Error when exiting program using hdf5 1.6.8

mike.jackson · June 5, 2009, 6:14pm

I am getting either one of the following errors when my program exits:

Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap

HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap

This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).

I googled a bit for the errors but nothing really jumped out at me. Has anyone seen this type of error before?

In the same project I have lots of other programs all using the same HDF5 library and I am not getting the error. Just kinda popped up today. I rebuilt the hdf5 library and reinstalled but I am still getting the errors. I have ensured that I am closing all the hdf5 files that are opened. I have tried several different hdf5 files and all will give the error.

Any help or nudges in the right direction would be appreciated.

Thanks

···

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

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Dominik_Szczerba · June 5, 2009, 6:17pm

I would run the code through valgrind.
-- Dominik

Michael Jackson wrote:

···

I am getting either one of the following errors when my program exits:

Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap

HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap

This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).

I googled a bit for the errors but nothing really jumped out at me. Has anyone seen this type of error before?

In the same project I have lots of other programs all using the same HDF5 library and I am not getting the error. Just kinda popped up today. I rebuilt the hdf5 library and reinstalled but I am still getting the errors. I have ensured that I am closing all the hdf5 files that are opened. I have tried several different hdf5 files and all will give the error.

Any help or nudges in the right direction would be appreciated.

Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

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Dimitris_Servis · June 6, 2009, 10:55am

I have seen such messages being due to an overrun unrelated to the library
itself. You can also get it when killing the process abruptly. Memory
checking is a good starting point.

HTH

-- dimitris

···

2009/6/5 Michael Jackson <mike.jackson@bluequartz.net>

I am getting either one of the following errors when my program exits:

Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file
/Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap

HDF5: infinite loop closing library

D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap

This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).

I googled a bit for the errors but nothing really jumped out at me. Has
anyone seen this type of error before?

In the same project I have lots of other programs all using the same HDF5
library and I am not getting the error. Just kinda popped up today. I
rebuilt the hdf5 library and reinstalled but I am still getting the errors.
I have ensured that I am closing all the hdf5 files that are opened. I have
tried several different hdf5 files and all will give the error.

Any help or nudges in the right direction would be appreciated.

Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

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nfortne2 · June 5, 2009, 6:38pm

Mike,

I have seen a similar problem before, but only when using 1.8 features. However, it could still be the same underlying problem with the shutdown routines in the free list code. I had originally assumed that it would be extremely rare, but now I will see if I can add that bug to the list of bugs to fix for 1.8.4, and hopefully 1.6.10. If you have an example program that would be helpful.

Thanks,
Neil Fortner
The HDF Group

Michael Jackson wrote:

···

And if I don't have valgrind?

---
Mike Jackson www.bluequartz.net

On Jun 5, 2009, at 2:17 PM, Dominik Szczerba wrote:

I would run the code through valgrind.
-- Dominik

Michael Jackson wrote:

I am getting either one of the following errors when my program exits:
Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap
HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

Abort trap
This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).
I googled a bit for the errors but nothing really jumped out at me. Has anyone seen this type of error before?
In the same project I have lots of other programs all using the same HDF5 library and I am not getting the error. Just kinda popped up today. I rebuilt the hdf5 library and reinstalled but I am still getting the errors. I have ensured that I am closing all the hdf5 files that are opened. I have tried several different hdf5 files and all will give the error.
Any help or nudges in the right direction would be appreciated.
Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio
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Quincey_Koziol · June 5, 2009, 6:38pm

Hi Mike,

And if I don't have valgrind?

Can you try with the recent 1.6.9 release? Even better would be to switch to the [also recent] 1.8.3 release. (Possibly with the v1.6 API compatibility switch enabled)

Quincey

···

On Jun 5, 2009, at 1:26 PM, Michael Jackson wrote:

---
Mike Jackson www.bluequartz.net

On Jun 5, 2009, at 2:17 PM, Dominik Szczerba wrote:

I would run the code through valgrind.
-- Dominik

Michael Jackson wrote:

I am getting either one of the following errors when my program exits:
Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap
HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap
This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).
I googled a bit for the errors but nothing really jumped out at me. Has anyone seen this type of error before?
In the same project I have lots of other programs all using the same HDF5 library and I am not getting the error. Just kinda popped up today. I rebuilt the hdf5 library and reinstalled but I am still getting the errors. I have ensured that I am closing all the hdf5 files that are opened. I have tried several different hdf5 files and all will give the error.
Any help or nudges in the right direction would be appreciated.
Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio
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nfortne2 · June 5, 2009, 6:47pm

Mike,

Neil Fortner wrote:

Mike,

I have seen a similar problem before, but only when using 1.8 features. However, it could still be the same underlying problem with the shutdown routines in the free list code. I had originally assumed that it would be extremely rare, but now I will see if I can add that bug to the list of bugs to fix for 1.8.4, and hopefully 1.6.10. If you have an example program that would be helpful.

As a work around, you can try using H5set_free_list_limits to set lower (or 0) limits for different types of free lists (probably array and/or block). Alternatively, you can try compiling the library with free lists disabled.

-Neil

···

Thanks,
Neil Fortner
The HDF Group

Michael Jackson wrote:

And if I don't have valgrind?

---
Mike Jackson www.bluequartz.net

On Jun 5, 2009, at 2:17 PM, Dominik Szczerba wrote:

I would run the code through valgrind.
-- Dominik

Michael Jackson wrote:

I am getting either one of the following errors when my program exits:
Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap
HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

Abort trap
This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).
I googled a bit for the errors but nothing really jumped out at me. Has anyone seen this type of error before?
In the same project I have lots of other programs all using the same HDF5 library and I am not getting the error. Just kinda popped up today. I rebuilt the hdf5 library and reinstalled but I am still getting the errors. I have ensured that I am closing all the hdf5 files that are opened. I have tried several different hdf5 files and all will give the error.
Any help or nudges in the right direction would be appreciated.
Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio
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Quincey_Koziol · June 5, 2009, 7:21pm

Hi Mike,

Thanks everyone for the suggestions. I did not know about the 1.6.9 release. I'll have to take some time this weekend to move that into my CMake build system for HDF5. Hopefully the changes from 1.6.8 to 1.6.9 are not too extreme.

Version 1.8 is not going to happen for a while (even with the 1.6 API enabled.)

I'll take a look into the H5set_free_list_limits function and documentation to see if that is causing any problems.

Is the reason for the error known? Maybe something I am doing in my code perhaps. Currently the hdf5 code was used in tandem with some ITK code, but only one specific program out of 10 that I wrote. Really odd. I guess I am just massaging something wrong.

Usually, when you get this kind of error, it means that the library is very confused about an object and has lost track of the reference count for it. Sometimes it is triggered by an application misusing the API, but could also be a bug in the library itself. Judging from the way the 'P' is repeated a couple of times before the 'FL' starts looping, I would take a look at your use of the property list API routines and see if you've done anything odd there.

Quincey

···

On Jun 5, 2009, at 2:09 PM, Michael Jackson wrote:

Thanks to all.
---
Mike Jackson www.bluequartz.net

On Jun 5, 2009, at 2:47 PM, Neil Fortner wrote:

Mike,

Neil Fortner wrote:

Mike,

I have seen a similar problem before, but only when using 1.8 features. However, it could still be the same underlying problem with the shutdown routines in the free list code. I had originally assumed that it would be extremely rare, but now I will see if I can add that bug to the list of bugs to fix for 1.8.4, and hopefully 1.6.10. If you have an example program that would be helpful.

As a work around, you can try using H5set_free_list_limits to set lower (or 0) limits for different types of free lists (probably array and/or block). Alternatively, you can try compiling the library with free lists disabled.

-Neil

Thanks,
Neil Fortner
The HDF Group

Michael Jackson wrote:

And if I don't have valgrind?

---
Mike Jackson www.bluequartz.net

On Jun 5, 2009, at 2:17 PM, Dominik Szczerba wrote:

I would run the code through valgrind.
-- Dominik

Michael Jackson wrote:

I am getting either one of the following errors when my program exits:
Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap
HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap
This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).
I googled a bit for the errors but nothing really jumped out at me. Has anyone seen this type of error before?
In the same project I have lots of other programs all using the same HDF5 library and I am not getting the error. Just kinda popped up today. I rebuilt the hdf5 library and reinstalled but I am still getting the errors. I have ensured that I am closing all the hdf5 files that are opened. I have tried several different hdf5 files and all will give the error.
Any help or nudges in the right direction would be appreciated.
Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio
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mike.jackson · June 5, 2009, 6:26pm

And if I don't have valgrind?

···

---
Mike Jackson www.bluequartz.net

On Jun 5, 2009, at 2:17 PM, Dominik Szczerba wrote:

I would run the code through valgrind.
-- Dominik

Michael Jackson wrote:

I am getting either one of the following errors when my program exits:
Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap
HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap
This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).
I googled a bit for the errors but nothing really jumped out at me. Has anyone seen this type of error before?
In the same project I have lots of other programs all using the same HDF5 library and I am not getting the error. Just kinda popped up today. I rebuilt the hdf5 library and reinstalled but I am still getting the errors. I have ensured that I am closing all the hdf5 files that are opened. I have tried several different hdf5 files and all will give the error.
Any help or nudges in the right direction would be appreciated.
Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio
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mike.jackson · June 5, 2009, 7:09pm

Thanks everyone for the suggestions. I did not know about the 1.6.9 release. I'll have to take some time this weekend to move that into my CMake build system for HDF5. Hopefully the changes from 1.6.8 to 1.6.9 are not too extreme.

Version 1.8 is not going to happen for a while (even with the 1.6 API enabled.)

I'll take a look into the H5set_free_list_limits function and documentation to see if that is causing any problems.

Is the reason for the error known? Maybe something I am doing in my code perhaps. Currently the hdf5 code was used in tandem with some ITK code, but only one specific program out of 10 that I wrote. Really odd. I guess I am just massaging something wrong.

Thanks to all.

···

---
Mike Jackson www.bluequartz.net

On Jun 5, 2009, at 2:47 PM, Neil Fortner wrote:

Mike,

Neil Fortner wrote:

Mike,

I have seen a similar problem before, but only when using 1.8 features. However, it could still be the same underlying problem with the shutdown routines in the free list code. I had originally assumed that it would be extremely rare, but now I will see if I can add that bug to the list of bugs to fix for 1.8.4, and hopefully 1.6.10. If you have an example program that would be helpful.

As a work around, you can try using H5set_free_list_limits to set lower (or 0) limits for different types of free lists (probably array and/or block). Alternatively, you can try compiling the library with free lists disabled.

-Neil

Thanks,
Neil Fortner
The HDF Group

Michael Jackson wrote:

And if I don't have valgrind?

---
Mike Jackson www.bluequartz.net

On Jun 5, 2009, at 2:17 PM, Dominik Szczerba wrote:

I would run the code through valgrind.
-- Dominik

Michael Jackson wrote:

I am getting either one of the following errors when my program exits:
Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap
HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap
This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).
I googled a bit for the errors but nothing really jumped out at me. Has anyone seen this type of error before?
In the same project I have lots of other programs all using the same HDF5 library and I am not getting the error. Just kinda popped up today. I rebuilt the hdf5 library and reinstalled but I am still getting the errors. I have ensured that I am closing all the hdf5 files that are opened. I have tried several different hdf5 files and all will give the error.
Any help or nudges in the right direction would be appreciated.
Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio
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Dominik_Szczerba · June 5, 2009, 6:42pm

standard gnu stuff, should be there for MAC too...

Michael Jackson wrote:

···

And if I don't have valgrind?

---
Mike Jackson www.bluequartz.net

On Jun 5, 2009, at 2:17 PM, Dominik Szczerba wrote:

I would run the code through valgrind.
-- Dominik

Michael Jackson wrote:

I am getting either one of the following errors when my program exits:
Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file /Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap
HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap
This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).
I googled a bit for the errors but nothing really jumped out at me. Has anyone seen this type of error before?
In the same project I have lots of other programs all using the same HDF5 library and I am not getting the error. Just kinda popped up today. I rebuilt the hdf5 library and reinstalled but I am still getting the errors. I have ensured that I am closing all the hdf5 files that are opened. I have tried several different hdf5 files and all will give the error.
Any help or nudges in the right direction would be appreciated.
Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio
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mike.jackson · June 6, 2009, 11:41am

Seems the problem followed me to another Mac when I came home do
definitely something wrong. Almost seems like I am stomping on some
memory somewhere. I'll try some other platforms and see what happens.
Unfortunately all I have at home this weekend is Windows XP via
Bootcamp but at least it would give me a sanity check. Just seems odd
that after almost a year of development I start hitting this bug now.
I guess more frustrating than anything else.

Thanks for the input.
Mike

···

On Sat, Jun 6, 2009 at 6:55 AM, Dimitris Servis<servisster@gmail.com> wrote:

I have seen such messages being due to an overrun unrelated to the library
itself. You can also get it when killing the process abruptly. Memory
checking is a good starting point.

HTH

-- dimitris

2009/6/5 Michael Jackson <mike.jackson@bluequartz.net>

I am getting either one of the following errors when my program exits:

Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file
/Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap

HDF5: infinite loop closing library

D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap

This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).

I googled a bit for the errors but nothing really jumped out at me. Has
anyone seen this type of error before?

In the same project I have lots of other programs all using the same HDF5
library and I am not getting the error. Just kinda popped up today. I
rebuilt the hdf5 library and reinstalled but I am still getting the errors.
I have ensured that I am closing all the hdf5 files that are opened. I have
tried several different hdf5 files and all will give the error.

Any help or nudges in the right direction would be appreciated.

Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net

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Dominik_Szczerba · June 6, 2009, 1:01pm

You may try the free Virtualbox, installing latest Ubuntu takes several minutes. Or just boot your Mac off the Live CDROM.
-- Dominik

Mike Jackson wrote:

···

Seems the problem followed me to another Mac when I came home do
definitely something wrong. Almost seems like I am stomping on some
memory somewhere. I'll try some other platforms and see what happens.
Unfortunately all I have at home this weekend is Windows XP via
Bootcamp but at least it would give me a sanity check. Just seems odd
that after almost a year of development I start hitting this bug now.
I guess more frustrating than anything else.

Thanks for the input.
Mike

On Sat, Jun 6, 2009 at 6:55 AM, Dimitris Servis<servisster@gmail.com> wrote:

I have seen such messages being due to an overrun unrelated to the library
itself. You can also get it when killing the process abruptly. Memory
checking is a good starting point.

HTH

-- dimitris

2009/6/5 Michael Jackson <mike.jackson@bluequartz.net>

I am getting either one of the following errors when my program exits:

Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file
/Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap

HDF5: infinite loop closing library

D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap

This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).

I googled a bit for the errors but nothing really jumped out at me. Has
anyone seen this type of error before?

In the same project I have lots of other programs all using the same HDF5
library and I am not getting the error. Just kinda popped up today. I
rebuilt the hdf5 library and reinstalled but I am still getting the errors.
I have ensured that I am closing all the hdf5 files that are opened. I have
tried several different hdf5 files and all will give the error.

Any help or nudges in the right direction would be appreciated.

Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net

----------------------------------------------------------------------
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To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

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sean · June 5, 2009, 7:22pm

Valgrind is basically an x86 emulator and the Mac only switched to Intel
a couple of years ago. When the Mac was PPC a Valgrind port was
basically impossible. Since the Intel switch people have been working
on porting Valgrind to the Mac, but it not yet fully baked. The current
state of Valgrind for the Mac is not for the faint of heart.

···

On 6/5/09 8:42 PM, Dominik Szczerba said:

standard gnu stuff, should be there for MAC too...

Michael Jackson wrote:

And if I don't have valgrind?

--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com
Rogue Research www.rogue-research.com
Mac Software Developer Montréal, Québec, Canada

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mike.jackson · June 6, 2009, 1:17pm

<off topic>I actually use Virtual Box at the office with 2 flavors of
Ubuntu (32 and 64 Bit) and Windows XP. My home machine is in need of a
hard drive upgrade at this point as it does not have the space left
for those virtual machines.</off topic>

Found the culprit. ITK was allowing me to walk of the end of an array
and set some values so basically I was stomping on some memory. I
would have thought the compiler or something would have asserted when
I tried to set a value off the end of an array or ITK would have
asserted when I tried it. Huh. So much for safety nets.

Valgrind probably would have told me all of this. I should get that
setup in the Virtual Machines.

Thanks everyone for the insight into my errors/bugs. Again, the list
has proved invaluable.

Mike Jackson

···

On Sat, Jun 6, 2009 at 9:01 AM, Dominik Szczerba<domi@vision.ee.ethz.ch> wrote:

You may try the free Virtualbox, installing latest Ubuntu takes several
minutes. Or just boot your Mac off the Live CDROM.
-- Dominik

Mike Jackson wrote:

Seems the problem followed me to another Mac when I came home do
definitely something wrong. Almost seems like I am stomping on some
memory somewhere. I'll try some other platforms and see what happens.
Unfortunately all I have at home this weekend is Windows XP via
Bootcamp but at least it would give me a sanity check. Just seems odd
that after almost a year of development I start hitting this bug now.
I guess more frustrating than anything else.

Thanks for the input.
Mike

On Sat, Jun 6, 2009 at 6:55 AM, Dimitris Servis<servisster@gmail.com> >> wrote:

I have seen such messages being due to an overrun unrelated to the
library
itself. You can also get it when killing the process abruptly. Memory
checking is a good starting point.

HTH

-- dimitris

2009/6/5 Michael Jackson <mike.jackson@bluequartz.net>

I am getting either one of the following errors when my program exits:

Assertion failed: (head->list_mem==0), function H5FL_blk_gc_list, file
/Users/mjackson/Workspace/hdf5-168/src/H5FL.c, line 1064.
Abort trap

HDF5: infinite loop closing library

D,G,A,S,T,F,FD,P,D,F,FD,P,FD,P,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Abort trap

This is with hdf5 V16.8 on OS X 10.5.7 Intel (Mac Pro).

I googled a bit for the errors but nothing really jumped out at me. Has
anyone seen this type of error before?

In the same project I have lots of other programs all using the same
HDF5
library and I am not getting the error. Just kinda popped up today. I
rebuilt the hdf5 library and reinstalled but I am still getting the
errors.
I have ensured that I am closing all the hdf5 files that are opened. I
have
tried several different hdf5 files and all will give the error.

Any help or nudges in the right direction would be appreciated.

Thanks
_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net

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Dominik_Szczerba · June 6, 2009, 10:30am

Checking the code on linux might be actually a good test to pass for the code consistency (and you have valgrind). You will know if the problem is your code or the environment.
-- Dominik

Sean McBride wrote:

···

Valgrind is basically an x86 emulator and the Mac only switched to Intel
a couple of years ago. When the Mac was PPC a Valgrind port was
basically impossible. Since the Intel switch people have been working
on porting Valgrind to the Mac, but it not yet fully baked. The current
state of Valgrind for the Mac is not for the faint of heart.

On 6/5/09 8:42 PM, Dominik Szczerba said:

standard gnu stuff, should be there for MAC too...

Michael Jackson wrote:

And if I don't have valgrind?

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