Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Failed to write core dump #82

Closed
helloworld1631 opened this issue May 12, 2023 · 4 comments
Closed

Failed to write core dump #82

helloworld1631 opened this issue May 12, 2023 · 4 comments

Comments

@helloworld1631
Copy link

When my search came to 58%, it stopped and reported a fatal error -

INFO: 58% processed (24273) 24378 read of 41620 Estimated remaining: 2hours 49minutes to 3hours 13minutes
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x0000000066f0aa78, pid=19560, tid=0x0000000000006554
#
# JRE version: Java(TM) SE Runtime Environment (8.0_371) (build 1.8.0_371-b11)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.371-b11 mixed mode windows-amd64 )
# Problematic frame:
# V  [jvm.dll+0x11aa78]
#
# Failed to write core dump. Minidumps are not enabled by default on client versions of Windows
#
# An error report file with more information is saved as:
# C:\CL_search_engine\xiSEARCH\xiSEARCH_1.7.6.7\hs_err_pid19560.log

Are there any problems with my Java setting? Or is that due to running out of memory(I assigned 32G memory)?

Thanks in advance for any help and suggestions.

@grandrea
Copy link
Contributor

hello, this could be out of memory, yes. How many proteins do you have in the database?
Could you post your config and the contents of the log file mentioned in the error message?

@helloworld1631
Copy link
Author

helloworld1631 commented May 17, 2023

Hi, I have ~7000 proteins in my database. If search against the whole proteome, e.g. 20k proteins, how much memory should I assign to it?
I tried again with 50 GB, but it still reported the same error. Attach the config and the log file in the link:
Thank you!

@lutzfischer
Copy link
Member

this actually does not look like memory problem. can you try with a different/newer java version?

@helloworld1631
Copy link
Author

Thank you, it works. I changed from the newest version to 16.0.2

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants