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<p>Hi Adam & Aaron,</p>
<p><br>
</p>
<p>Thank you for your time and help!</p>
<p>I am using serial HDF5 for AMR grid. I cleaned my Makefile
further and tried running FLASH 4.6.2 again with HDF5 1.10.5 and
1.12.0 (both using<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><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>intel/19.0.5
and impi/2019.5.281). I am getting the following error:</p>
<p dir="ltr"
style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"
id="docs-internal-guid-42540eba-7fff-19f4-fb67-5ab2fb09123c"><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;">Gravity initialized</span></p>
<p dir="ltr"
style="line-height:1.38;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;"> Initial dt verified</span></p>
<p dir="ltr"
style="line-height:1.38;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;"> Particles_sinkAccelSinksOnGasAndSinksOnGas:: sink_softening_type_gas = linear</span></p>
<p dir="ltr"
style="line-height:1.38;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;">HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 46912496411200:</span></p>
<p dir="ltr"
style="line-height:1.38;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;"> #000: H5Ddeprec.c line 126 in H5Dcreate1(): not a location ID</span></p>
<p dir="ltr"
style="line-height:1.38;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 class="Apple-tab-span" style="white-space:pre;"> </span></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;">major: Invalid arguments to routine</span></p>
<p dir="ltr"
style="line-height:1.38;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 class="Apple-tab-span" style="white-space:pre;"> </span></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;">minor: Inappropriate type</span></p>
<p dir="ltr"
style="line-height:1.38;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;"> #001: H5Gloc.c line 246 in H5G_loc(): invalid object ID</span></p>
<p dir="ltr"
style="line-height:1.38;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 class="Apple-tab-span" style="white-space:pre;"> </span></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;">major: Invalid arguments to routine</span></p>
<p dir="ltr"
style="line-height:1.38;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 class="Apple-tab-span" style="white-space:pre;"> </span></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;">minor: Bad value</span></p>
<p dir="ltr"
style="line-height:1.38;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;">Driver_abortC called</span></p>
<p dir="ltr"
style="line-height:1.38;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;">Error: H5Dcreate particle names, io_h5write_particles</span></p>
<br>
<p dir="ltr"
style="line-height:1.38;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;">Calling MPI_Abort for immediate shutdown</span></p>
<p dir="ltr"
style="line-height:1.38;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;">Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0</span></p>
<p><br>
</p>
<p>Please find attached the log (flash*.log) and output files
(op*.log) for each hdf5 version for more details and the Makefile
used. I checked that this query has been addressed before
<a class="moz-txt-link-freetext" href="https://flash.rochester.edu/pipermail/flash-users/2019-September/003039.html">https://flash.rochester.edu/pipermail/flash-users/2019-September/003039.html</a>
but I do not quite understand how to proceed further. <br>
</p>
<p><br>
</p>
<p>Best regards,</p>
<p>Deepali<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 19.12.22 19:05, Adam Reyes wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CACcm6AfMGFmtmQt1e2kHcSpwdabDjc_6yyEFVG6gYkTxRAkrQA@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Deepali,
<div><br>
</div>
<div>FLASH should work with hdf5 1.12.0. Which IO implementation
did you set up with (+hdftTypeIO, +parallelIO)? You could try
the other one. If you could share the log file from the run it
might be helpful as well.</div>
<br clear="all">
<div>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div dir="ltr"
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">*************************************************************************</div>
<div dir="ltr"
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">Adam
Reyes
<div><img
src="https://flash.rochester.edu/site/common/images/email_signature/FLASH.jpg"
moz-do-not-send="true"><br>
</div>
<div>Code Group Leader, Flash Center for Computational
Science <span> </span><br>
</div>
<div>Research Scientist, Dept. of Physics and Astronomy</div>
<div>University of Rochester</div>
<div>River Campus: Bausch and Lomb Hall, 369 <span> </span><br>
</div>
<div>500 Wilson Blvd. PO Box 270171, Rochester, NY 14627</div>
<div dir="ltr">Email<span> </span><a
href="mailto:adam.reyes@rochester.edu"
target="_blank" moz-do-not-send="true">adam.reyes@rochester.edu</a></div>
<div>Web<span> </span><a
href="https://flash.rochester.edu/" target="_blank"
moz-do-not-send="true">https://flash.rochester.edu</a><br>
</div>
<div> (he / him / his)</div>
<div><img
src="https://flash.rochester.edu/site/common/images/email_signature/FLASH-pride-sml.png"
moz-do-not-send="true"><br>
</div>
*************************************************************************</div>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Dec 19, 2022 at 12:00
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>I am using FLASH4.6.2. I tried other available HDF5
versions - <span style="font-size:11pt;font-family:Arial;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/1.12.0, </span><span style="font-size:11pt;font-family:Arial;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/1.12.1</span>
, but received different errors with 10.5 and 12.x (tried
with <span style="font-size:11pt;font-family:Arial;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" id="m_6718985364133676126docs-internal-guid-96418bff-7fff-cfaf-7644-de176ef92480">-DH5_USE_16_API, </span><span style="font-size:11pt;font-family:Arial;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" id="m_6718985364133676126docs-internal-guid-96418bff-7fff-cfaf-7644-de176ef92480">-DH5_USE_110_API, </span><span style="font-size:11pt;font-family:Arial;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" id="m_6718985364133676126docs-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: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:Arial;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:Arial;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>
<div>On 15.12.22 18:40, Ryan Farber wrote:<br>
</div>
<blockquote type="cite">
<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
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
style="text-decoration-line:underline;font-variant-ligatures:no-common-ligatures">hdf5-mpi/1.8.21</span><span
style="font-variant-ligatures:no-common-ligatures"><span> </span></span></p>
<div>
<div dir="ltr">
<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"
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>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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