HDFView 2.5 Error

HDFView / Java HDF Object Package
1

I used the installer on linux to install HDFView 2.5. When I try to run it, I get this error (JVM is crashing).

$ ./hdfview

hs_err_pid26153.log.gz (5.23 KB)

···

#
# An unexpected error has been detected by Java Runtime Environment:
#
# SIGFPE (0x8) at pc=0x40008016, pid=26153, tid=1075682224
#
# Java VM: Java HotSpot(TM) Server VM (1.6.0-b105 mixed mode)
# Problematic frame:
# C [ld-linux.so.2+0x8016]
#
# An error report file with more information is saved as hs_err_pid26153.log
#
# If you would like to submit a bug report, please visit:
# Bug Report
#
Aborted

I've attached the file mentioned.

I've also tried this with the "with VM" version as well as downloading hdf-java and compiling myself from scratch. And I always am getting a SIGFPE in ld-linux on a call from System.loadLibrary.

Anyone have any ideas about this problem?

Some more info below:
$ uname -a
Linux circlew 2.6.5-7.244-bigsmp #1 SMP Mon Dec 12 18:32:25 UTC 2005 i686 i686 i386 GNU/Linux

$ /develop/unix/sccoe_tools/opt/java/jdk1.6.0_14-32/bin/java -version
java version "1.6.0_14"
Java(TM) SE Runtime Environment (build 1.6.0_14-b08)
Java HotSpot(TM) Server VM (build 14.0-b16, mixed mode)

(Tried with this and an older version mentioned in the hs err log.)

David McCloskey
Lead Programmer Analyst
Software Development
Core Engineering
Nuclear Fuel

Westinghouse Electric Company
Energy Center
4350 Northern Pike
Monroeville, PA, 15146, USA
Phone: +1 (412) 374-3789
Fax: +1 (412) 374-4500
Email: mcclosdl@westinghouse.com
Home Page: www.westinghousenuclear.com

2

It may be a problem of the old linux kernel. HDFView was build on Linux 2.6.18 and
you are using 2.6.5. Or it may be a problem of gcc library. HDFView was built with
gcc version 4.1.2.

Did you try 2.6 beta (ftp://ftp.hdfgroup.org/HDF5/hdf-java/v26b1/ )?

A couple of things you can try,
1) upgrade gcc (simplest solution, most likely it will solve the problem)
2) upgrade linux kernel or
3) build hdfview from the source

Thanks
--pc

McCloskey, David L. wrote:

···

I used the installer on linux to install HDFView 2.5. When I try to run it, I get this error (JVM is crashing).

$ ./hdfview

#

# An unexpected error has been detected by Java Runtime Environment:

#

# SIGFPE (0x8) at pc=0x40008016, pid=26153, tid=1075682224

#

# Java VM: Java HotSpot(TM) Server VM (1.6.0-b105 mixed mode)

# Problematic frame:

# C [ld-linux.so.2+0x8016]

#

# An error report file with more information is saved as hs_err_pid26153.log

#

# If you would like to submit a bug report, please visit:

# http://java.sun.com/webapps/bugreport/crash.jsp

#

Aborted

I've attached the file mentioned.

I've also tried this with the "with VM" version as well as downloading hdf-java and compiling myself from scratch. And I always am getting a SIGFPE in ld-linux on a call from System.loadLibrary.

Anyone have any ideas about this problem?

Some more info below:

$ uname -a

Linux circlew 2.6.5-7.244-bigsmp #1 SMP Mon Dec 12 18:32:25 UTC 2005 i686 i686 i386 GNU/Linux

$ /develop/unix/sccoe_tools/opt/java/jdk1.6.0_14-32/bin/java -version

java version "1.6.0_14"

Java(TM) SE Runtime Environment (build 1.6.0_14-b08)

Java HotSpot(TM) Server VM (build 14.0-b16, mixed mode)

(Tried with this and an older version mentioned in the hs err log.)

*David McCloskey*

Lead Programmer Analyst

Software Development

Core Engineering

Nuclear Fuel

Westinghouse Electric Company

Energy Center

4350 Northern Pike

Monroeville, PA, 15146, USA

Phone: +1 (412) 374-3789

Fax: +1 (412) 374-4500

Email: mcclosdl@westinghouse.com

Home Page: www.westinghousenuclear.com

------------------------------------------------------------------------

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

3

I tried the beta, and I got a similar error.

This is a controlled system, so I cannot upgrade gcc or the kernel. However, I tried to run on a SUSE 10 machine that looks like the following and got the same problem with both 2.5 and 2.6.
Linux duckster 2.6.16.60-0.21-smp #1 SMP Tue May 6 12:41:02 UTC 2008 x86_64 x86_64 x86_64 GNU/Linux
$ gcc -v
Using built-in specs.
Target: x86_64-suse-linux
Configured with: ../configure --enable-threads=posix --prefix=/usr --with-local-prefix=/usr/local --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,java,ada --enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 --enable-ssp --disable-libssp --disable-libgcj --with-slibdir=/lib64 --with-system-zlib --enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=new --program-suffix= --enable-version-specific-runtime-libs --without-system-libunwind --with-cpu=generic --host=x86_64-suse-linux
Thread model: posix
gcc version 4.1.2 20070115 (SUSE Linux)

Also, I did build HDFView from the source for 2.5 and got the same problem.

Since ld-linux.so.2 is the crashing library, I think it's crashing when trying to load the HDF5 library, but I couldn't figure out where. I tried putting prints above the various loadLibrary calls but nothing was showing up. Do you think I should try harder down that route?

David McCloskey
(412) 374-3789

···

_____________________________________________
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of Peter Cao
Sent: Monday, December 07, 2009 4:36 PM
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] HDFView 2.5 Error

It may be a problem of the old linux kernel. HDFView was build on Linux
2.6.18 and
you are using 2.6.5. Or it may be a problem of gcc library. HDFView was
built with
gcc version 4.1.2.

Did you try 2.6 beta (ftp://ftp.hdfgroup.org/HDF5/hdf-java/v26b1/ )?

A couple of things you can try,
1) upgrade gcc (simplest solution, most likely it will solve the problem)
2) upgrade linux kernel or
3) build hdfview from the source

Thanks
--pc

McCloskey, David L. wrote:

I used the installer on linux to install HDFView 2.5. When I try to
run it, I get this error (JVM is crashing).

$ ./hdfview

#

# An unexpected error has been detected by Java Runtime Environment:

#

# SIGFPE (0x8) at pc=0x40008016, pid=26153, tid=1075682224

#

# Java VM: Java HotSpot(TM) Server VM (1.6.0-b105 mixed mode)

# Problematic frame:

# C [ld-linux.so.2+0x8016]

#

# An error report file with more information is saved as
hs_err_pid26153.log

#

# If you would like to submit a bug report, please visit:

# http://java.sun.com/webapps/bugreport/crash.jsp

#

Aborted

I've attached the file mentioned.

I've also tried this with the "with VM" version as well as downloading
hdf-java and compiling myself from scratch. And I always am getting a
SIGFPE in ld-linux on a call from System.loadLibrary.

Anyone have any ideas about this problem?

Some more info below:

$ uname -a

Linux circlew 2.6.5-7.244-bigsmp #1 SMP Mon Dec 12 18:32:25 UTC 2005
i686 i686 i386 GNU/Linux

$ /develop/unix/sccoe_tools/opt/java/jdk1.6.0_14-32/bin/java -version

java version "1.6.0_14"

Java(TM) SE Runtime Environment (build 1.6.0_14-b08)

Java HotSpot(TM) Server VM (build 14.0-b16, mixed mode)

(Tried with this and an older version mentioned in the hs err log.)

*David McCloskey*

Lead Programmer Analyst

Software Development

Core Engineering

Nuclear Fuel

Westinghouse Electric Company

Energy Center

4350 Northern Pike

Monroeville, PA, 15146, USA

Phone: +1 (412) 374-3789

Fax: +1 (412) 374-4500

Email: mcclosdl@westinghouse.com

Home Page: www.westinghousenuclear.com

------------------------------------------------------------------------

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

4

It seems that your SUS 10 system is a 64bit linux.

Try the 64-bit hdfivew
ftp://ftp.hdfgroup.org/HDF5/hdf-java/v26b1/hdfview/hdfview_install_linux64.bin

If you build from the source on your 64-bit system, make sure to use 64-bit
flags. Some examples are at Config/config.sh.

Thanks
--pc

McCloskey, David L. wrote:

···

I tried the beta, and I got a similar error.
This is a controlled system, so I cannot upgrade gcc or the kernel. However, I tried to run on a SUSE 10 machine that looks like the following and got the same problem with both 2.5 and 2.6.
Linux duckster 2.6.16.60-0.21-smp #1 SMP Tue May 6 12:41:02 UTC 2008 x86_64 x86_64 x86_64 GNU/Linux
$ gcc -v
Using built-in specs.
Target: x86_64-suse-linux
Configured with: ../configure --enable-threads=posix --prefix=/usr --with-local-prefix=/usr/local --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,java,ada --enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 --enable-ssp --disable-libssp --disable-libgcj --with-slibdir=/lib64 --with-system-zlib --enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=new --program-suffix= --enable-version-specific-runtime-libs --without-system-libunwind --with-cpu=generic --host=x86_64-suse-linux
Thread model: posix
gcc version 4.1.2 20070115 (SUSE Linux)
Also, I did build HDFView from the source for 2.5 and got the same problem.
Since ld-linux.so.2 is the crashing library, I think it's crashing when trying to load the HDF5 library, but I couldn't figure out where. I tried putting prints above the various loadLibrary calls but nothing was showing up. Do you think I should try harder down that route?
David McCloskey
(412) 374-3789

*From:* hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] *On Behalf Of *Peter Cao
*Sent:* Monday, December 07, 2009 4:36 PM
*To:* hdf-forum@hdfgroup.org
*Subject:* Re: [Hdf-forum] HDFView 2.5 Error

2.6.18 and
you are using 2.6.5. Or it may be a problem of gcc library. HDFView was
built with
gcc version 4.1.2.
Did you try 2.6 beta (ftp://ftp.hdfgroup.org/HDF5/hdf-java/v26b1/ )?
A couple of things you can try,
1) upgrade gcc (simplest solution, most likely it will solve the problem)
2) upgrade linux kernel or
3) build hdfview from the source
Thanks
--pc

>
> I used the installer on linux to install HDFView 2.5. When I try to
> run it, I get this error (JVM is crashing).
>
> >
> $ ./hdfview
>
> #
>
> # An unexpected error has been detected by Java Runtime Environment:
>
> #
>
> # SIGFPE (0x8) at pc=0x40008016, pid=26153, tid=1075682224
>
> #
>
> # Java VM: Java HotSpot(TM) Server VM (1.6.0-b105 mixed mode)
>
> # Problematic frame:
>
> # C [ld-linux.so.2+0x8016]
>
> #
>
> # An error report file with more information is saved as
> hs_err_pid26153.log
>
> #
>
> # If you would like to submit a bug report, please visit:
>
> # http://java.sun.com/webapps/bugreport/crash.jsp
>
> #
>
> Aborted
>
> >
> I've attached the file mentioned.
>
> >
> I've also tried this with the "with VM" version as well as downloading
> hdf-java and compiling myself from scratch. And I always am getting a
> SIGFPE in ld-linux on a call from System.loadLibrary.
>
> >
> Anyone have any ideas about this problem?
>
> >
> >
> >
> Some more info below:
>
> $ uname -a
>
> Linux circlew 2.6.5-7.244-bigsmp #1 SMP Mon Dec 12 18:32:25 UTC 2005
> i686 i686 i386 GNU/Linux
>
> >
> $ /develop/unix/sccoe_tools/opt/java/jdk1.6.0_14-32/bin/java -version
>
> java version "1.6.0_14"
>
> Java(TM) SE Runtime Environment (build 1.6.0_14-b08)
>
> Java HotSpot(TM) Server VM (build 14.0-b16, mixed mode)
>
> >
> (Tried with this and an older version mentioned in the hs err log.)
>
> >
> >
> *David McCloskey*
>
> Lead Programmer Analyst
>
> Software Development
>
> Core Engineering
>
> Nuclear Fuel
>
> >
> Westinghouse Electric Company
>
> Energy Center
>
> 4350 Northern Pike
>
> Monroeville, PA, 15146, USA
>
> Phone: +1 (412) 374-3789
>
> Fax: +1 (412) 374-4500
>
> Email: mcclosdl@westinghouse.com
>
> Home Page: www.westinghousenuclear.com <http://www.westinghousenuclear.com>
>
> >
> >
> ------------------------------------------------------------------------
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@hdfgroup.org
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org