Hey, someone else having trouble running Java-programs on midas right now? Did IT change anything (Java version, whatever) over the weekend? I wanted to run the exact same program I ran on Friday (just with a different file as input) , and i constantly get this: # # An unexpected error has been detected by Java Runtime Environment: # # Internal Error (exceptions.cpp:367), pid=4792, tid=4160019344 # Error: ExceptionMark destructor expects no pending exceptions # # Java VM: Java HotSpot(TM) Server VM (11.0-b11 mixed mode linux-x86) # An error report file with more information is saved as: # /tmp/hs_err_pid4792.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # and those error logs are also not really helpful :-( -- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
Fixed. Cause was some really weird problem with linux i-nodes . I could list the contents of the directory - it was just /group/biocomp/users/mibel/ - but when typing the pwd - command, i got this nice error: pwd: couldn't find directory entry in `../../../../..' with matching i-node heavy metal! Anyway, going to the root directory and then going back to the same (/group/biocomp/users/mibel/ ) directory, solved the problem :/ Apparently some weird problem with mount points i think Michiel Van Bel wrote:
Hey, someone else having trouble running Java-programs on midas right now? Did IT change anything (Java version, whatever) over the weekend? I wanted to run the exact same program I ran on Friday (just with a different file as input) , and i constantly get this:
# # An unexpected error has been detected by Java Runtime Environment: # # Internal Error (exceptions.cpp:367), pid=4792, tid=4160019344 # Error: ExceptionMark destructor expects no pending exceptions # # Java VM: Java HotSpot(TM) Server VM (11.0-b11 mixed mode linux-x86) # An error report file with more information is saved as: # /tmp/hs_err_pid4792.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp #
and those error logs are also not really helpful :-(
-- ================================================================== Michiel Van Bel PhD student Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel@psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================
I think I had a similar problem last friday. I couldn't use pwd anymore either, and my jobs on the cluster had simply stopped running in the middle of the program, without outputting any errors.. I thought it was because a small network interruption or anything, but everything was fine again after logging out & back in... Sofie Michiel Van Bel wrote:
Fixed. Cause was some really weird problem with linux i-nodes . I could list the contents of the directory - it was just /group/biocomp/users/mibel/ - but when typing the pwd - command, i got this nice error: pwd: couldn't find directory entry in `../../../../..' with matching i-node
heavy metal! Anyway, going to the root directory and then going back to the same (/group/biocomp/users/mibel/ ) directory, solved the problem :/ Apparently some weird problem with mount points i think
Michiel Van Bel wrote:
Hey, someone else having trouble running Java-programs on midas right now? Did IT change anything (Java version, whatever) over the weekend? I wanted to run the exact same program I ran on Friday (just with a different file as input) , and i constantly get this:
# # An unexpected error has been detected by Java Runtime Environment: # # Internal Error (exceptions.cpp:367), pid=4792, tid=4160019344 # Error: ExceptionMark destructor expects no pending exceptions # # Java VM: Java HotSpot(TM) Server VM (11.0-b11 mixed mode linux-x86) # An error report file with more information is saved as: # /tmp/hs_err_pid4792.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp #
and those error logs are also not really helpful :-(
-- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be
participants (2)
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Michiel Van Bel -
Sofie Van Landeghem