error in installing astral-mp

[Aannaw]

Hello, Professor,
I am installing the astral-mp, my command is :
git clone https://github.com/smirarab/ASTRAL/
cd ASTRAL
git checkout MP
./make.sh
java -D"java.library.path=/data/01/user157/software/ASTRAL/lib/" -jar native_library_tester.jar
The path of lib is current path,and I get the error :

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=0x00007f627452234a, pid=732789, tid=0x00007f62f3ad7700
JRE version: OpenJDK Runtime Environment (8.0_192-b01) (build 1.8.0_192-b01)
Java VM: OpenJDK 64-Bit Server VM (25.192-b01 mixed mode linux-amd64 compressed oops)
Problematic frame:
C [libAstral.so+0x234a] Java_phylonet_coalescent_Polytree_00024PTNative_cppBatchCompute+0x10a
Core dump written. Default location: /data/01/user157/software/ASTRAL/core or core.732789
An error report file with more information is saved as:
/data/01/user157/software/ASTRAL/hs_err_pid732789.log
[1] 732789 segmentation fault (core dumped) java -D"java.library.path=/data/01/user157/software/ASTRAL/lib/" -jar

Can you help me about the problem? Looking forward to your reply.

[smirarab]

when you run make.sh, can you capture and send me the content of the standard out and standard error? Perhaps there is an error that went unnoticed here.

…

On Mon, Aug 9, 2021 at 11:50 PM Aannaw ***@***.***> wrote: Reopened #78 <#78>. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#78 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJXOGXRSMWCKNFD5SWPFLT4DD2JANCNFSM5B3PR4IQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

-- Siavash Mirarab

[Aannaw]

Hi，Professor,

Thanks for your reply.

This out_error.txt is the standard out and error captured when running ./make.sh.There is warning that : Build finished successfully. You can distribute Astral.5.15.4.zip or simply run astral.5.15.4.jar. Note that if you are moving astral.5.15.4.jar to some other location, you need to also move the lib directory.But the astral.5.15.4.jar is in the current path---/data/01/user157/software/ASTRAL. Should I remove the Astral.5.15.4.zip? I can not understand the meaning.

Thanks for again.

[smirarab]

Hmm. I see no errors in the make. You do not need to move Astral.5.15.4.zip.

The error you are reporting is something we have not seen before. I am not quite sure what is driving it. The important part seems to be:

OpenJDK 64-Bit Server VM (25.192-b01 mixed mode linux-amd64 compressed oops)

When I google this, it seems to be an error with either gcc, java, or both. The error is probably specific to some versions of Java (or gcc). Are you able to change the java version or gcc version on your machine? For example, if you are doing this on a cluster, sometimes, you can load new "modules" that change C or java compilers. If you are able to do that, perhaps try that to see if it fixes anything?

In particular, your java seems slightly old. You seem to have 1.8.0_192-b01 whereas, on all linux machines I have, I seem to have 1.8.0_252-b09. Is it possible to update java and try again?