Help with Error: PANIC: fatal region error detected; run recovery

Question

Here's what I'm trying to do:
I am trying to us BDBXML in a webapp using tomcat 5.5. I have a class that is responsible for opening and closing the db. This class is accessed by a servlet for some AJAX RCP stuff and it also serves as an access point for a Web Service (Apache Axis). This class looks like this:
public class DG implements Serializable {
private javax.xml.datatype.DatatypeFactory datatypeFactory;
private Environment environment;
private EnvironmentConfig environmentConf;
private XmlContainer xmlContainer = null;
private XmlManager xmlManager = null;
private XmlManagerConfig xmlManagerConfig;
public DG() {
try {
File envHome = new File("C:\\bdbxml\\database");
environmentConf = new EnvironmentConfig();
environmentConf.setAllowCreate(true);
environmentConf.setInitializeCache(true);
environmentConf.setInitializeLocking(true);
environmentConf.setInitializeLogging(true);
environmentConf.setRunRecovery(true);
environmentConf.setTransactional(true);
environmentConf.setLockDetectMode(LockDetectMode.MINWRITE);
     //tried the following with default and 10000
     environmentConf.setMaxLockers(100000);
environmentConf.setMaxLockObjects(100000);
environmentConf.setMaxLocks(100000);
environmentConf.setTxnMaxActive(100000);
environment = new Environment(envHome, environmentConf);
CheckpointConfig cpc = new CheckpointConfig();
cpc.setKBytes(500);
environment.checkpoint(cpc);
xmlManagerConfig = new XmlManagerConfig();
xmlManagerConfig.setAdoptEnvironment(true);
xmlManager = new XmlManager(environment, xmlManagerConfig);
XmlContainerConfig xmlContainerConfig = new XmlContainerConfig();
xmlContainerConfig.setIndexNodes(true);
xmlContainerConfig.setTransactional(true);
xmlContainerConfig.setNodeContainer(true);
xmlContainer = xmlManager.openContainer("container.dbxml", xmlContainerConfig);
xmlContainer.sync();
datatypeFactory = javax.xml.datatype.DatatypeFactory.newInstance();
} catch (FileNotFoundException e) {
     e.printStackTrace();
} catch (DatabaseException e) {
     e.printStackTrace();
} catch (DatatypeConfigurationException e) {
     e.printStackTrace();
public void close() {
try {
if (xmlContainer != null) {
xmlContainer.close();
if (xmlManager != null) {
xmlManager.close();
} catch (DatabaseException e) {
e.printStackTrace();
public String getDocument(String docId) {
try {
XmlDocument doc = xmlContainer.getDocument(docId);
String docString = doc.getContentAsString();
doc.delete();
return docString;
} catch (XmlException e) {
e.printStackTrace();
public Result[] search(Search search) {
try {
     //normally I construct the query string using the Search object
StringBuffer q = new StringBuffer("subsequence(collection('container.dbxml')/metadata[contains(./idinfo//title, 'Ecology')], 1,10)");
XmlQueryContext xqc = xmlManager.createQueryContext();
XmlQueryExpression xqe = xmlManager.prepare(q.toString(), xqc);
XmlResults xr = xqe.execute(xqc);
int i = 0;
Vector<Result> vec = new Vector<Result>();
while (xr.hasNext()) {
XmlValue xv = xr.next();
XmlDocument xd = xv.asDocument();
Result r = new Result();
r.setMetadata(xd.getContentAsString());
r.setDocumentId(xd.getName());
XmlValue groupVal = new XmlValue(XmlValue.STRING);
xd.getMetaData("", "group", groupVal);
r.setGroup(groupVal.asString());
XmlValue ownerVal = new XmlValue(XmlValue.STRING);
xd.getMetaData("", "owner", ownerVal);
r.setOwner(ownerVal.asString());
XmlValue createdVal = new XmlValue(XmlValue.DATE_TIME);
xd.getMetaData("", "created", createdVal);
r.setCreated(createdVal.asString());
XmlValue updatedVal = new XmlValue(XmlValue.DATE_TIME);
xd.getMetaData("", "updated", updatedVal);
r.setModified(updatedVal.asString());
r.setPosition(search.getStartPosition() + i);
updatedVal.delete();
createdVal.delete();
ownerVal.delete();
groupVal.delete();
xd.delete();
xv.delete();
vec.add(r);
i++;
xr.delete();
xqe.delete();
xqc.delete();
return vec.toArray(new Result[vec.size()]);
} catch (XmlException e) {
e.printStackTrace();
// PLUS SOME OTHER METHODS, BUT USING ONLY THESE TO TEST
The Servlet looks like this:
public class DGServlet extends javax.servlet.http.HttpServlet implements javax.servlet.Servlet {
private DG dg;
private final XPathFactory xpf = XPathFactory.newInstance();
private final XPath xp = xpf.newXPath();
private final SimpleDateFormat df = new SimpleDateFormat("EEE MMM d HH:mm:ss z yyyy");
public DGServlet() {
super();
@Override
public void destroy() {
try {
dg.close();
} catch (Exception e) {
log(e.getMessage());
e.printStackTrace();
super.destroy();
protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
String action = request.getParameter("action");
if (action != null && !action.equals("")) {
if (action.equals("search")) {
response.setContentType("text/xml");
Result[] result = null;
try {
result = dg.search(constructSearch(request));
} catch (Exception e1) {
log(e1.getMessage());
e1.printStackTrace();
if (result==null || result.length==0) {
response.getWriter().print("0");
return;
StringBuffer sb = new StringBuffer("<results>");
for (int i = 0; result != null && i < result.length; i++) {
try {
sb.append("<result"
+ " title='"
+ xp.evaluate("/metadata/idinfo//title", new InputSource(new StringReader(result[i]
.getMetadata()))));
sb.append("' northbc='"
+ xp.evaluate("//northbc", new InputSource(new StringReader(result.getMetadata())))
+ "' southbc='"
+ xp.evaluate("//southbc", new InputSource(new StringReader(result[i].getMetadata())))
+ "' eastbc='"
+ xp.evaluate("//eastbc", new InputSource(new StringReader(result[i].getMetadata())))
+ "' westbc='"
+ xp.evaluate("//westbc", new InputSource(new StringReader(result[i].getMetadata())))
+ "' docid='" + result[i].getDocumentId() + "' group='" + result[i].getGroup()
+ "' owner='" + result[i].getOwner() + "' position='" + result[i].getPosition()
+ "' modified='" + result[i].getModified() + "' created='" + result[i].getCreated()
+ "'>");
NodeList nodes = (NodeList) xp.evaluate("//digform", new InputSource(new StringReader(result[i]
.getMetadata())), XPathConstants.NODESET);
for (int j = 0; j < nodes.getLength(); j++) {
sb.append("<resource download='"
+ StringEscapeUtils.escapeXml(xp.evaluate("//networkr", new InputSource(
new StringReader(XMLUtil.printDOMTree(nodes.item(j)))))));
sb.append("' format='"
+ StringEscapeUtils.escapeXml(xp.evaluate("//formname", new InputSource(
new StringReader(XMLUtil.printDOMTree(nodes.item(j)))))));
sb.append("'></resource>");
sb.append("</result>");
} catch (XPathExpressionException e) {
e.printStackTrace();
log(e.getMessage());
} catch (TransformerConfigurationException e) {
e.printStackTrace();
log(e.getMessage());
} catch (TransformerFactoryConfigurationError e) {
e.printStackTrace();
log(e.getMessage());
} catch (TransformerException e) {
e.printStackTrace();
log(e.getMessage());
sb.append("</results>");
response.getWriter().print(sb.toString());
else if (action.equals("details")) {
response.setContentType("text/html");
String str = "";
try {
str = dg.getDocument(request.getParameter("docId"));
response.getWriter().print(
setTranslatePage(str, new java.net.URL(
"http://localhost:8080/datastream/stylesheets/fgdc/fgdc_classic.xsl")));
} catch (Exception e) {
e.printStackTrace();
log(e.getMessage());
public void init() throws ServletException {
super.init();
dg = new DG();
It seems to work fine for a while, but then I get errors like the following:
PANIC: fatal region error detected; run recovery
PANIC: fatal region error detected; run recovery
PANIC: fatal region error detected; run recovery
PANIC: fatal region error detected; run recovery
PANIC: fatal region error detected; run recovery
PANIC: fatal region error detected; run recovery
PANIC: fatal region error detected; run recovery
PANIC: fatal region error detected; run recovery
PANIC: fatal region error detected; run recovery
com.sleepycat.dbxml.XmlException: Error: DB_RUNRECOVERY: Fatal error, run database recovery, errcode = DATABASE_ERROR
at com.sleepycat.dbxml.dbxml_javaJNI.XmlManager_prepare__SWIG_0(Native Method)
at com.sleepycat.dbxml.XmlManager.prepare(XmlManager.java:586)
at edu.washington.cev.datastream.api.DG.search(DG.java:935)
at edu.washington.cev.datastream.servlets.DGServlet.doGet(DGServlet.java:83)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:619)
I've set this up on a Window XP machine using tomcat 5.5 and java 5 as well as a Redhat Linux machine with tomcat 5.5 and java 5. I'm using the Web Service point for other servers to access the database. Everything starts up and runs for a little while, but I can't seem to pin down what causes the errors. I've run recovery multiple times as well as started new databases. Any help is appreciated.

Answer 1

There's a bug in your use of DB XML somewhere. Are you committing or aborting every transaction that you start, and calling delete() explicitly on all the DB XML objects that you use?
Those errors mean your database has become corrupted somehow.
John