<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><span>Hi Tim,</span><div><span><br></span><span>Thanks for the very detailed bug report! </span></div><div><span><br></span><span>I would guess that the issue has to do with the use of the runtime parameter “output_dir” leading to an absolute path for the io output files being too long for the allocated strings. If that’s the case it should be pretty fixable.</span></div><div><span><br></span><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);"><span>As a workaround you should be able to copy the flash4 executable as well as any par and data files (such as EoS/opacity tables) to the desired output directory and launch FLASH directly from there. This way you can leave out the “output_dir” runtime parameter and have FLASH output directly to the CWD.</span><br style="caret-color: rgb(255, 255, 255); color: rgb(255, 255, 255);"></div><br class="Apple-interchange-newline" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);"><div>
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;">*********************************************<br>Adam Reyes</div><br class="Apple-interchange-newline"><span><img alt="FLASH.jpg" src="cid:EA5A7E59-94B9-4162-879C-B52E774AEA24"></span><meta charset="UTF-8"><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">Code Group Leader, Flash Center for </span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">Computational Science</span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">Research Scientist, Dept. of Physics and </span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">Astronomy</span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">University of Rochester</span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">River Campus: Bausch and Lomb Hall, </span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">369</span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;"> </span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;"> </span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">500 Wilson Blvd. PO Box 270171, </span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">Rochester, NY 14627</span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">Email</span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;"> </span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">adam.reyes@rochester.edu</span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; 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font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">https://flash.rochester.edu</span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;"> </span><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none; display: inline !important; float: none;">(he / him / his)</span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;"><span><img alt="FLASH-pride-sml.png" src="cid:CE45460D-2261-4A69-865C-5CF7BEACF620"></span><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;"><br>*********************************************</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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; text-decoration: none;"><br></div><br class="Apple-interchange-newline">
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<div><br><blockquote type="cite"><div>On Sep 5, 2023, at 7:20 PM, Timothy Mark Johnson <tmarkj@mit.edu> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Hi FLASH users and developers,<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">I seem to have found a bug in the code that saves output files in HDF5. I originally noticed this problem with my own simulation, but I was able to replicate the issue with the laserslab example simulation. I’m using the MIT Engaging cluster to run the simulations which has a high performance Lustre file system. I get the errors specifically when I set the FLASH output_directory to the Lustre file system while the simulation directory is in an NFS file system. The issue also only arises if I’m using more than one MPI process.<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">I’ve attached a copy of the error messages without my added debugging statements. I’ve also attached a copy with some debugging statements that I’ve added. The thing I’ve gleaned from the debugging statements is that if my filename in Fortran is too long, the filename in C gets messed up and includes extra bits at the end which cause the problem. This should be visible in the debugging output. I’ve also attached the modified io_h5file_interface.c and io_initFile.F90 files so you can see where I’ve added debugging statements. The io_h5file_interface.c function in question is io_h5init_file. To get the code to crash, I’ve changed the basenm in the flash.par to be “gasjetexp_”, the same as when I discovered this issue.<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">I’ve also attached output from when I changed the basenm to be “test_”. The code works fine in this case, but you can see weird characters at the end of strings. I had to set ignoreForcedPlot to true to get it to work. With the additional characters of “forced” added to the filename, it still crashes. It might just be that my filename plus path is too long.<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Note that the crash code doesn’t give a good “stack trace”. I managed to get a good one with my own simulation which I’ve attached as “original_stacktrace.txt”. This is how I figured out to look at the files discussed earlier.<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">For additional details, I’m using FLASH4.6.2, gcc 6.3.0, openmpi 2.1.1, and HDF5 1.10.5. The gcc is provided by the cluster in a module file but I’ve built openmpi and HDF5 from source. I can provide more details about how I configured/built these libraries if needed. Some information (not very comprehensive) about the engaging cluster can be found here:<span class="Apple-converted-space"> </span><a href="https://engaging-web.mit.edu/eofe-wiki/" style="color: rgb(5, 99, 193); text-decoration: underline;">https://engaging-web.mit.edu/eofe-wiki/</a>.<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">For even more context, here is my FLASH setup command: ./setup -auto LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +uhd3t +mgd mgd_meshgroups=6 -parfile=example.par -without-unit=physics/sourceTerms/EnergyDeposition/EnergyDepositionMain/Laser/LaserIO +hdf5typeIO +parallelIO -objdir=test_laserslab<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">I’ve had to disable LaserIO due to some other problems I’ve had with parallel HDF5 output. I’ve also attached my flash.par file.<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">I hope what I’ve written here is enough to describe the problem. Hopefully other users using Lustre filesystems can be aware of this potential issue.<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Best,<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Tim Johnson<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">PhD Candidate<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">High Energy Density Physics Group<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">MIT Plasma Science and Fusion Center<o:p></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><span id="cid:BA5A2B85-9B95-4247-B1A4-AF86C726F74E"><flash.par></span><span id="cid:A3333425-77DC-4570-9F65-4075E74D8F33"><io_h5file_interface.c></span><span id="cid:F33E33E9-EAA3-446C-A77A-3B7202B24379"><io_initFile.F90></span><span id="cid:E7096A8C-B82B-41A1-A626-A88D1C66F382"><original_stacktrace.txt></span><span id="cid:B04CED15-5D64-4587-96A0-286D651CC0FC"><output_no_debug.txt></span><span id="cid:F62B117F-2BB6-43B1-8613-3FB7ACC817FA"><output_with_debug.txt></span><span id="cid:954E97AE-C0EF-492D-8771-37D271D72339"><output_working.txt></span><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">flash-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><a href="mailto:flash-users@flash.rochester.edu" style="color: rgb(5, 99, 193); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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;">flash-users@flash.rochester.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">For list info, including unsubscribe:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><a href="https://flash.rochester.edu/mailman/listinfo/flash-users" style="color: rgb(5, 99, 193); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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;">https://flash.rochester.edu/mailman/listinfo/flash-users</a></div></blockquote></div><br><div></div></div></body></html>