<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="">Hi Jacob,<div class=""><br class=""></div><div class="">I don’t have a solution, but I will chime in and say that you’re not crazy and not doing anything wrong. I’ve seen exactly this type of behavior with VisIt many times. It’s like each process allocates enough memory for the entire dataset… What’s more is that there are clearly memory leaks to boot. For example, when making movies of a series of large FLASH plot files, I would see memory crashes after roughly the same number of frame creations. Then restarting the movie making from where it left off would work fine, until the magic number of frames had again been made… </div><div class=""><br class=""></div><div class="">As far as file size go, VisIt should have no problem with ~16 Gb files. I routinely visualize plot files that are 100s of Gb in size. But doing it in parallel is always a pain… </div><div class=""><br class=""></div><div class="">I’ve looked briefly into the FLASH reader for VisIt and I don’t think the bug is there. The reader is extremely simple. I think the bug must be in the VisIt source itself. And it’s been there for a very long time…</div><div class=""><br class=""></div><div class="">Sorry, this is not helpful but I don’t have a good solution. Except to switch to yt as John suggests (but in my experience that’s no panacea, either…).</div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">Sean</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class="">----------------------------------------------------------------------------------------------------------<br class="">Sean M. Couch</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Assistant Professor<br class="">Department of Physics and Astronomy<br class="">Department of Computational Mathematics, Science, and Engineering<br class="">National Superconducting Cyclotron Laboratory/Facility for Rare Isotope Beams<br class="">Michigan State University<br class="">567 Wilson Rd, 3250 BPS<br class="">East Lansing, MI 48824<br class="">(517) 884-5035 —— <a href="mailto:couch@pa.msu.edu" class="">couch@pa.msu.edu</a> —— <a href="http://www.pa.msu.edu/~couch" class="">www.pa.msu.edu/~couch</a></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""><div class=""><br class=""><br class=""><br class=""></div></div></div></div></div></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Jul 8, 2016, at 10:02 AM, John ZuHone <<a href="mailto:jzuhone@space.mit.edu" class="">jzuhone@space.mit.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Jacob,<div class=""><br class=""></div><div class="">I know this question is about VisIt, but I should point out that FLASH support for VisIt has lingered for quite some time now. </div><div class=""><br class=""></div><div class="">yt is a pretty powerful package for dealing with FLASH data—it’s one of the data types that has the fullest support in yt, and you can do a lot more than you can in VisIt.</div><div class=""><br class=""></div><div class="">Find out more at <a href="http://yt-project.org/" class="">http://yt-project.org</a>, or ping me off-list at <a href="mailto:john.zuhone@cfa.harvard.edu" class="">john.zuhone@cfa.harvard.edu</a> if you have more questions. </div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">John Z<br class="">
<br class=""><div class=""><blockquote type="cite" class=""><div class="">On Jul 8, 2016, at 9:59 AM, McFarland, Jacob A. <<a href="mailto:mcfarlandja@missouri.edu" class="">mcfarlandja@missouri.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; direction: ltr; font-family: Tahoma; font-size: 10pt;" class="">All,<br class=""><br class="">I just wanted to ping the community one more time to see if anyone has any suggestions on this issue. I have not received any feedback yet but I have received emails from some other users with this issue.<span class="Apple-converted-space"> </span><br class=""><br class="">Thanks for any help you can provide.<span class="Apple-converted-space"> </span><br class=""><br class="">- Jacob<br class=""><div style="font-family: 'Times New Roman'; font-size: 16px;" class=""><hr tabindex="-1" class=""><div id="divRpF925082" style="direction: ltr;" class=""><font face="Tahoma" size="2" class=""><b class="">From:</b><span class="Apple-converted-space"> </span><a href="mailto:flash-users-bounces@flash.uchicago.edu" class="">flash-users-bounces@flash.uchicago.edu</a><span class="Apple-converted-space"> </span>[<a href="mailto:flash-users-bounces@flash.uchicago.edu" class="">flash-users-bounces@flash.uchicago.edu</a>] on behalf of McFarland, Jacob A.<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, July 05, 2016 9:00 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:flash-users@flash.uchicago.edu" class="">flash-users@flash.uchicago.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[FLASH-USERS] larger FLASH hdf5 files in visit<br class=""></font><br class=""></div><div class=""></div><div class=""><div style="direction: ltr; font-family: Tahoma; font-size: 10pt;" class="">Hello all,<br class=""><br class="">I emailed the visit users group with this issue but I have not received any info back yet. As this is a problem many of you may have encountered with FLASH data I thought the FLASH users group might have some advice as well.<span class="Apple-converted-space"> </span><br class=""><br class="">I am having a problem with Visit consuming a lot of memory when opening FLASH hdf5 files. I have simulations with about 50E6 nodes on the fluid mesh and about 20k particles. The hdf5 files are written with parallel hdf5 (I ran the setup with +hdf5TypeIO). The chk files are 5-16gb or so in size, getting larger in time as there are more nodes at later times.<span class="Apple-converted-space"> </span><br class=""><br class="">When I open the files with Visit each processor seems to consume enough memory to open the whole chk file no matter how many processor I throw at it. This means I end up memory limited and have to rune with very few processor on each computer node.<span class="Apple-converted-space"> </span><br class=""><br class="">I expected visit would be able to break up the hdf5 files so that each processor would not need the whole file in memory. This is the behavior I have seen when using other codes with data in the silo format.<span class="Apple-converted-space"> </span><br class=""><br class="">Is this the normal behavior for visit with large FLASH data files?<span class="Apple-converted-space"> </span><br class=""><br class="">If not, any suggestions on what I am doing wrong?<br class=""><br class="">If so, any suggestions on how to mitigate this memory problem?<br class=""><br class="">Thanks,<br class="">Jacob</div></div></div></div></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></body></html>