com.sleepycat.je.EnvironmentFailureException: (JE 4.1.6) Environment must be closed, caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 4.1.6) /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state fetchTarget of 0x112/0x941961 parent IN=62673966 IN class=com.sleepycat.je.tree.BIN lastFullVersion=0x183/0x2a17d parent.getDirty()=true state=0 LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed.

JIRA | Jean-Pierre Bergamin | 3 years ago
  1. 0

    If encounterting SEVERE errors, running jobs should be tried to get stopped and the heritrix engine should be shutdown. An NFS mount that contained heritrix's job directory went down last night. This lead to gazillion of Exceptions of the form: {noformat} Oct 06, 2013 5:19:40 PM org.archive.crawler.frontier.BdbWorkQueue peekItem SEVERE: peekItem failure; retrying (in thread 'ToeThread #23: ') com.sleepycat.je.EnvironmentFailureException: (JE 4.1.6) Environment must be closed, caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 4.1.6) /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state fetchTarget of 0x112/0x941961 parent IN=62673966 IN class=com.sleepycat.je.tree.BIN lastFullVersion=0x183/0x2a17d parent.getDirty()=true state=0 LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed. at com.sleepycat.je.EnvironmentFailureException.wrapSelf(EnvironmentFailureException.java:196) at com.sleepycat.je.dbi.EnvironmentImpl.checkIfInvalid(EnvironmentImpl.java:1439) at com.sleepycat.je.Database.checkEnv(Database.java:1778) at com.sleepycat.je.Database.openCursor(Database.java:625) at org.archive.crawler.frontier.BdbMultipleWorkQueues.getNextNearestItem(BdbMultipleWorkQueues.java:297) at org.archive.crawler.frontier.BdbMultipleWorkQueues.get(BdbMultipleWorkQueues.java:258) at org.archive.crawler.frontier.BdbWorkQueue.peekItem(BdbWorkQueue.java:103) at org.archive.crawler.frontier.WorkQueue.peek(WorkQueue.java:173) at org.archive.crawler.frontier.WorkQueueFrontier.findEligibleURI(WorkQueueFrontier.java:651) at org.archive.crawler.frontier.AbstractFrontier.next(AbstractFrontier.java:452) at org.archive.crawler.framework.ToeThread.run(ToeThread.java:133) Caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 4.1.6) /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state fetchTarget of 0x112/0x941961 parent IN=62673966 IN class=com.sleepycat.je.tree.BIN lastFullVersion=0x183/0x2a17d parent.getDirty()=true state=0 LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed. at com.sleepycat.je.tree.IN.fetchTarget(IN.java:1332) at com.sleepycat.je.tree.BIN.fetchTarget(BIN.java:1367) at com.sleepycat.je.dbi.CursorImpl.fetchCurrent(CursorImpl.java:2499) at com.sleepycat.je.dbi.CursorImpl.getCurrentAlreadyLatched(CursorImpl.java:1545) at com.sleepycat.je.dbi.CursorImpl.getNextWithKeyChangeStatus(CursorImpl.java:1692) at com.sleepycat.je.dbi.CursorImpl.getNext(CursorImpl.java:1617) at com.sleepycat.je.Cursor.retrieveNextAllowPhantoms(Cursor.java:2485) at com.sleepycat.je.Cursor.retrieveNext(Cursor.java:2304) at com.sleepycat.je.Cursor.getNext(Cursor.java:1013) at org.archive.crawler.frontier.BdbMultipleWorkQueues.getNextNearestItem(BdbMultipleWorkQueues.java:313) ... 6 more Caused by: java.io.FileNotFoundException: /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state/00000112.jdb (Input/output error) at java.io.RandomAccessFile.open(Native Method) at java.io.RandomAccessFile.<init>(RandomAccessFile.java:233) at java.io.RandomAccessFile.<init>(RandomAccessFile.java:118) at com.sleepycat.je.log.FileManager$1.<init>(FileManager.java:995) at com.sleepycat.je.log.FileManager.openFileHandle(FileManager.java:994) at com.sleepycat.je.log.FileManager.getFileHandle(FileManager.java:890) at com.sleepycat.je.log.LogManager.getLogSource(LogManager.java:1074) {noformat} The local disk that contains the heritrix_out.log ran full within minutes because of this flood of exceptions. In such non recoverable cases, the engine should be shutdown while trying to save as much state as possible.

    JIRA | 3 years ago | Jean-Pierre Bergamin
    com.sleepycat.je.EnvironmentFailureException: (JE 4.1.6) Environment must be closed, caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 4.1.6) /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state fetchTarget of 0x112/0x941961 parent IN=62673966 IN class=com.sleepycat.je.tree.BIN lastFullVersion=0x183/0x2a17d parent.getDirty()=true state=0 LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed.
  2. 0

    If encounterting SEVERE errors, running jobs should be tried to get stopped and the heritrix engine should be shutdown. An NFS mount that contained heritrix's job directory went down last night. This lead to gazillion of Exceptions of the form: {noformat} Oct 06, 2013 5:19:40 PM org.archive.crawler.frontier.BdbWorkQueue peekItem SEVERE: peekItem failure; retrying (in thread 'ToeThread #23: ') com.sleepycat.je.EnvironmentFailureException: (JE 4.1.6) Environment must be closed, caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 4.1.6) /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state fetchTarget of 0x112/0x941961 parent IN=62673966 IN class=com.sleepycat.je.tree.BIN lastFullVersion=0x183/0x2a17d parent.getDirty()=true state=0 LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed. at com.sleepycat.je.EnvironmentFailureException.wrapSelf(EnvironmentFailureException.java:196) at com.sleepycat.je.dbi.EnvironmentImpl.checkIfInvalid(EnvironmentImpl.java:1439) at com.sleepycat.je.Database.checkEnv(Database.java:1778) at com.sleepycat.je.Database.openCursor(Database.java:625) at org.archive.crawler.frontier.BdbMultipleWorkQueues.getNextNearestItem(BdbMultipleWorkQueues.java:297) at org.archive.crawler.frontier.BdbMultipleWorkQueues.get(BdbMultipleWorkQueues.java:258) at org.archive.crawler.frontier.BdbWorkQueue.peekItem(BdbWorkQueue.java:103) at org.archive.crawler.frontier.WorkQueue.peek(WorkQueue.java:173) at org.archive.crawler.frontier.WorkQueueFrontier.findEligibleURI(WorkQueueFrontier.java:651) at org.archive.crawler.frontier.AbstractFrontier.next(AbstractFrontier.java:452) at org.archive.crawler.framework.ToeThread.run(ToeThread.java:133) Caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 4.1.6) /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state fetchTarget of 0x112/0x941961 parent IN=62673966 IN class=com.sleepycat.je.tree.BIN lastFullVersion=0x183/0x2a17d parent.getDirty()=true state=0 LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed. at com.sleepycat.je.tree.IN.fetchTarget(IN.java:1332) at com.sleepycat.je.tree.BIN.fetchTarget(BIN.java:1367) at com.sleepycat.je.dbi.CursorImpl.fetchCurrent(CursorImpl.java:2499) at com.sleepycat.je.dbi.CursorImpl.getCurrentAlreadyLatched(CursorImpl.java:1545) at com.sleepycat.je.dbi.CursorImpl.getNextWithKeyChangeStatus(CursorImpl.java:1692) at com.sleepycat.je.dbi.CursorImpl.getNext(CursorImpl.java:1617) at com.sleepycat.je.Cursor.retrieveNextAllowPhantoms(Cursor.java:2485) at com.sleepycat.je.Cursor.retrieveNext(Cursor.java:2304) at com.sleepycat.je.Cursor.getNext(Cursor.java:1013) at org.archive.crawler.frontier.BdbMultipleWorkQueues.getNextNearestItem(BdbMultipleWorkQueues.java:313) ... 6 more Caused by: java.io.FileNotFoundException: /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state/00000112.jdb (Input/output error) at java.io.RandomAccessFile.open(Native Method) at java.io.RandomAccessFile.<init>(RandomAccessFile.java:233) at java.io.RandomAccessFile.<init>(RandomAccessFile.java:118) at com.sleepycat.je.log.FileManager$1.<init>(FileManager.java:995) at com.sleepycat.je.log.FileManager.openFileHandle(FileManager.java:994) at com.sleepycat.je.log.FileManager.getFileHandle(FileManager.java:890) at com.sleepycat.je.log.LogManager.getLogSource(LogManager.java:1074) {noformat} The local disk that contains the heritrix_out.log ran full within minutes because of this flood of exceptions. In such non recoverable cases, the engine should be shutdown while trying to save as much state as possible.

    JIRA | 3 years ago | Jean-Pierre Bergamin
    com.sleepycat.je.EnvironmentFailureException: (JE 4.1.6) Environment must be closed, caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 4.1.6) /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state fetchTarget of 0x112/0x941961 parent IN=62673966 IN class=com.sleepycat.je.tree.BIN lastFullVersion=0x183/0x2a17d parent.getDirty()=true state=0 LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed.
  3. 0

    [Launcher] Loading Cache... Exception in thread "main" java.io.FileNotFoundException:

    rune-server.org | 1 year ago
    java.io.FileNotFoundException: data\cache\main_file_c ache.dat2 (The system cannot find the path specified)
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  5. 0

    Error loading large files

    GitHub | 1 year ago | GoogleCodeExporter
    java.io.FileNotFoundException: /home/phains/bin/PeptideShaker-0.22.6/I:/MassspecCoreGroup/Search Engine/DB/SearchGUI/ICKP_140_seq_concatenated_target_decoy.fasta (No such file or directory)
  6. 0

    Issue with DiskOrderedCursor and WriteDeferredDB 5.0.97

    Oracle Community | 2 years ago | 5267b12c-9d06-4ac5-b3ae-02e876ffc12a
    com.sleepycat.je.EnvironmentFailureException: (JE 5.0.97) Environment must be closed, caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 5.0.97) F:\calculationservice\workspace\workflow-uatcrttorqt2wf3\replication java.io.FileNotFoundException: F:\calculationservice\workspace\workflow-uatcrttorqt2wf3\replication\ffffffff.jdb (The system cannot find the file specified) LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed.

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Root Cause Analysis

  1. java.io.FileNotFoundException

    /mnt/sammy-data/heritrix_jobs/two-hops-no-requests-html-only/state/00000112.jdb (Input/output error)

    at java.io.RandomAccessFile.open()
  2. Java RT
    RandomAccessFile.<init>
    1. java.io.RandomAccessFile.open(Native Method)
    2. java.io.RandomAccessFile.<init>(RandomAccessFile.java:233)
    3. java.io.RandomAccessFile.<init>(RandomAccessFile.java:118)
    3 frames
  3. Berkeley DB Java Edition
    LogManager.getLogSource
    1. com.sleepycat.je.log.FileManager$1.<init>(FileManager.java:995)
    2. com.sleepycat.je.log.FileManager.openFileHandle(FileManager.java:994)
    3. com.sleepycat.je.log.FileManager.getFileHandle(FileManager.java:890)
    4. com.sleepycat.je.log.LogManager.getLogSource(LogManager.java:1074)
    4 frames