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<div class="moz-cite-prefix">Hi Xuan,<br>
<br>
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.<br>
<br>
I'd think your java is somehow corrupted. Does it work for other
things?<br>
<br>
Erik Sonnhammer<br>
<br>
On 2014-03-27 05:50, Xuan Wang wrote:<br>
</div>
<blockquote
cite="mid:CAOu9gnnG3db7GRy560ckH3SZaF6L+sVKNMea0v8LPpVST3mP1A@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>
<div>
<div>Hi, developers!<br>
<br>
</div>
First of all, thank you very much for developing the
user-friendly ortholog find program.<br>
<br>
</div>
I used the stand alone inparanoid in many cases. Recently, I
used it on a HPC， but a bug appeared.<br>
<br>
</div>
The system info:<br>
$ cat /proc/version<br>
Linux version 2.6.32-279.el6.x86_64 (<a moz-do-not-send="true"
href="mailto:mockbuild@c6b9.bsys.dev.centos.org">mockbuild@c6b9.bsys.dev.centos.org</a>)
(gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP
Fri Jun 22 12:19:21 UTC 2012<br>
$ lsb_release -a<br>
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<br>
Distributor ID: CentOS<br>
Description: CentOS release 6.3 (Final)<br>
Release: 6.3<br>
Codename: Final<br>
###################################<br>
</div>
<div>First try:<br>
</div>
$ /usr/bin/java -version<br>
<div>
<div>java version "1.6.0_24"<br>
OpenJDK Runtime Environment (IcedTea6 1.11.1)
(rhel-1.45.1.11.1.el6-x86_64)<br>
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)<br>
<br>
<div>
<div>
<div>
<div>
<div>ERRs like this:<br>
*** glibc detected *** java: double free or
corruption (fasttop): 0x00002baa3000ae70 ***<br>
*** glibc detected *** java: double free or
corruption (fasttop): 0x00002baa30007f40 ***<br>
*** glibc detected *** java: double free or
corruption (fasttop): 0x00002baa30014f00 ***<br>
*** glibc detected *** java: double free or
corruption (fasttop): 0x00002baa3000afe0 ***<br>
*** glibc detected *** java: double free or
corruption (fasttop): 0x00002baa30007f40 ***<br>
*** glibc detected *** java: double free or
corruption (fasttop): 0x00002baa3000b080 ***<br>
*** glibc detected *** java: double free or
corruption (fasttop): 0x00002baa3001e5e0 ***<br>
*** glibc detected *** java: double free or
corruption (out): 0x00002baa3001b5e0 ***<br>
sh: line 1: 6311 Aborted (core
dumped) java -jar seqstat.jar -m BLOSUM80 -n 1000
-i 237.faa > <a moz-do-not-send="true"
href="http://237.bs">237.bs</a><br>
Error: Could not create the Java Virtual Machine.<br>
Error: A fatal exception has occurred. Program
will exit.<br>
sh: line 1: 6374 Aborted (core
dumped) java -jar seqstat.jar -m BLOSUM80 -n 1000
-i 589.faa > <a moz-do-not-send="true"
href="http://589.bs">589.bs</a><br>
<br>
</div>
<div>Second try:<br>
</div>
<div>$ my_java/java -version<br>
java version "1.7.0_51"<br>
Java(TM) SE Runtime Environment (build
1.7.0_51-b13)<br>
Java HotSpot(TM) 64-Bit Server VM (build
24.51-b03, mixed mode)<br>
<br>
</div>
<div>The same ERR as first try.<br>
<br>
</div>
<div>Third try:<br>
</div>
<div>$ my_java_32/java -version<br>
java version "1.7.0_51"<br>
Java(TM) SE Runtime Environment (build
1.7.0_51-b13)<br>
Java HotSpot(TM) Server VM (build 24.51-b03, mixed
mode)<br>
<br>
</div>
<div>Under the 32 bit java environment, no error
reports.<br>
<br>
#####################<br>
<br>
</div>
<div>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.<br>
</div>
<div>Looking forward to your early reply :)<br>
</div>
<div><br>
</div>
<div>Xuan Wang<br>
</div>
<div>-- <br>
<div dir="ltr">
<div><font size="1">Xuan Wang <br>
</font></div>
<div><font size="1">Biology, Cuiying Honors
College, Lanzhou University, China <br>
</font></div>
<div><font size="1">Kunming institute of
zoology, CAS<br>
</font></div>
<div><font size="1">Email: <a
moz-do-not-send="true"
href="mailto:xmaswang26@gmail.com">xmaswang26@gmail.com</a><br>
</font></div>
</div>
</div>
</div>
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