<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 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 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 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 href="mailto:xmaswang26@gmail.com">xmaswang26@gmail.com</a><br></font></div></div>
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