Hi
I compiled hdf5-1.8.3 with the GrADs system and found many memory leaks on
H5FL.c
It is substantial.
John Huddleston, PhD, PE
···
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Today's Topics:
1. Re: Support for the third party filters with the HDF5
library: Re: [hdf-forum] Lzf support (Mark Miller)
2. Re: Support for the third party filters with the HDF5
library: Re: [hdf-forum] Lzf support (Mark Miller)
3. typo in page name: Re: Support for the third party filters
with the HDF5 library: Re: [hdf-forum] Lzf support (Elena Pourmal)
4. sanity check error (Dimitry Ayzenberg)
5. Re: sanity check error (Elena Pourmal)
6. Re: sanity check error (Dimitry Ayzenberg)
7. Re: sanity check error (Dimitry Ayzenberg)
----------------------------------------------------------------------
Message: 1
Date: Thu, 13 Aug 2009 08:58:01 -0700
From: Mark Miller <miller86@llnl.gov>
Subject: Re: [Hdf-forum] Support for the third party filters with the
HDF5 library: Re: [hdf-forum] Lzf support
To: hdf-forum@hdfgroup.org
Message-ID: <1250179081.6785.423.camel@114 miller86-1.llnl.gov
miller86-1
Content-Type: text/plain; charset=iso-8859-13
Hi Elena,
I'll provide my comments, here, via email.
First, great idea. I like this (service) HDF5 group is trying to offer.
The policy discusses the identifier and what information is required to
'request' an identifier. Are there any requirements on the language its
written it (I assume it has to be C), the platorm(s) it is known to
compile/run on?
Finally, it would be good to establish a small set of benchmark datasets
that compression filters can be tested on. These (uncompressed) HDF5
files could be provided for download from the community filters page
along with the same files with datasets compressed by each of the
filters published there. And, for each filter performance (both time to
compress/decompress as well as amount of compression) of the filter on a
canonical cpu (some machine HDFgroup owns -- all thats important is that
performance results are all obtained from the same machine) be given
along with the link to the filter 'details'
Mark
On Thu, 2009-08-13 at 08:59, Elena Pourmal wrote:
Good morning,
The HDF Group has been working on setting up the process
of registering the third party filters to be used with the HDF5
library (to see the process description go to
http://*wiki.hdfgroup.org/Communite-HDF5-filters-policy)Please visit http://*wiki.hdfgroup.org/ --> "Community Support for
HDF5" (it is the first link on the Front Page) --> HDF5 Filters
to find more about the process and the third party filters LZO, BZIP2,
LZF and BLOSC that have been registered with The HDF Group using the
proposed process.Comment, suggestions are more than welcome.
Thank you!
Elena
On Jul 6, 2009, at 11:45 AM, Elena Pourmal wrote:
> Mag,
>
> The HDF Group doesn't have plans to support any new types of
> compression except GZIP and SZIP supported now, but we have been
> working on defining a process of registering new filters and making
> them available to the HDF5 users? community. Compressions used by
> PyTables and H5Py (i.e., LZF) were our "guinea pigs" and have
> been registered already. More information is coming soon.
>
> Francesc and Andrew,
>
> Thank you for your patience
>
> Elena
>
> On Jul 5, 2009, at 7:48 AM, Mag Gam wrote:
> > Are there any plans to support Lzf natively for HDF5?
> >
> > http://*h5py.alfven.org/lzf/ seems to already implement it but it
> > would
> > be nice if we had it natively...
> >
> > ----------------------------------------------------------------------
> > This mailing list is for HDF software users discussion.
> > 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.
> >
> >
> >
>
>
> _______________________________________________
> 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
--
Mark C. Miller, Lawrence Livermore National Laboratory
email: mailto:miller86@llnl.gov
(M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
(Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
------------------------------
Message: 2
Date: Thu, 13 Aug 2009 09:10:17 -0700
From: Mark Miller <miller86@llnl.gov>
Subject: Re: [Hdf-forum] Support for the third party filters with the
HDF5 library: Re: [hdf-forum] Lzf support
To: hdf-forum@hdfgroup.org
Message-ID: <1250179817.23125.435.camel@114 miller86-1.llnl.gov
miller86-1
Content-Type: text/plain; charset=iso-8859-13
Hi Elena,
One other thing it might be worth mentioning about a compression filter
is whether the compresser supports ONLY lossless compression or both
lossy and lossless compression. Sometimes lossy is useful. Most times
not.
On Thu, 2009-08-13 at 08:58, Mark Miller wrote:
Hi Elena,
I'll provide my comments, here, via email.
First, great idea. I like this (service) HDF5 group is trying to offer.
The policy discusses the identifier and what information is required to
'request' an identifier. Are there any requirements on the language its
written it (I assume it has to be C), the platorm(s) it is known to
compile/run on?Finally, it would be good to establish a small set of benchmark datasets
that compression filters can be tested on. These (uncompressed) HDF5
files could be provided for download from the community filters page
along with the same files with datasets compressed by each of the
filters published there. And, for each filter performance (both time to
compress/decompress as well as amount of compression) of the filter on a
canonical cpu (some machine HDFgroup owns -- all thats important is that
performance results are all obtained from the same machine) be given
along with the link to the filter 'details'Mark
On Thu, 2009-08-13 at 08:59, Elena Pourmal wrote:
> Good morning,
>
> The HDF Group has been working on setting up the process
> of registering the third party filters to be used with the HDF5
> library (to see the process description go to
> http://*wiki.hdfgroup.org/Communite-HDF5-filters-policy)
>
> Please visit http://*wiki.hdfgroup.org/ --> "Community Support for
> HDF5" (it is the first link on the Front Page) --> HDF5 Filters
> to find more about the process and the third party filters LZO, BZIP2,
> LZF and BLOSC that have been registered with The HDF Group using the
> proposed process.
>
> Comment, suggestions are more than welcome.
>
> Thank you!
>
> Elena
>
>
> On Jul 6, 2009, at 11:45 AM, Elena Pourmal wrote:
> > Mag,
> >
> > The HDF Group doesn't have plans to support any new types of
> > compression except GZIP and SZIP supported now, but we have been
> > working on defining a process of registering new filters and making
> > them available to the HDF5 users? community. Compressions used by
> > PyTables and H5Py (i.e., LZF) were our "guinea pigs" and have
> > been registered already. More information is coming soon.
> >
> > Francesc and Andrew,
> >
> > Thank you for your patience
> >
> > Elena
> >
> > On Jul 5, 2009, at 7:48 AM, Mag Gam wrote:
> > > Are there any plans to support Lzf natively for HDF5?
> > >
> > > http://*h5py.alfven.org/lzf/ seems to already implement it but it
> > > would
> > > be nice if we had it natively...
> > >
> > >
----------------------------------------------------------------------
> > > This mailing list is for HDF software users discussion.
> > > 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.
> > >
> > >
> > >
> >
> >
> > _______________________________________________
> > 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
--
Mark C. Miller, Lawrence Livermore National Laboratory
email: mailto:miller86@llnl.gov
(M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
(Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
------------------------------
Message: 3
Date: Thu, 13 Aug 2009 11:27:26 -0500
From: Elena Pourmal <epourmal@hdfgroup.org>
Subject: [Hdf-forum] typo in page name: Re: Support for the third
party filters with the HDF5 library: Re: [hdf-forum] Lzf support
To: hdf-forum@hdfgroup.org
Message-ID: <A4034C0F-520E-4020-BAD2-101683CF9398@hdfgroup.org>
Content-Type: text/plain; charset="windows-1252"; Format="flowed";
DelSp="yes"
I apologize for the multiple emails.
There was a typo in the page name that was brought to my attention. It
was fixed. Here is the new link to the policy description
https://hdf5dev.pbworks.com/Community-HDF5-filters-policy
Elena
On Aug 13, 2009, at 10:59 AM, Elena Pourmal wrote:
Good morning,
The HDF Group has been working on setting up the process of
registering the third party filters to be used with the HDF5 library
(to see the process description go to
http://wiki.hdfgroup.org/Communite-HDF5-filters-policy)
Please visit http://wiki.hdfgroup.org/ --> "Community Support for
HDF5" (it is the first link on the Front Page) --> HDF5 Filters
to find more about the process and the third party filters LZO,
BZIP2, LZF and BLOSC that have been registered with The HDF Group
using the proposed process.Comment, suggestions are more than welcome.
Thank you!
Elena
On Jul 6, 2009, at 11:45 AM, Elena Pourmal wrote:
Mag,
The HDF Group doesn't have plans to support any new types of
compression except GZIP and SZIP supported now, but we have been
working on defining a process of registering new filters and making
them available to the HDF5 users? community. Compressions used by
PyTables and H5Py (i.e., LZF) were our "guinea pigs" and have been
registered already. More information is coming soon.Francesc and Andrew,
Thank you for your patience
Elena
On Jul 5, 2009, at 7:48 AM, Mag Gam wrote:
Are there any plans to support Lzf natively for HDF5?
http://h5py.alfven.org/lzf/ seems to already implement it but it
would
be nice if we had it natively...----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
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._______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org_______________________________________________
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http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
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Message: 4
Date: Thu, 13 Aug 2009 21:56:37 -0400
From: "Dimitry Ayzenberg" <dayzenbe@andrew.cmu.edu>
Subject: [Hdf-forum] sanity check error
To: hdf-forum@hdfgroup.org
Message-ID:
<9bdcb4014a19f57337c6e7912ae08e5f.squirrel@webmail.andrew.cmu.edu>
Content-Type: text/plain;charset=iso-8859-1
I'm trying to configure hdf5 through cygwin on vista and I'm getting an
error saying that: C++ preprocessor "/lib/cpp" fails sanity check. I was
wondering if anyone could help me out with why that's coming up. I have
installed g++ into cygwin and everything else that hdf5 should need. I
didn't email the helpdesk because I figure I'll get a faster response from
here. Thanks for any help.
--
Dimitry Ayzenberg
Carnegie Mellon University
Physics - Class of 2012
Email: dayzenbe@andrew.cmu.edu
------------------------------
Message: 5
Date: Thu, 13 Aug 2009 21:08:05 -0500
From: Elena Pourmal <epourmal@hdfgroup.org>
Subject: Re: [Hdf-forum] sanity check error
To: hdf-forum@hdfgroup.org
Message-ID: <E135A7F9-6009-4F10-AB29-672983085014@hdfgroup.org>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Dimitry,
Did you set any CPP flags before doing configure? (don't do it)
Please also see instructions in the release_docs directory, the
INSTALL_Cygwin.txt file
Elena
On Aug 13, 2009, at 8:56 PM, Dimitry Ayzenberg wrote:
I'm trying to configure hdf5 through cygwin on vista and I'm getting
an
error saying that: C++ preprocessor "/lib/cpp" fails sanity check. I
was
wondering if anyone could help me out with why that's coming up. I
have
installed g++ into cygwin and everything else that hdf5 should need. I
didn't email the helpdesk because I figure I'll get a faster
response from
here. Thanks for any help.--
Dimitry Ayzenberg
Carnegie Mellon University
Physics - Class of 2012
Email: dayzenbe@andrew.cmu.edu_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
------------------------------
Message: 6
Date: Thu, 13 Aug 2009 22:24:36 -0400
From: "Dimitry Ayzenberg" <dayzenbe@andrew.cmu.edu>
Subject: Re: [Hdf-forum] sanity check error
To: hdf-forum@hdfgroup.org
Message-ID:
<76ca99c9e7eff893082f78008e2276f1.squirrel@webmail.andrew.cmu.edu>
Content-Type: text/plain;charset=iso-8859-1
No I didn't set any flags and I looked at those instructions. They don't
really say much. I just need a basic install anyway. Do you want me to
post the config.log file?
On Thu, August 13, 2009 22:08, Elena Pourmal wrote:
Dimitry,
Did you set any CPP flags before doing configure? (don't do it)
Please also see instructions in the release_docs directory, the
INSTALL_Cygwin.txt fileElena
On Aug 13, 2009, at 8:56 PM, Dimitry Ayzenberg wrote:I'm trying to configure hdf5 through cygwin on vista and I'm getting
an error saying that: C++ preprocessor "/lib/cpp" fails sanity check. I
was wondering if anyone could help me out with why that's coming up. I
have installed g++ into cygwin and everything else that hdf5 should
need. I didn't email the helpdesk because I figure I'll get a faster
response from here. Thanks for any help.--
Dimitry Ayzenberg
Carnegie Mellon University
Physics - Class of 2012
Email: dayzenbe@andrew.cmu.edu_______________________________________________
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
--
Dimitry Ayzenberg
Carnegie Mellon University
Physics - Class of 2012
Cell:(732)-425-4534
Email: dayzenbe@andrew.cmu.edu
------------------------------
Message: 7
Date: Thu, 13 Aug 2009 23:45:16 -0400
From: "Dimitry Ayzenberg" <dayzenbe@andrew.cmu.edu>
Subject: Re: [Hdf-forum] sanity check error
To: hdf-forum@hdfgroup.org
Message-ID:
<6ea1944d540207de4647e1c0400718a8.squirrel@webmail.andrew.cmu.edu>
Content-Type: text/plain;charset=iso-8859-1
So I found that the problem is that the configuration is looking for
lib/cpp but no such file exists in lib. I don't know how to fix that
though.
On Thu, August 13, 2009 22:08, Elena Pourmal wrote:
Dimitry,
Did you set any CPP flags before doing configure? (don't do it)
Please also see instructions in the release_docs directory, the
INSTALL_Cygwin.txt fileElena
On Aug 13, 2009, at 8:56 PM, Dimitry Ayzenberg wrote:I'm trying to configure hdf5 through cygwin on vista and I'm getting
an error saying that: C++ preprocessor "/lib/cpp" fails sanity check. I
was wondering if anyone could help me out with why that's coming up. I
have installed g++ into cygwin and everything else that hdf5 should
need. I didn't email the helpdesk because I figure I'll get a faster
response from here. Thanks for any help.--
Dimitry Ayzenberg
Carnegie Mellon University
Physics - Class of 2012
Email: dayzenbe@andrew.cmu.edu_______________________________________________
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
--
Dimitry Ayzenberg
Carnegie Mellon University
Physics - Class of 2012
Cell:(732)-425-4534
Email: dayzenbe@andrew.cmu.edu
------------------------------
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
End of Hdf-forum Digest, Vol 2, Issue 18
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