[Inparanoid] A bug report for inparanoid4.1

[Xuan Wang]

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)
(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
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

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
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