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<div class="moz-cite-prefix">Hello,<br>
<br>
I opened <a class="moz-txt-link-freetext" href="https://redmine.gromacs.org/issues/3269">https://redmine.gromacs.org/issues/3269</a> for this and
should have a fix for it soon.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Cheers<br>
<br>
Paul<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 27/12/2019 10:12, Erik Lindahl
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAEJJM8HSF0ZqCuc9G63LZkrEM-Y4Nk0ctqYijtBhmVdaTvLANA@mail.gmail.com">
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<div dir="ltr">Hi Len & Jonathan,
<div><br>
</div>
<div>Paul found an issue related to different-endianness-reading
that has apparently slipped through the Debian tests (since
they didn't run the regression tests by default). We'll get a
fix in for that before the release.</div>
<div><br>
</div>
<div>The reason for the change is that the XDR I/IO layer is
becoming very outdated. First, while it made a lot of sense to
stick to the standard (big) "network endian" in the late 90s,
today the problem is that virtually every single architecture
is little endian, so you incur all the overhead of swapping
both on writing and reading. Second, the way this is
implemented in XDR means it's very slow - we're basically
doing byte-by-byte reading.</div>
<div><br>
</div>
<div>This change will instead allow all architectures to use
highly efficient buffered I/O in their default endian, and
then we only have to bother about swapping endianness in the
rare cases an actual big-endian machine is involved.</div>
<div><br>
</div>
<div>We'll also look into the one-padding; for Gromacs it
doesn't matter, but avoiding that might indeed make the life
of other codes easier.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Erik</div>
<div><br>
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<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Dec 26, 2019 at 11:04
PM Jonathan Barnoud <<a href="mailto:jonathan@barnoud.net"
moz-do-not-send="true">jonathan@barnoud.net</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div>
<div>Hello everyone,<br>
</div>
<div><br>
</div>
<div>I upgraded the code of MDAnalysis to read the latest
TPR version. To add to Len's comments, it appears indeed
that the new TPR body is 4 times as big as it use to be
for the same content, and is not portable between
architectures. gmx dump does fail at reading a file with a
different byte order than native, and there is no obvious
way to determine the endianness of the body. While the TPR
format is not meant to really be portable, it seemed
commonly agreed that it was a good file to share (<a
href="https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00665"
target="_blank" moz-do-not-send="true">https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00665</a>),
it is for sure a good input file in MDAnalysis. TPR files
are commonly produced on a local machine before being
actually run on a cluster, that may use a different byte
order.<br>
</div>
<div><br>
</div>
<div>> Second the individual bytes of a value are padded
to 4 bytes per original bytes (each byte is packed as
`char`). <br>
</div>
<div><br>
</div>
<div>To be noted that the in-file XDR decoder in gromacs
(used for the header and prior to gromacs 2020) uses 4
bytes for "char", hence the padding. The in-memory one
reads 1 padded byte (1 byte of information, 4 bytes in the
file).</div>
<div><br>
</div>
<div>As my use case for noticing these differences is fairly
niche, I may be missing the reason for them. In such case,
I would be curious to read about them.<br>
</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Jonathan<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>On 12/26/19 7:39 PM, Len Kimms wrote:<br>
</div>
<blockquote type="cite">
<pre>Hello everyone,
while fooling around with the new (i.e. version 2020 rc1) TPR file format I noticed some strange behaviors that I don’t understand. As far as I understand the body of the new format is written by the `gmx::InMemorySerializer`. My following questions are basically about this module.
First it seems that the memory serializer writes the values in native byte order. This means that the body of TPR files differ between big- and little-endian systems. The XDR standard used before requires big-endian data. For me, a novice user, the new implementation seems to be less portable and robust. Endian swapping seems to be implemented but not currently used for TPR files.
Is this intentional, if so, why?
Second the individual bytes of a value are padded to 4 bytes per original bytes (each byte is packed as `char`). Therefore the size increases accordingly.
Do those padding bytes serve a special purpose?
Also regarding the padding bytes: Some bytes are not, like most others, padded with zeros. In some places they are padded with ones. At first glance this seem to happen to the second byte (big-endian) of a float. From some initial testing my best guess is, that this is caused by the union conversion in `CharBuffer`. With an `unsigned char` in the private union `u` those values would be zero padded.
In the attachment one could find example files from a big- and little-endian system as well as a file created with GROMACS 2019.
I also brought this to the attention of the MDAnalysis devs here:
<a href="https://github.com/MDAnalysis/mdanalysis/issues/2428" target="_blank" moz-do-not-send="true">https://github.com/MDAnalysis/mdanalysis/issues/2428</a>
Best regards,
Len</pre>
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-- <br>
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<div dir="ltr">
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<div dir="ltr">
<div>
<div dir="ltr">
<div>Erik Lindahl <<a
href="mailto:erik.lindahl@dbb.su.se"
target="_blank" moz-do-not-send="true">erik.lindahl@dbb.su.se</a>></div>
<div>Professor of Biophysics, Dept. Biochemistry
& Biophysics, Stockholm University</div>
<div>Science for Life Laboratory, Box 1031, 17121
Solna, Sweden</div>
</div>
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<pre class="moz-signature" cols="72">--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594</pre>
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