<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear all,<div class=""><br class=""></div><div class="">after some fights with dependencies and pip I finally managed to get a working version of YT using h5py 2.5.0.</div><div class=""><br class=""></div><div class="">Thank you very much for the fast support.</div><div class="">Philipp</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 19 Oct 2016, at 18:57, Dominik Derigs <<a href="mailto:derigs@ph1.uni-koeln.de" class="">derigs@ph1.uni-koeln.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi again,<div class=""><br class=""></div><div class="">I can confirm that downgrading h5py from 2.6.0 to 2.5.0 fixed the issue for me.</div><div class=""><br class=""></div><div class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><font face="monospace, monospace" class="">>>> ds = yt.load("DensTurbMag_hdf5_plt_cnt_0015")<br class=""></font><font face="monospace, monospace" class="">yt : [INFO ] 2016-10-19 18:56:40,998 Parameters: current_time = 751000000000.0<br class=""></font><font face="monospace, monospace" class="">yt : [INFO ] 2016-10-19 18:56:40,999 Parameters: domain_dimensions = [8 8 8]<br class=""></font><font face="monospace, monospace" class="">yt : [INFO ] 2016-10-19 18:56:40,999 Parameters: domain_left_edge = [ -2.00000000e+18 -2.00000000e+18 -2.00000000e+18]<br class=""></font><font face="monospace, monospace" class="">yt : [INFO ] 2016-10-19 18:56:40,999 Parameters: domain_right_edge = [ 2.00000000e+18 2.00000000e+18 2.00000000e+18]<br class=""></font><font face="monospace, monospace" class="">yt : [INFO ] 2016-10-19 18:56:40,999 Parameters: cosmological_simulation = 0.0</font></blockquote></div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Dominik</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2016-10-19 18:11 GMT+02:00 Nathan Goldbaum <span dir="ltr" class=""><<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">So it turns out this is due to a regression in the h5py library:<div class=""><br class=""></div><div class=""><a href="https://github.com/h5py/h5py/issues/764" target="_blank" class="">https://github.com/h5py/h5py/<wbr class="">issues/764</a><br class=""></div><div class=""><br class=""></div><div class="">If you'd like a quick workaround without Kacper's pull request, you just need to forcibly downgrade h5py:</div><div class=""><br class=""></div><div class=""> $ conda uninstall h5py</div><div class=""> $ conda install h5py==2.5.0</div><div class=""><br class=""></div><div class="">or if you use pip:</div><div class=""><br class=""></div><div class=""> $ pip uninstall h5py</div><div class=""> $ pip install h5py==2.5.0</div><div class=""><br class=""></div><div class="">Hopefully Kacper's fix will be in by the time we release yt 3.3.2 and you'll be able to upgrade h5py once again and hopefully the h5py bug will be fixed by the time the next version fo h5py comes out.</div><span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">-Nathan</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Oct 19, 2016 at 11:05 AM, Philipp <span dir="ltr" class=""><<a href="mailto:keule-phg@gmx.de" target="_blank" class="">keule-phg@gmx.de</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Kacper,<br class="">
<br class="">
sure you can add those files to the official testing suite!<br class="">
<br class="">
<br class="">
Dear Alex,<br class="">
<br class="">
I installed yt on a “clean” machine using pip and I still get the error that also Dominik confirmed.<br class="">
<br class="">
Thank you and best regards,<br class="">
Philipp<br class="">
<div class="m_2495466698145701960HOEnZb"><div class="m_2495466698145701960h5"><br class="">
<br class="">
> On 19 Oct 2016, at 17:33, Kacper Kowalik <<a href="mailto:xarthisius.kk@gmail.com" target="_blank" class="">xarthisius.kk@gmail.com</a>> wrote:<br class="">
><br class="">
> On 10/18/2016 09:11 AM, Philipp wrote:<br class="">
>> Hi Nathan,<br class="">
>><br class="">
>> thank you for the fast reply. Sorry, I didn’t check the sample data<br class="">
>> for F2.5 files. I uploaded a small test file here:<br class="">
>> <a href="http://use.yt/upload/b895e885" rel="noreferrer" target="_blank" class="">http://use.yt/upload/b895e885</a> <<a href="http://use.yt/upload/b895e885" rel="noreferrer" target="_blank" class="">http://use.yt/upload/b895e885</a><wbr class="">> which<br class="">
>> is at time 0 (maybe not a very clever idea if the time is read<br class="">
>> incorrectly) and another file (<a href="http://use.yt/upload/1106d6c4" rel="noreferrer" target="_blank" class="">http://use.yt/upload/1106d6c4</a><br class="">
>> <<a href="http://use.yt/upload/1106d6c4" rel="noreferrer" target="_blank" class="">http://use.yt/upload/1106d6c4</a><wbr class="">>) at time 23.8 kyr. The block size is<br class="">
>> [8,8,8].<br class="">
>><br class="">
>> With best regards,<br class="">
>> Philipp<br class="">
><br class="">
> Hi Phillip,<br class="">
> can I add those datasets to yt's testing suite? That mandates having<br class="">
> them publicly available at <a href="http://yt-project.org/data/" rel="noreferrer" target="_blank" class="">http://yt-project.org/data/</a><br class="">
><br class="">
> I've also opened PR 2421 [1] that hopefully will fix the issue you're<br class="">
> seeing.<br class="">
><br class="">
> Cheers,<br class="">
> Kacper<br class="">
><br class="">
> [1] <a href="https://bitbucket.org/yt_analysis/yt/pull-requests/2421" rel="noreferrer" target="_blank" class="">https://bitbucket.org/yt_analy<wbr class="">sis/yt/pull-requests/2421</a><br class="">
><br class="">
><br class="">
>>> On 18 Oct 2016, at 15:37, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>><br class="">
>>> wrote:<br class="">
>>><br class="">
>>> Hi Phillip,<br class="">
>>><br class="">
>>> I don't think we have any Flash2.5 test data on <a href="http://yt-project.org/data" rel="noreferrer" target="_blank" class="">yt-project.org/data</a><br class="">
>>> <<a href="http://yt-project.org/data" rel="noreferrer" target="_blank" class="">http://yt-project.org/data</a>>. We use the datasets there in our test<br class="">
>>> suite, so if we don't have any such data that means that our<br class="">
>>> support for a data format isn't tested and is subject to breakage.<br class="">
>>><br class="">
>>> Would you be willing to share some test data that the yt project<br class="">
>>> can use for debugging purposes? It should be relatively small,<br class="">
>>> should trigger the error you're seeing, and should be ok to host<br class="">
>>> publicly on <a href="http://yt-project.org/data" rel="noreferrer" target="_blank" class="">yt-project.org/data</a> <<a href="http://yt-project.org/data" rel="noreferrer" target="_blank" class="">http://yt-project.org/data</a>> and<br class="">
>>> use in our test suite. If so, we can look into restoring support<br class="">
>>> and making sure we don't regress again.<br class="">
>>><br class="">
>>> You can share the data using e.g. Dropbox, google drive, or by<br class="">
>>> using the yt curldrop:<br class="">
>>><br class="">
>>> <a href="https://docs.hub.yt/services.html#curldrop" rel="noreferrer" target="_blank" class="">https://docs.hub.yt/services.h<wbr class="">tml#curldrop</a><br class="">
>>> <<a href="https://docs.hub.yt/services.html#curldrop" rel="noreferrer" target="_blank" class="">https://docs.hub.yt/services.<wbr class="">html#curldrop</a>><br class="">
>>><br class="">
>>> Nathan<br class="">
>>><br class="">
>>> On Tuesday, October 18, 2016, Philipp Girichidis <<a href="mailto:keule-phg@gmx.de" target="_blank" class="">keule-phg@gmx.de</a><br class="">
>>> <mailto:<a href="mailto:keule-phg@gmx.de" target="_blank" class="">keule-phg@gmx.de</a>>> wrote: Dear YT users,<br class="">
>>><br class="">
>>> I upgraded my version of YT from an older version that still<br class="">
>>> installed the libraries on its own (version downloaded 2016/06/21)<br class="">
>>> to a more recent version using yt-conda. With the new version I<br class="">
>>> cannot read old FLASH2.5 data any more. The previous version of yt<br class="">
>>> gave me the correct output<br class="">
>>><br class="">
>>> yt : [INFO ] 2016-09-09 16:37:59,285 Parameters: current_time<br class="">
>>> = 1260000000.0 yt : [INFO ] 2016-09-09 16:37:59,286 Parameters:<br class="">
>>> domain_dimensions = [8 8 8] yt : [INFO ] 2016-09-09<br class="">
>>> 16:37:59,289 Parameters: domain_left_edge = [<br class="">
>>> -4.00000000e+17 -4.00000000e+17 -4.00000000e+17] yt : [INFO ]<br class="">
>>> 2016-09-09 16:37:59,290 Parameters: domain_right_edge = [<br class="">
>>> 4.00000000e+17 4.00000000e+17 4.00000000e+17] yt : [INFO ]<br class="">
>>> 2016-09-09 16:37:59,291 Parameters: cosmological_simulation =<br class="">
>>> 0.0<br class="">
>>><br class="">
>>> the new version does not read some of the numbers properly,<br class="">
>>><br class="">
>>> yt : [INFO ] 2016-09-09 16:39:11,692 Parameters: current_time<br class="">
>>> = 1.06099789548e-313 yt : [INFO ] 2016-09-09 16:39:11,692<br class="">
>>> Parameters: domain_dimensions = [1104332420 0<br class="">
>>> 1102957925] yt : [INFO ] 2016-09-09 16:39:11,693 Parameters:<br class="">
>>> domain_left_edge = [ -4.00000000e+17 -4.00000000e+17<br class="">
>>> -4.00000000e+17] yt : [INFO ] 2016-09-09 16:39:11,694<br class="">
>>> Parameters: domain_right_edge = [ 4.00000000e+17<br class="">
>>> 4.00000000e+17 4.00000000e+17] yt : [INFO ] 2016-09-09<br class="">
>>> 16:39:11,695 Parameters: cosmological_simulation = 0.0<br class="">
>>><br class="">
>>> The time value as well as the dimensions are messed up and thus yt<br class="">
>>> crashes with a memory error at some point. To me it looks like a<br class="">
>>> conversion problem between big and little endian or some similar<br class="">
>>> conversion problem between single and double precision. I tried<br class="">
>>> various combinations of MAC and linux and the problem does not seem<br class="">
>>> to operating system dependent.<br class="">
>>><br class="">
>>> Quite a few functions have changed in terms of reading particle<br class="">
>>> data, but the simulation does not contain particles. I tried to<br class="">
>>> find the part of the code that reads the domain_dimensions and<br class="">
>>> looked at file<br class="">
>>> yt-conda/lib/python2.7/site-pa<wbr class="">ckages/yt/frontends/flash/data<wbr class="">_structures.py<br class="">
>>><br class="">
>>><br class="">
> where in line 99ff the block dimensions are read. But this part of the<br class="">
> code is not executed (checked with print statements in iyt). Loading the<br class="">
> hdf5 file with h5py and using the code in line 104 gives me the correct<br class="">
> numbers, but I guess yt reads the data from somewhere else?<br class="">
>>><br class="">
>>> Any hints on how the hierarchy of reading data is organized or<br class="">
>>> where to search? I know FLASH2.5 is very old but we still have a<br class="">
>>> lot of (quite expensive) F2.5 data.<br class="">
>>><br class="">
>>> With best regards, Philipp Girichidis<br class="">
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<br class=""></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Dominik Derigs<br class="">I. Physikalisches Institut<br class="">Universität zu Köln<br class="">Zülpicher Straße 77<br class="">50937 Köln<br class="">GERMANY</div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class=""><a href="https://hera.ph1.uni-koeln.de/~derigs/" target="_blank" class="">https://hera.ph1.uni-koeln.de/~derigs/</a><br class=""><br class="">Tel. (+49|0) 221 470-8352<br class="">Fax. (+49|0) 221 470-5162<br class=""><br class="">Diese Email ist vertraulich und nur für den angegebenen Empfänger bestimmt. Zugang, Freigabe, die Kopie, die Verteilung oder Weiterleitung durch jemand anderen außer dem Empfänger selbst ist verboten und kann eine kriminelle Handlung sein. Bitte löschen Sie die Email, wenn Sie sie durch einen Fehler erhalten haben und informieren Sie den Absender.<br class=""><br class="">This email and any files transmitted with it may contain confidential and/or privileged material and is intended only for the person or entity to which it is addressed. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you have received this email in error, please notify the sender immediately and delete this material from all known records.</div></div></div></div></div></div></div></div>
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