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<p>Hi Ryan,</p>
<p><br>
</p>
<p>I am using FLASH4.6.2. I tried other available HDF5 versions - <span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">hdf5/intel/1.12.0, </span><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">hdf5/intel/1.12.1</span>
, but received different errors with 10.5 and 12.x (tried with <span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;" id="docs-internal-guid-96418bff-7fff-cfaf-7644-de176ef92480">-DH5_USE_16_API, </span><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;" id="docs-internal-guid-96418bff-7fff-cfaf-7644-de176ef92480">-DH5_USE_110_API, </span><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;" id="docs-internal-guid-96418bff-7fff-cfaf-7644-de176ef92480">-DH5_USE_112_API</span>).<br>
</p>
<p>I also went through the mailing lists where a patch was made
available for FLASH4.5, but it didn't work for me.</p>
<p>Could someone tell me which library versions are compatible with
FLASH 4.6.2? Is there a documentation available for the compatible
HDF5 library and FLASH versions?<br>
</p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt;"><br>
</p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt;">Best,</p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt;">Deepali<br>
</p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt;"><br>
<span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;"></span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;"></span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">
</span></p>
<div class="moz-cite-prefix">On 15.12.22 18:40, Ryan Farber wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAF9W8=3VYhSHjc_wQ=Y+ppYqK-q9pMd9GCgkSi0Kkt+Xr5WAZg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Deepali,
<div><br>
</div>
<div>I think if you search the flash-users mailing list there
were issues with hdf5 1.10.x a few years ago. I think those
were patched but definitely worth trying different hdf5
versions. For reference I'm using
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span
class="gmail-s1"
style="text-decoration-line:underline;font-variant-ligatures:no-common-ligatures">hdf5-mpi/1.8.21</span><span
class="gmail-s2"
style="font-variant-ligatures:no-common-ligatures"><span
class="gmail-Apple-converted-space"> </span></span></p>
<div>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr"><br>
</div>
<div>but I'm still on FLASH4.2.2...which version of
FLASH are you using?</div>
<div><br>
</div>
<div>Best,</div>
<div dir="ltr">--------
<div>Ryan</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Dec 15, 2022 at 12:33
PM Deepali <<a href="mailto:ddeepali@hs.uni-hamburg.de"
moz-do-not-send="true">ddeepali@hs.uni-hamburg.de</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi Ryan,</p>
<p><br>
</p>
<p>Thank you for your reply!</p>
<p>I checked the space on hard drive and majority of it is
available (~ 3 TB). So no problem there. Also I have the
permission to write. Could it be a problem between flash
and the HLRN cluster HDF5 library version?<br>
</p>
<p><br>
</p>
<p>Best,</p>
<p>Deepali<br>
</p>
<p><br>
</p>
<p><br>
</p>
<div>On 12.12.22 18:54, Ryan Farber wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Deepali,
<div><br>
</div>
<div>I haven't seen your error before:<br>
flash4: io_h5create_dataset.c:29: io_h5create_dataset:
Assertion `diskSize[i] > 0' failed.</div>
<div><br>
</div>
<div>But from the sound of it, that file doesn't think
you have space on the hard drive it's trying to write
to. Maybe a permissions problem(?)</div>
<div><br>
</div>
<div>Best,<br clear="all">
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">--------
<div>Ryan</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Dec 12, 2022
at 5:44 PM Deepali <<a
href="mailto:ddeepali@hs.uni-hamburg.de"
target="_blank" moz-do-not-send="true">ddeepali@hs.uni-hamburg.de</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>
<p><span> </span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Dear Flash users & developers,</span></p>
<br>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">I am trying to simulate a 3D Bonnor-Ebert sphere type setup using AMR grid on HLRN machine (<a href="https://www.hlrn.de/doc/display/PUB/Usage+Guide" target="_blank" moz-do-not-send="true">https://www.hlrn.de/doc/display/PUB/Usage+Guide</a>). I use the following compiler and hdf5 modules:</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">
</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">intel/18.0.6 </span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">impi/2018.5(default) </span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">hdf5/intel/1.10.5</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">
</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">But I am facing a problem with the writing of initial HDF5 checkpoint and plot files. FLASH initializes all the units needed and then produces the error mentioned in the simulation log file (flash.log) attached with this email.
</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">
</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">I would appreciate any help or suggestions </span><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">in order to resolve this error. </span>Please
let me know if I should share <span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"></span><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap"></span><span style="font-size:11pt;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">any other information.</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Nunito,sans-serif;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">
</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Nunito,sans-serif;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">
</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Nunito,sans-serif;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Thanks and regards,</span></p>
<p dir="ltr"
style="line-height:1.2;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Nunito,sans-serif;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Deepali</span></p>
</div>
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