ADL_Unpacke segmentation fault (core dumped)

Issues related to runtime execution of algorithms in ADL

ADL_Unpacke segmentation fault (core dumped)

Postby zion0210 » Wed Apr 29, 2015 8:57 am

Hi,

I took ADL_Unpacker.exe, contained within SDR Software v2.1, for unpack VIIRS RDR file.

$ ADL_Unpacker.exe VIIRS-RDR.h5

But ADL_Unpacker.exe run is failed:
Segmentation fault (core dumped).

Though run ADL_Unpacker.exe within SDR Software v2.1 not have problem.

After, i installed ADL 4.2 in compliance with instruction
https://jpss.ssec.wisc.edu/jpss-data/ht ... lation.pdf
and again started ADL_Unpacker.exe.

$ ADL_Unpacker.exe VIIRS-RDR.h5

But again ADL_Unpacker.exe run is failed:
Segmentation fault (core dumped).

My OS is CentOS 6.6.

Does need ADL_Unpacker.exe to export variables, such as $CSPP_HOME?

Is there a only ADL tools package (${CSPP_HOME}/common/ADL/tools)?

Can anyone help with this?


Regards,
zion0210
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Re: ADL_Unpacke segmentation fault (core dumped)

Postby tsimpson » Thu Apr 30, 2015 9:15 am

I have not seen a segmentation fault with the ADL Unpacker so far. I have a couple of questions that could help me look into this problem:

- Can you give any details on the core dump? You should have the gdb debugger on your system. Run the command:

gdb $ADL_HOME/tools/bin/ADL_Unpacker.exe <corefile>

where <corefile> should be replaced by the actual name of the core dump file. After you type this command, you will get a gdb prompt. Enter the "where" command and post the output to the forum, then enter "quit" to quit gdb.

- Where did the file you are trying to unpack come from? The ADL Unpacker should work on HDF5 files produced by IDPS, such as the kind you can get from CLASS, but I don't know if it works on files from other sources.

Concerning your question about whether ADL_Unpacker.exe needs to export variables: You should not need any variables beyond those that are defined when you source the envSetup.csh or envSetup.ksh file in your ADL installation.

Hope this helps ... please let me know if there are more questions or comments.
Todd Simpson
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Re: ADL_Unpacke segmentation fault (core dumped)

Postby houchin » Fri May 01, 2015 6:24 am

Hi all,

Crashing of the ADL Unpacker is a well known issue, resulting from a difference between the version of the HDF library installed as part of the UWisc integration of ADL, and the officially supported version. The crash occurs on application cleanup in the bowels of C++ as part of the exit system call. By this point, the actual unpacked files have all been written and everything is done.

You can either downgrade your version of the HDF library to the exact version listed in the ADL Users guide (can't remember what it is off the top of my head), or just ignore the segmentation fault.
Scott Houchin, Senior Engineering Specialist, The Aerospace Corporation
15049 Conference Center Dr CH3/310, Chantilly, VA 20151; 571-307-3914; scott.houchin@aero.org
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Re: ADL_Unpacke segmentation fault (core dumped)

Postby tsimpson » Fri May 01, 2015 8:08 am

Thanks for the information Scott. The current ADL user guide lists 1.8.6 as the official version of the HDF software, and it lists 1.8.7 as a compatible version. The ADL environment I use has HDF version 1.8.6 and I don't remember ever seeing a core dump from the ADL Unpacker.
Todd Simpson
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Re: ADL_Unpacke segmentation fault (core dumped)

Postby houchin » Fri May 01, 2015 10:54 am

tsimpson wrote:Thanks for the information Scott. The current ADL user guide lists 1.8.6 as the official version of the HDF software, and it lists 1.8.7 as a compatible version. The ADL environment I use has HDF version 1.8.6 and I don't remember ever seeing a core dump from the ADL Unpacker.


Yup, that's it. There's a small difference in how the HDF libraries close things down between 1.8.6 and 1.8.7, and that's what's causing the crash. I believe either a DR or a PCR has been put in for this issue, so a correction could be made if it's prioritized.

I do not know why UWisc uses 1.8.7 in their integration, as they're installing it explicitly as part of the ADL install. I would think anyone could modify the support script to get 1.8.6 and install that version instead.
Scott Houchin, Senior Engineering Specialist, The Aerospace Corporation
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Re: ADL_Unpacke segmentation fault (core dumped)

Postby zion0210 » Fri May 08, 2015 7:59 am

Hi,

Where did the file you are trying to unpack come from?

I getting *.h5 VIIRS RDR for processing from http://www.nsof.class.noaa.gov.

Can you give any details on the core dump?

Sorry, i not know how create <core dump> file.
I have gdb mesage only:
Code: Select all
gdb $ADL_HOME/tools/bin/ADL_Unpacker.exe
(gdb) run RNSCA-RVIRS*.h5
Starting program:  $ADL_HOME/tools/bin/ADL_Unpacker.exe RNSCA-RVIRS*.h5
[Thread debugging using libthread_db enabled]
Program received signal SIGSEGV, Segmentation fault.
0x000000369af34012 in __strcpy_ssse3 () from /lib64/libc.so.6
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.149.el6_6.7.x86_64 libgcc-4.4.7-11.el6.x86_64 libgfortran-4.4.7-11.el6.x86_64 libgomp-4.4.7-11.el6.x86_64 libstdc++-4.4.7-11.el6.x86_64
(gdb) where
#0  0x000000369af34012 in __strcpy_ssse3 () from /lib64/libc.so.6
#1  0x0000000000472823 in main (argc=2, argv=0x7fffffffda88) at ADL_Main.cpp:163


cat $ADL_HOME/CMN/Utilities/DDS/ADL_Unpacker/src/ADL_Main.cpp | sed -n "161,164p"
Code: Select all
161   char *dConfig = getenv( "DCONFIG" );
162   char *configFile=new char [255];
163   strcpy( configFile, dConfig);
164   strcat( configFile,"/unpacker.xml");


next i defined DCONFIG

export DCONFIG=$DCONFIG ; $ADL_HOME/tools/bin/ADL_Unpacker.exe *.h5
Code: Select all
LogLog: Configurator file key inf_util_dbg_cfg_file not specified
LogLog: Configurator class key inf_util_dbg_cfg_class not specified
LogLog: Configurator aborted
Error initializing with infrastructure ../../util/src/InfTk_ConfigStore.cpp|465|getInstance|SINGLETON_NOT_CREATED_ERR



About version hdf5 library:

ldd $ADL_HOME/tools/bin/ADL_Unpacker.exe | grep hdf5
Code: Select all
libhdf5.so.7 => $ADL_HOME/../common/local/lib/libhdf5.so.7


libhdf5.so.7 was builded using hdf5-1.8.7.

I did replace hdf5-1.8.7 by hdf5-1.8.6, and again builded COTS and ADL 4.2.

ldd $ADL_HOME/tools/bin/ADL_Unpacker.exe | grep hdf5
Code: Select all
libhdf5.so.6 => $ADL_HOME/../common/local/lib/libhdf5.so.6


But again ADL_Unpacker.exe run is failed:
Segmentation fault (core dumped).

What can i do next?

Regards,
zion0210
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Re: ADL_Unpacke segmentation fault (core dumped)

Postby houchin » Fri May 08, 2015 8:56 am

Enter the command "backtrace" in gdb and see what you get. The well known error is inside the call to "exit()" as the C++ environment starts destructing the HDF objects. If that's it, you're simplest bet right now is to just ignore the crash.

Scott Mindock might now the specific code change to the unpacker to fix the error; in fact I am thinking that there is a patch to this available.
Scott Houchin, Senior Engineering Specialist, The Aerospace Corporation
15049 Conference Center Dr CH3/310, Chantilly, VA 20151; 571-307-3914; scott.houchin@aero.org
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Re: ADL_Unpacke segmentation fault (core dumped)

Postby zion0210 » Mon May 11, 2015 8:27 am

Hi Scott.

After i defined DCONFIG variable, gdb reported only next log:

Code: Select all
$ gdb ADL_Unpacker.exe
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-75.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from ADL_Unpacker.exe...done.
(gdb) run RNSCA-RVIRS_*.h5
Starting program: ADL_Unpacker.exe RNSCA-RVIRS_*.h5
[Thread debugging using libthread_db enabled]
LogLog: Configurator file key inf_util_dbg_cfg_file not specified
LogLog: Configurator class key inf_util_dbg_cfg_class not specified
LogLog: Configurator aborted
Error initializing with infrastructure ../../util/src/InfTk_ConfigStore.cpp|465|getInstance|SINGLETON_NOT_CREATED_ERR

Program exited with code 01.
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.149.el6_6.7.x86_64 libgcc-4.4.7-11.el6.x86_64 libgfortran-4.4.7-11.el6.x86_64 libgomp-4.4.7-11.el6.x86_64 libstdc++-4.4.7-11.el6.x86_64
(gdb) backtrace
No stack.
(gdb)


Regards,
zion0210
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Re: ADL_Unpacke segmentation fault (core dumped)

Postby houchin » Mon May 11, 2015 11:18 am

Hi,

This is definitely a different error, and in this case the code didn't crash but just exited with an error. It looks like you have a DCONFIG error.
Scott Houchin, Senior Engineering Specialist, The Aerospace Corporation
15049 Conference Center Dr CH3/310, Chantilly, VA 20151; 571-307-3914; scott.houchin@aero.org
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Re: ADL_Unpacke segmentation fault (core dumped)

Postby scottm » Mon May 11, 2015 11:21 am

Good Morning,

What version of ADL are you working with? On what platform Centos6?
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