[Inparanoid] A bug report for inparanoid4.1

Erik Sonnhammer erik.sonnhammer at scilifelab.se
Fri May 23 14:37:50 CEST 2014


Hi Xuan,

Have you solved this yourself?  All I can say is that when I run on a 
64-bit ubuntu 12.04 there is no problem.

I'd think your java is somehow corrupted.  Does it work for other things?

Erik Sonnhammer

On 2014-03-27 05:50, Xuan Wang wrote:
> Hi, developers!
>
> First of all, thank you very much for developing the user-friendly 
> ortholog find program.
>
> I used the stand alone inparanoid in many cases. Recently, I used it 
> on a HPC, but a bug appeared.
>
> The system info:
> $ cat /proc/version
> Linux version 2.6.32-279.el6.x86_64 
> (mockbuild at c6b9.bsys.dev.centos.org 
> <mailto:mockbuild at c6b9.bsys.dev.centos.org>) (gcc version 4.4.6 
> 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP Fri Jun 22 12:19:21 UTC 2012
> $ lsb_release -a
> LSB Version: 
> :core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
> Distributor ID: CentOS
> Description:    CentOS release 6.3 (Final)
> Release:        6.3
> Codename:       Final
> ###################################
> First try:
> $ /usr/bin/java -version
> java version "1.6.0_24"
> OpenJDK Runtime Environment (IcedTea6 1.11.1) 
> (rhel-1.45.1.11.1.el6-x86_64)
> OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)
>
> ERRs like this:
> *** glibc detected *** java: double free or corruption (fasttop): 
> 0x00002baa3000ae70 ***
> *** glibc detected *** java: double free or corruption (fasttop): 
> 0x00002baa30007f40 ***
> *** glibc detected *** java: double free or corruption (fasttop): 
> 0x00002baa30014f00 ***
> *** glibc detected *** java: double free or corruption (fasttop): 
> 0x00002baa3000afe0 ***
> *** glibc detected *** java: double free or corruption (fasttop): 
> 0x00002baa30007f40 ***
> *** glibc detected *** java: double free or corruption (fasttop): 
> 0x00002baa3000b080 ***
> *** glibc detected *** java: double free or corruption (fasttop): 
> 0x00002baa3001e5e0 ***
> *** glibc detected *** java: double free or corruption (out): 
> 0x00002baa3001b5e0 ***
> sh: line 1:  6311 Aborted                 (core dumped) java -jar 
> seqstat.jar -m BLOSUM80 -n 1000 -i 237.faa > 237.bs <http://237.bs>
> Error: Could not create the Java Virtual Machine.
> Error: A fatal exception has occurred. Program will exit.
> sh: line 1:  6374 Aborted                 (core dumped) java -jar 
> seqstat.jar -m BLOSUM80 -n 1000 -i 589.faa > 589.bs <http://589.bs>
>
> Second try:
> $ my_java/java -version
> java version "1.7.0_51"
> Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
> Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)
>
> The same ERR as first try.
>
> Third try:
> $ my_java_32/java -version
> java version "1.7.0_51"
> Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
> Java HotSpot(TM) Server VM (build 24.51-b03, mixed mode)
>
> Under the 32 bit java environment, no error reports.
>
> #####################
>
> Because I have to use 64bit java for other big ram programs, it's not 
> convenient for me to change the shell env frequently. Also, I don't 
> know if the bug will affect the calculating results(I dug some infos 
> on the net. A explanation is that the jar used free() twice to access 
> a same RAM address, so when glibc checked, it was considered as a 
> fatal error), I hope you can check the java src and help me solve the 
> problem in 64bit java and CentOS environment.
> Looking forward to your early reply :)
>
> Xuan Wang
> -- 
> Xuan Wang
> Biology, Cuiying Honors College, Lanzhou University, China
> Kunming institute of zoology, CAS
> Email: xmaswang26 at gmail.com <mailto:xmaswang26 at gmail.com>
>
>
> _______________________________________________
> InParanoid mailing list
> InParanoid at lists.su.se
> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20140523/55ef2a46/attachment.html>


More information about the InParanoid mailing list