We are testing a update to our app on a couple of qa instances 
(applications, not just JVMs) of AppEngine.  Both are getting 
DeadlineExceededException pretty often.  However, we have only a single user 
hitting the database and it has little data in it - basically, there is no 
contention for the database, but sometimes it simply does not respond. 
 Below is an example log.  You can see that we use JDO to emit a query for a 
single entity.  However, the datastore never responds.  We have the same 
exact code running on two different AppEngine applications.  One of them has 
instant-on enabled (so it has 3 instances running all the time) and the 
other does not (so it needs to spin up an instance relatively regularly). 
 We are using JDO and Restlet, but not Spring or Grooving or other packages 
that take a very long time to initialize (initializing a new instance takes 
our app about 7 seconds).  The very similar code on our live application 
seems to be fine - we are not seeing the same thing.  This makes me worry 
about deploying to live.  Is anyone else seeing this kind of behavior with 
the datastore?

Caused by: com.google.apphosting.api.DeadlineExceededException: This request 
(d5cf2cc1a60c6af7) started at 2011/03/17 22:49:48.468 UTC and was still 
executing at 2011/03/17 22:50:17.887 UTC.
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:502)
at com.google.apphosting.runtime.AsyncFuture.get(AsyncFuture.java:54)
at com.google.appengine.api.utils.FutureWrapper.get(FutureWrapper.java:67)
at com.google.appengine.api.utils.FutureWrapper.get(FutureWrapper.java:67)
at 
com.google.appengine.api.datastore.FutureHelper.getInternal(FutureHelper.java:71)
at 
com.google.appengine.api.datastore.FutureHelper.quietGet(FutureHelper.java:32)
at 
com.google.appengine.api.datastore.QueryResultsSourceImpl.loadMoreEntities(QueryResultsSourceImpl.java:69)
at 
com.google.appengine.api.datastore.QueryResultsSourceImpl.loadMoreEntities(QueryResultsSourceImpl.java:56)
at 
com.google.appengine.api.datastore.QueryResultIteratorImpl.ensureLoaded(QueryResultIteratorImpl.java:156)
at 
com.google.appengine.api.datastore.QueryResultIteratorImpl.hasNext(QueryResultIteratorImpl.java:65)
at 
org.datanucleus.store.appengine.query.RuntimeExceptionWrappingIterator.hasNext(RuntimeExceptionWrappingIterator.java:44)
at 
org.datanucleus.store.appengine.query.LazyResult.resolveAll(LazyResult.java:115)
at 
org.datanucleus.store.appengine.query.LazyResult.size(LazyResult.java:110)
at 
org.datanucleus.store.appengine.query.StreamingQueryResult.size(StreamingQueryResult.java:124)
at org.datanucleus.store.query.Query.executeQuery(Query.java:1508)
at org.datanucleus.store.query.Query.executeWithArray(Query.java:1371)
at org.datanucleus.jdo.JDOQuery.execute(JDOQuery.java:266)
at 
com.conceptualcalculations.model.Group.GroupMembershipDAO.testSecondaryKey(GroupMembershipDAO.java:185)
at 
com.conceptualcalculations.model.Group.GroupMembershipDAO.testSecondaryKey(GroupMembershipDAO.java:1)
at 
com.conceptualcalculations.persistence.JDOTemplate.innerGetBySecondaryKey(JDOTemplate.java:403)

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