<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">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">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">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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