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smirarab / ASTRAL

Accurate Species TRee ALgorithm
Apache License 2.0
234 stars 68 forks source link

fatal error by the Java Runtime Environmen #67

Closed siberianhigh closed 3 years ago

siberianhigh commented 3 years ago

Hi,

Just downloaded ASTRAL and run java -D"java.library.path=lib/" -jar native_library_tester.jar

and got the following error: hs_err_pid1249854.log

There are 2 threads used to run. Native AVX library found.

A fatal error has been detected by the Java Runtime Environment:

SIGILL (0x4) at pc=0x00007f789ad7e34a, pid=1249854, tid=1249855

JRE version: OpenJDK Runtime Environment (11.0.9+11) (build 11.0.9+11-Ubuntu-0ubuntu1.20.04) Java VM: OpenJDK 64-Bit Server VM (11.0.9+11-Ubuntu-0ubuntu1.20.04, mixed mode, sharing, tiered, compressed oops, g1 gc, linux-amd64) Problematic frame: C [libAstral.so+0x234a] Java_phylonet_coalescent_Polytree_00024PTNative_cppBatchCompute+0x10a

Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport %p %s %c %d %P %E" (or dumping to /home/evgeniy/soft/Astral/core.1249854)

An error report file with more information is saved as: /home/evgeniy/soft/Astral/hs_err_pid1249854.log

If you would like to submit a bug report, please visit: https://bugs.launchpad.net/ubuntu/+source/openjdk-lts The crash happened outside the Java Virtual Machine in native code. See problematic frame for where to report the bug.

Aborted (core dumped)

The hs_err_pid1249854.log is attached.

best,

Evgeniy

smirarab commented 3 years ago

Two questions.

  1. Are you using the ASTRAL-MP branch? The command you mentioned is related to ASTRAL-MP. What is the version of ASTRAL you are using?

  2. If you are using ASTRAL-MP and you are getting this error, have you tried running make.sh on your machine to see if that solves the problem?

Thanks Siavash

On Thu, Nov 12, 2020 at 8:51 AM Evgeniy notifications@github.com wrote:

Hi,

Just downloaded ASTRAL and run java -D"java.library.path=lib/" -jar native_library_tester.jar

and got the following error: hs_err_pid1249854.log https://github.com/smirarab/ASTRAL/files/5531991/hs_err_pid1249854.log

There are 2 threads used to run. Native AVX library found.

A fatal error has been detected by the Java Runtime Environment:

SIGILL (0x4) at pc=0x00007f789ad7e34a, pid=1249854, tid=1249855

JRE version: OpenJDK Runtime Environment (11.0.9+11) (build 11.0.9+11-Ubuntu-0ubuntu1.20.04) Java VM: OpenJDK 64-Bit Server VM (11.0.9+11-Ubuntu-0ubuntu1.20.04, mixed mode, sharing, tiered, compressed oops, g1 gc, linux-amd64) Problematic frame: C [libAstral.so+0x234a] Java_phylonet_coalescent_Polytree_00024PTNative_cppBatchCompute+0x10a

Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport %p %s %c %d %P %E" (or dumping to /home/evgeniy/soft/Astral/core.1249854)

An error report file with more information is saved as: /home/evgeniy/soft/Astral/hs_err_pid1249854.log

If you would like to submit a bug report, please visit: https://bugs.launchpad.net/ubuntu/+source/openjdk-lts The crash happened outside the Java Virtual Machine in native code. See problematic frame for where to report the bug.

Aborted (core dumped)

The hs_err_pid1249854.log is attached.

best,

Evgeniy

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-- Siavash Mirarab

siberianhigh commented 3 years ago
  1. Thanks Siavash, it solved the problem. And sorry, this somehow escaped my mind, now I see this issue in the README.