DataONE Tasks: Issueshttps://redmine.dataone.org/https://redmine.dataone.org/favicon.ico2019-06-19T02:03:44ZDataONE Tasks
Redmine Infrastructure - Story #8823 (New): Recent Apache and OpenSSL combinations break connectivity on ...https://redmine.dataone.org/issues/88232019-06-19T02:03:44ZDave Vieglaisdave.vieglais@gmail.com
<p>The latest Ubuntu 18.04 release of Apache is 2.4.29 and OpenSSL is 1.1.1.</p>
<p>This combination creates a significant delay in TLS renegotiation that results from the Apache config option on the CNs:</p>
<pre>SSLVerifyClient none
<Location "/cn">
<If " ! ( %{HTTP_USER_AGENT} =~ /(windows|chrome|mozilla|safari|webkit)/i )">
SSLVerifyClient optional
</If>
</Location>
</pre>
<p>Which is intended to disable client certificate authentication for web browsers, but allow it for others. This approach worked fine on older Apache / OpenSSL but the new combination creates a several second wait when the server discovers the client is not a web browser and tells it to reconnect with the option of including a client certificate.</p>
<p>The latest released version of Apache is 2.4.39 and this is available through a PPA intended for Debian developers. This has been installed so far on dev-2, sandbox, stage, and stage-2 with the process:</p>
<pre>sudo add-apt-repository ppa:ondrej/apache2
sudo apt update
sudo apt dist-upgrade
sudo systemctl restart apache2
</pre>
<p>This installs Apache 2.4.39 and OpenSSL 1.1.1c which appears to resolve the apparent bug in the 2.4.29 / 1.1.1 combination.</p>
<p>One issue with the update is that by default, Apache now offers TLSv1.3, which is great except that it appears to cause problems with at least Python clients failing to connect and getting a 403 error. For example:</p>
<pre>$ python3
>>> import requests
>>> r = requests.get("https://cn-sandbox-ucsb-1.test.dataone.org/cn/v2/monitor/ping")
>>> r.status_code
403
</pre>
<p>That TLSv1.3 is the problem was verified with cn-stage-unm-2 by configuring Apache with:</p>
<pre> SSLProtocol all -TLSv1.3 -SSLv2 -SSLv3
</pre>
<p>to disable TLSv1.3. After this change the Python client was able to connect as expected.</p>
<p>A workaround has not yet been researched.</p>
<p>It is not clear if this issue applies to other clients such as R and Java, so until we learn one way or the other, TLSv1.3 will be disabled on the CNs.</p>
<p>--This issue will likely apply to Member Nodes as well once TLSv1.3 is generally available or if MNs choose to install Apache 2.4.39.-- CORRECTION: this issue only applies when attempting to renegotiate TLS after headers have been transferred, so will not typically apply to a MN.</p>
Infrastructure - Story #8525 (In Progress): timeout exceptions thrown from Hazelcast disable sync...https://redmine.dataone.org/issues/85252018-03-27T22:36:54ZRob Nahfrnahf@epscor.unm.edu
<p>Very occasionally, synchronization disables itself when RuntimeExceptions bubble up. The most common of these is when the Hazelcast client seemingly disconnects, or can't complete an operation, and a java.util.concurrent.TimeoutException is thrown.</p>
<p>These are usually due to network problems, as evidenced by timeout exceptions appearing in both the Metacat hazelcast-storage.log files as well as d1-processing logs.</p>
<p>Temporary problems like this should be recoverable, and so a retry or bypass for those timeouts should be implemented. It's not clear whether or not a new HazelcastClient should be instantiated, or whether the same client is still usable. (Is the client tightly bound to a session, or does it recover?) If a new client is needed, preliminary searching through the code indicates that refactoring the HazelcastClientFactory.getProcessingClient() method is only used in a few places, and the singleton behavior it uses can be sidestepped by removing the method and replacing it with a getLock() wrapper method (that seems to be the dominant use case for it). See the newer SyncQueueFacade in d1_synchronization for guidance on that. If the client is never exposed, it can be refreshed as needed.</p>
<pre>root@cn-unm-1:/var/metacat/logs# grep FATAL hazelcast-storage.log.1
[FATAL] 2018-03-27 03:15:19,380 (BaseManager$2:run:1402) [64.106.40.6]:5701 [DataONE] Caught error while calling event listener; cause: [CONCURRENT_MAP_CONTAINS_KEY] Operation Timeout (with no response!): 0
</pre><pre>[ERROR] 2018-03-27 03:15:19,781 [ProcessDaemonTask1] (SyncObjectTaskManager:run:84) java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent
.TimeoutException: [CONCURRENT_MAP_REMOVE] Operation Timeout (with no response!): 0
java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.TimeoutException: [CONCURRENT_MAP_REMOVE] Operation Timeout (with no response!): 0
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.dataone.cn.batch.synchronization.SyncObjectTaskManager.run(SyncObjectTaskManager.java:76)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: java.util.concurrent.TimeoutException: [CONCURRENT_MAP_REMOVE] Operation Timeout (with no response!): 0
at com.hazelcast.impl.ClientServiceException.readData(ClientServiceException.java:63)
at com.hazelcast.nio.Serializer$DataSerializer.read(Serializer.java:104)
at com.hazelcast.nio.Serializer$DataSerializer.read(Serializer.java:79)
at com.hazelcast.nio.AbstractSerializer.toObject(AbstractSerializer.java:121)
at com.hazelcast.nio.AbstractSerializer.toObject(AbstractSerializer.java:156)
at com.hazelcast.client.ClientThreadContext.toObject(ClientThreadContext.java:72)
at com.hazelcast.client.IOUtil.toObject(IOUtil.java:34)
at com.hazelcast.client.ProxyHelper.getValue(ProxyHelper.java:186)
at com.hazelcast.client.ProxyHelper.doOp(ProxyHelper.java:146)
at com.hazelcast.client.ProxyHelper.doOp(ProxyHelper.java:140)
at com.hazelcast.client.QueueClientProxy.innerPoll(QueueClientProxy.java:115)
at com.hazelcast.client.QueueClientProxy.poll(QueueClientProxy.java:111)
at org.dataone.cn.batch.synchronization.type.SyncQueueFacade.poll(SyncQueueFacade.java:231)
at org.dataone.cn.batch.synchronization.tasks.SyncObjectTask.call(SyncObjectTask.java:131)
at org.dataone.cn.batch.synchronization.tasks.SyncObjectTask.call(SyncObjectTask.java:73)
</pre> Testing MN Management - Story #8463 (New): test: Testing & Developmenthttps://redmine.dataone.org/issues/84632018-03-01T21:04:41ZAmy Forresteraforres4@utk.edu
<p>Install or develop a functional member node to be registered to a non-production environment. </p>
Testing MN Management - Story #8352 (New): Move to Productionhttps://redmine.dataone.org/issues/83522018-02-08T15:28:13ZMonica Ihliemail@monicaihli.comTesting MN Management - Story #8347 (New): Testing & Developmenthttps://redmine.dataone.org/issues/83472018-02-08T15:28:11ZMonica Ihliemail@monicaihli.com
<p>Install or develop a functional member node to be registered to a non-production environment. </p>
Testing MN Management - Story #8343 (New): Planninghttps://redmine.dataone.org/issues/83432018-02-08T15:28:10ZMonica Ihliemail@monicaihli.com
<p>The repository and DataONE have agreed to proceed with deployment as a member node. Decisions will be made as to how to proceed with development. Node operators will receive training.</p>
Testing MN Management - Story #8340 (New): Discoveryhttps://redmine.dataone.org/issues/83402018-02-08T15:28:09ZMonica Ihliemail@monicaihli.com
<p>Discovery is about establishing contact and building a relationship with a potential new member node. In this phase, it is determined if DataONE and the repository are a good fit for one another and if the repository generally meets the requirements of DataONE member nodes. Broad discussions of deployment options may be reviewed as well.<br>
This story is complete when a determination is made to either proceed with planning a new deployment, or that joining DataONE is not an option for the repository at this time.</p>
Infrastructure - Story #8208 (New): Review and adjust memory allocated to d1-index-task-generator...https://redmine.dataone.org/issues/82082017-10-24T16:09:06ZDave Vieglaisdave.vieglais@gmail.com
<p>Configuration for these services is located at:<br>
<br>
/etc/default/d1-index-task-generator<br>
/etc/default/d1-index-task-processor</p>
<p>d1-index-task-generator is probably fine, however d1-index-task-processor may benefit from increased allocation especially for processing resource maps.</p>
Infrastructure - Story #8207 (New): review and adjust memory allocated to d1-processinghttps://redmine.dataone.org/issues/82072017-10-24T16:06:24ZDave Vieglaisdave.vieglais@gmail.com
<p>d1-processing settings are under @/etc/default/d1-processing@</p>
<p>Currently runs like: <br>
<br>
jsvc.exec -home /usr/lib/jvm/java-1.8.0-openjdk-amd64 -cp /usr/share/java/commons-daemon.jar:/usr/share/j<br>
ava/d1_process_daemon.jar -debug -outfile /var/log/dataone/daemon/d1-processing-jsvc.log -errfile /var/log/dataone/daemon/d1-process<br>
ing-jsvc.err -pidfile /var/run/d1-processing.pid -user tomcat7 -Djava.awt.headless=true -XX:UseParallelGC -Xmx4096M -Xms1024M -Xss12<br>
80k -XX:MaxPermSize=512M org.dataone.cn.batch.daemon.SchedulerDaemon</p>
Infrastructure - Story #8204 (New): Adjust memory allocation for services running under JVM on CNshttps://redmine.dataone.org/issues/82042017-10-24T15:29:28ZDave Vieglaisdave.vieglais@gmail.com
<p>Most services on CNs run in JVM instances, each with separate restrictions on memory use.</p>
<p>Current configurations were mostly based on defaults and have not changed much despite significantly higher memory use for systems such as Solr and Hazelcast.</p>
<p>The goal of this story is to evaluate the memory configuration of each JVM instance on the CNs and tune as necessary with the primary goal of avoiding out of memory errors, secondary goal is improving performance.</p>
<p>Note that with increased heap allocation, garbage collection may become a significant bottleneck, with application freeze in the order of several minutes possible or likely with higher heap allocations (e.g. 16GB)</p>
Infrastructure - Story #8173 (New): add checks for retrograde systemMetadata changeshttps://redmine.dataone.org/issues/81732017-09-01T19:42:33ZRob Nahfrnahf@epscor.unm.edu
<p>with the ability to prioritize and the introduction of parallelized index task processing, the effective queue is not guaranteed to be time-ordered. If there are two valid system metadata changes resulting in two tasks and the second change hits the index first, the earlier task should be rejected, as its changes are out of date.</p>
Infrastructure - Story #8049 (In Progress): Support synchronization of system metadata for unhost...https://redmine.dataone.org/issues/80492017-03-21T05:34:38ZRob Nahfrnahf@epscor.unm.edu
<p>As part of mutable-content MN support, allow the MemberNode to keep the system metadata records for all resultant versions of its changeable entities. this allows them to keep accurate system metadata for every version even though they do not have the object bytes anymore for that version.</p>
<p>Benefits:<br>
1. MN does not orphan any objects<br>
2. MN can administer objects from past versions on their own MN. Adjust the access policy of all versions, for example.<br>
3. don't need to call cn.setObsoletedBy or leave that field empty.</p>
<p>Costs:<br>
1. requires new logic for indexing (possibly)<br>
2. requires new logic for registerSystemMEtadata (possibly)<br>
3. require new logic for synchronization </p>
<p>very similar to how we synchronize DATA objects, but don't trigger MN replication.</p>
Member Nodes - Story #5833 (In Progress): GBIF: Developinghttps://redmine.dataone.org/issues/58332014-07-17T21:05:32ZRoger Dahldahl@unm.edu
<p>Determine which software stack to use, etc.</p>
Infrastructure - Story #4091 (New): ESRI GeoPortal MN stackhttps://redmine.dataone.org/issues/40912013-10-15T13:36:56ZBruce Wilsonbwilso27@utk.edu
<p>The objective is to design, develop, and implement a MN Stack to integrate with the ESRI GeoPortal server (<a href="http://www.esri.com/software/arcgis/geoportal">http://www.esri.com/software/arcgis/geoportal</a>).</p>
Infrastructure - Story #4052 (In Progress): OPeNDAP MN Storyhttps://redmine.dataone.org/issues/40522013-10-06T20:07:50ZBruce Wilsonbwilso27@utk.edu
<p>There are a large number of possible DataONE MN's running Data Access Protocol (DAP) compliant servers, particularly servers based on the OPeNDAP Hyrax and UCAR THREDDS servers. The objective of this work is to develop a MN stack that can be used with at least one of these DAP-compliant software stacks as a low-barrier route to becoming a Tier 1 MN.</p>