37:31.000Z2024-03-20T10:37:31.000Zcom.atlassian.jirahttp://activitystrea.ms/schema/1.0/posturn:uuid:76d636a9-de87-3a06-b764-5315b13846afJAL-4391Job details & Memoryhttp://streams.atlassian.com/syndication/types/issue+0000urn:uuid:03075130-6523-30ea-8820-e40c5559dcba<a href="https://issues.jalview.org/secure/ViewProfile.jspa?name=morellthomas" class="activity-item-user activity-item-author">Thomas Morell</a> created <a href="https://issues.jalview.org/browse/JAL-4390">JAL-4390 - PairwiseAlignPanel running out of heap space</a> <div class="user-content"> Java runs out of heap space when performing a pairwise alignment of 340 sequences or more, seemingly due to creating too many AlignSeq objects.<br> <br> Is there a way to get around this?<br> I have tried initialising an AlignSeq prior to the main loop and <a class="content-more" href="https://issues.jalview.org/browse/JAL-4390">Read more</a></div> <div class="user-content"> Java runs out of heap space when performing a pairwise alignment of 340 sequences or more, seemingly due to creating too many AlignSeq objects.<br> <br> Is there a way to get around this?<br> I have tried initialising an AlignSeq prior to the main loop and re-using the object with its seqInit method. This makes it incredibly slow and it was not able to finish this in any feasible time. I have also tried splitting the Alignment internally into smaller groups, align those and all combinations of them to not have one big PairwiseAlignPanel, but that only crashed during the 340th. </div> Thomas Morellhttps://issues.jalview.org/secure/ViewProfile.jspa?name=morellthomasmorellthomashttp://activitystrea.ms/schema/1.0/person2024-03-20T08:15:24.000Z2024-03-20T08:15:24.000Zcom.atlassian.jirahttp://activitystrea.ms/schema/1.0/posturn:uuid:03075130-6523-30ea-8820-e40c5559dcbaJAL-4390PairwiseAlignPanel running out of heap spacehttp://streams.atlassian.com/syndication/types/issue+0000urn:uuid:ae1eca73-27b7-3e61-8208-e91dda0ebb9b<a href="https://builds.jalview.org/browse/JB-GDB577-1">Jalview Builds &rsaquo; Gradle Develop Build &rsaquo; <span class="icon icon-branch"/> bug-JAL-4389-web-services-prefs-panel &rsaquo; #1</a> &rsaquo; <a href="https://builds.jalview.org/browse/JB-GDB577-JOB1-1">Clover and Tests</a> <span class="stream-build-summary stream-build-success">was successful</span> Initial clean build, build took 5 minutes, <span class="stream-build-status stream-tests-passed">1,706 tests passed</span> Anonymous Useranonymoushttp://activitystrea.ms/schema/1.0/person2024-03-15T17:21:50.560Z2024-03-15T17:21:50.560Zcom.atlassian.bamboohttp://streams.atlassian.com/syndication/verbs/bamboo/passurn:uuid:ae1eca73-27b7-3e61-8208-e91dda0ebb9bClover and Testshttp://streams.atlassian.com/syndication/types/joburn:uuid:ae1eca73-27b7-3e61-8208-e91dda0ebb9bJalview Builds &rsaquo; Gradle Develop Build &rsaquo; <span class="icon icon-branch"/> bug-JAL-4389-web-services-prefs-panel &rsaquo; #1http://streams.atlassian.com/syndication/types/build+0000https://builds.jalview.org/activity?use-accept-lang=true&authOnly=true&local=true&maxResults=10Activity Stream for all projects+0000Activity for Bamboo2024-03-29T00:20:24.935Z