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Hi, Divyanshu When PnetCDF is configured with option "--enable-debug" and the environment variable PNETCDF_VERBOSE_DEBUG_MODE is set to 1, additional error messages describing the bound violation will be printed on screen. It may help</div>
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Hi, Divyanshu
<div><br>
</div>
<div>When PnetCDF is configured with option "--enable-debug" and</div>
<div>the environment variable PNETCDF_VERBOSE_DEBUG_MODE is set to 1,</div>
<div>additional error messages describing the bound violation will</div>
<div>be printed on screen. It may help you find the source code location</div>
<div>that produces the error.</div>
<div><br id="lineBreakAtBeginningOfMessage">
<div>
<div>Wei-keng</div>
</div>
<div><br>
<blockquote type="cite">
<div>On Jul 14, 2025, at 7:56 AM, Divyanshu Gola <divyans@umich.edu> wrote:</div>
<br class="Apple-interchange-newline">
<div>
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contain: revert !important; container-name: revert !important; container-type: revert !important; content: revert !important; content-visibility: revert !important; counter-increment: revert !important; counter-reset: revert !important; counter-set: revert !important; cursor: revert !important; cx: revert !important; cy: revert !important; d: revert !important; dominant-baseline: revert !important; empty-cells: revert !important; field-sizing: revert !important; fill: revert !important; fill-opacity: revert !important; fill-rule: revert !important; filter: revert !important; flex: revert !important; flex-flow: revert !important; float: revert !important; flood-color: revert !important; flood-opacity: revert !important; glyph-orientation-horizontal: revert !important; glyph-orientation-vertical: revert !important; grid: revert !important; grid-column-end: revert !important; grid-column-start: revert !important; grid-row-end: revert !important; grid-row-start: revert !important; hanging-punctuation: revert !important; 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z-index: revert !important; -apple-color-filter: revert !important; -apple-pay-button-style: revert !important; -apple-pay-button-type: revert !important; -apple-visual-effect: revert !important; -internal-text-autosizing-status: revert !important; -webkit-backdrop-filter: revert !important; -webkit-background-clip: revert !important; -webkit-background-origin: revert !important; border-spacing: revert !important; -webkit-box-align: revert !important; -webkit-box-decoration-break: revert !important; -webkit-box-direction: revert !important; -webkit-box-flex: revert !important; -webkit-box-flex-group: revert !important; -webkit-box-lines: revert !important; -webkit-box-ordinal-group: revert !important; -webkit-box-orient: revert !important; -webkit-box-pack: revert !important; -webkit-box-reflect: revert !important; -webkit-box-shadow: revert !important; -webkit-column-axis: revert !important; -webkit-column-progression: revert !important; -webkit-cursor-visibility: revert !important; -webkit-font-size-delta: revert !important; -webkit-hyphenate-limit-after: revert !important; -webkit-hyphenate-limit-before: revert !important; -webkit-hyphenate-limit-lines: revert !important; -webkit-initial-letter: revert !important; -webkit-line-align: revert !important; -webkit-line-box-contain: revert !important; -webkit-line-clamp: revert !important; -webkit-line-grid: revert !important; -webkit-line-snap: revert !important; -webkit-marquee-direction: revert !important; -webkit-marquee-increment: revert !important; -webkit-marquee-repetition: revert !important; -webkit-marquee-speed: revert !important; -webkit-marquee-style: revert !important; -webkit-mask: revert !important; -webkit-mask-composite: revert !important; -webkit-mask-source-type: revert !important; -webkit-nbsp-mode: revert !important; -webkit-rtl-ordering: revert !important; -webkit-ruby-position: revert !important; -webkit-text-combine: revert !important; -webkit-text-decorations-in-effect: revert !important; -webkit-text-fill-color: revert !important; -webkit-text-security: revert !important; 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inset: revert !important; contain-intrinsic-block-size: revert !important; contain-intrinsic-size: revert !important; contain-intrinsic-inline-size: revert !important; height: revert !important; inline-size: revert !important; inset-block: revert !important; inset-inline: revert !important; margin-block: revert !important; margin-inline: revert !important; max-block-size: revert !important; max-height: revert !important; max-inline-size: revert !important; max-width: revert !important; min-block-size: revert !important; min-height: revert !important; min-inline-size: revert !important; overscroll-behavior-block: revert !important; overscroll-behavior-inline: revert !important; overscroll-behavior: revert !important; padding-block: revert !important; padding-inline: revert !important; scroll-margin-block: revert !important; scroll-margin: revert !important; scroll-margin-inline: revert !important; scroll-padding-block: revert !important; scroll-padding: revert !important; scroll-padding-inline: revert !important; width: revert !important; margin: 16px 0px !important; padding: 8px 16px !important; border-radius: 4px !important; min-width: 200px !important; border-top-width: 4px !important; border-top-style: solid !important; border-top-color: rgb(144, 164, 174) !important;">
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Hi Jim,
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<div>Thank you for your reply. I use openmpi/5.0.3 under intel/2022.1.2. I have tried with pnetcdf versions 12 , 13 and 14 but get the same error. I really think that there is some inconsistency during writing the file and as I said in the previous email, this
only happens on one specific cluster. Here's a result of a test script: Using pnetcdf and mpi I write a global variable named<span class="Apple-converted-space"> </span><b>var</b> that is an array consisting of the indices of each process, i.e., each process
writes only its own index. Example if I use 96 processes, var is [1, 2, 3, 4, ..., 95, 96]. However when I try writing the same variable using , say, 384 processes, some of the values in the middle remain zero (default element value) instead of the respective
process index. Like you said, I am pretty sure this is<span class="Apple-converted-space"> </span><b>NOT</b> an issue with pnetcdf but some other inconsistency within the cluster, but I just don't know how to identify it and thought maybe people on the mailing
list might have encountered this before. Meanwhile I got my code to work by doing simple binary IO instead of pnetcdf files, which tells me the MPI in itself is also okay I guess?</div>
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<div>I appreciate your time with this.</div>
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<div>Best</div>
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<div>Divyanshu</div>
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<div dir="ltr" class="gmail_attr">On Fri, Jul 11, 2025 at 4:23 PM Jim Edwards <<a href="mailto:jedwards@ucar.edu">jedwards@ucar.edu</a>> wrote:<br>
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Hi Divyanshu,</div>
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>From your description it sounds like the file written is corrupted? And when you say "The error also doesn't appear when I use fewer processes on a single node on the cluster." Do you</div>
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mean use fewer processes to write the file or to read the file? It really sounds to me like an application problem and not a pnetcdf or mpi issue. I think that you may need to provide</div>
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an exact description of how the problem is created including the system you are using, the mpi library and version as well as the pnetcdf version and the application. </div>
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Jim</div>
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<div dir="ltr" class="gmail_attr">On Fri, Jul 11, 2025 at 4:13 PM Divyanshu Gola <<a href="mailto:divyans@umich.edu" target="_blank">divyans@umich.edu</a>> wrote:<br>
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<div dir="ltr">Hi,
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<div>This is a shot in the dark but I thought why not. </div>
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<div>The exact same code that I had been using until a few weeks ago gives me an error when I am trying to read restart files using PNetcdf. The error is<span class="Apple-converted-space"> </span><b>Index exceeds dimension bounds, or Start+Count exceeds dimension
bounds.<span class="Apple-converted-space"> </span></b>Based on days of debugging, I have narrowed it down to some problem during the writing of the restart files (and not the reading itself). All of these errors seem to originate from the way PNetcdf is built
and the MPI file system used on the cluster (because I can run the same code on a different cluster), but I can't seem to identify the root cause. The error also doesn't appear when I use fewer processes on a single node on the cluster.</div>
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<div>I know this is most likely not a bug in the PNetcdf library but something else, but I was wondering if people on this mailing list have encountered a similar issue.</div>
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<div>Apologies for the long email and thanks</div>
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<div>Divyanshu </div>
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<div>Postdoctoral Researcher</div>
<div>University of Michigan</div>
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<div>Jim Edwards<br>
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<div>STAND UP FOR SCIENCE</div>
<font size="1">CESM Software Engineer<br>
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<font size="1">National Center for Atmospheric Research<br>
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<div><font size="1">Boulder, CO</font></div>
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