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Dear Barry:
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<div>You were right!! The problem is I am using the background DMDA mesh for the domain partitioning of the DMSWarm as in “dm/tutorials/swarm_ex3.c”. And then “<span style="white-space: pre;">DMGetNeighbors</span>” to locate the neighbour ranks, including those
in the other side of the domain when I am using periodic bcc. </div>
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<div>Therefore, if I define the background DMDA to use periodic bcc the particle domain partitioning is uneven but I can locate precisely the periodic ranks. </div>
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<div>Thanks,</div>
<div>Miguel<br id="lineBreakAtBeginningOfMessage">
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<div>On 20 Nov 2024, at 23:40, MIGUEL MOLINOS PEREZ <mmolinos@us.es> wrote:</div>
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<div dir="auto">I see… that might be the problem. I’ll check it tomorrow. Thank you!
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<div>Miguel<br>
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<blockquote type="cite">On 20 Nov 2024, at 22:57, Barry Smith <bsmith@petsc.dev> wrote:<br>
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<div>On Nov 20, 2024, at 2:38 PM, MIGUEL MOLINOS PEREZ <mmolinos@us.es> wrote:</div>
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<div style="caret-color: rgb(0, 0, 0);">Yes, I use the vertex (nodes) of the elements. </div>
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Then the length between each vertex will be different between periodic and non-periodic case. With 10 points and non-periodic, it will be 1/9, and with periodic it will be 1/10th. Is this what you are asking about?</div>
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<div style="caret-color: rgb(0, 0, 0);">I am using the DMDA as an auxiliar mesh to do the domain partitioning in the DMSWARM. </div>
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<div style="caret-color: rgb(0, 0, 0);">Thanks,</div>
<div style="caret-color: rgb(0, 0, 0);">Miguel</div>
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<div>On 20 Nov 2024, at 19:54, Barry Smith <bsmith@petsc.dev> wrote:</div>
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Are you considering your degrees of freedom as vertex or cell-centered?
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<div> Say three "elements" per edge.</div>
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<div> If vertex centered then discretization size is 1/3 if periodic and 1/2 if not periodic</div>
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<div> If cell-centered then each cell has width 1/3 for both periodic and not periodic</div>
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<div> but in both cases you can think of the discretization size as constant along the whole cube edge.</div>
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<div> Is this related to DMSWARM in particular?</div>
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<div>On Nov 20, 2024, at 12:56 PM, MIGUEL MOLINOS PEREZ <mmolinos@us.es> wrote:</div>
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<div>I mean that if the dimensions of the cube are 1x1x1 (for example). And I want 10 elements per edge, the discretization size must be 0.1 constant over the whole cube edge. </div>
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<div>This is not in the code, I just impose the number of elements per edge. </div>
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<div>Thank you,</div>
<div>Miguel</div>
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<div>On 20 Nov 2024, at 18:52, Barry Smith <bsmith@petsc.dev> wrote:</div>
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What do you mean by discretization size, and how do I see it in the code?
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<div> Barry</div>
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<div>On Nov 20, 2024, at 12:48 PM, MIGUEL MOLINOS PEREZ <mmolinos@us.es> wrote:</div>
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Sorry, I meant that the discretisation size is not constant across the edges of the cube.
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<div>Miguel<br id="lineBreakAtBeginningOfMessage">
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<div>On 20 Nov 2024, at 18:36, Barry Smith <bsmith@petsc.dev> wrote:</div>
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I am sorry, I don't understand the problem. When I run by default with -da_view I get
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<span style="font-variant-ligatures: no-common-ligatures">Processor [0] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 0 2, Y range of indices: 0 2, Z range of indices: 0 2</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [1] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 2 3, Y range of indices: 0 2, Z range of indices: 0 2</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [2] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 0 2, Y range of indices: 2 3, Z range of indices: 0 2</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [3] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 2 3, Y range of indices: 2 3, Z range of indices: 0 2</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [4] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 0 2, Y range of indices: 0 2, Z range of indices: 2 3</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [5] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 2 3, Y range of indices: 0 2, Z range of indices: 2 3</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [6] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 0 2, Y range of indices: 2 3, Z range of indices: 2 3</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [7] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 2 3, Y range of indices: 2 3, Z range of indices: 2 3</span></div>
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</span></div>
<div><span style="font-variant-ligatures: no-common-ligatures">which seems right because you are trying to have three cells in each direction. The distribution has to be uneven, hence </span><span style="font-family: Menlo; font-size: 14px;">0 2 and </span><span style="font-family: Menlo; font-size: 14px;">2
3</span></div>
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</span></div>
<div><span style="font-family: Menlo; font-size: 14px;">When I change the code to use </span>ndiv_mesh_* = 4 and run with periodic or not I get </div>
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<span style="font-variant-ligatures: no-common-ligatures">$ PETSC_OPTIONS="" mpiexec -n 8 ./atoms-3D -dm_view</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">DM Object: 8 MPI processes</span></div>
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<span style="font-variant-ligatures: no-common-ligatures"> type: da</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">Processor [0] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 0 2, Y range of indices: 0 2, Z range of indices: 0 2</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">Processor [1] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 2 4, Y range of indices: 0 2, Z range of indices: 0 2</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">Processor [2] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 0 2, Y range of indices: 2 4, Z range of indices: 0 2</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [3] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 2 4, Y range of indices: 2 4, Z range of indices: 0 2</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [4] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 0 2, Y range of indices: 0 2, Z range of indices: 2 4</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Processor [5] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1</span></div>
<div style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;">
<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 2 4, Y range of indices: 0 2, Z range of indices: 2 4</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">Processor [6] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 0 2, Y range of indices: 2 4, Z range of indices: 2 4</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">Processor [7] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">X range of indices: 2 4, Y range of indices: 2 4, Z range of indices: 2 4</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">so it is splitting as expected each rank gets a 2 by 2 by 2 set of indices.</span></div>
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<span style="font-variant-ligatures: no-common-ligatures">Could you please let me know what the problem is that I should be seeing.</span></div>
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<span style="font-variant-ligatures: no-common-ligatures"> Barry</span></div>
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<div>On Nov 20, 2024, at 7:06 AM, MIGUEL MOLINOS PEREZ <mmolinos@us.es> wrote:</div>
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<div>Dear Barry,</div>
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<div>Please, find attached to this email a minimal example of the problem. Run it using 8 MPI processes. </div>
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<div>Thanks,</div>
<div>Miguel</div>
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<div>On 20 Nov 2024, at 11:48, Miguel Molinos <mmolinos@us.es> wrote:</div>
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<div>Hi Bary:</div>
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<div>I will check the example you suggest. Anyhow, I’ll send a reproducible example ASAP.</div>
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<div>Thanks,</div>
<div>Miguel<br id="x_lineBreakAtBeginningOfMessage">
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<div>On 19 Nov 2024, at 18:55, Barry Smith <bsmith@petsc.dev> wrote:</div>
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<span style="font-size:14.666667px">I modify src/dm/tests/ex25.c and always see a nice even split when possible with both DM_BOUNDARY_NONE and DM_BOUNDARY_PERIODIC</span>
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<div><span style="font-size:14.666667px"> Can you please send a reproducible example?</span></div>
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<div><span style="font-size:14.666667px"> Thanks</span></div>
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<div>On Nov 19, 2024, at 6:14 AM, MIGUEL MOLINOS PEREZ <mmolinos@us.es> wrote:</div>
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<div class="x_PlainText">Dear all:<br>
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It seems that if I mesh a cubic domain with “DMDACreate3d” using 8 bricks for discretization and with periodic boundaries, each of the bricks has a different size. In contrast, if I use DM_BOUNDARY_NONE, all 8 bricks have the same size.
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I have used this together with the DMSWarm discretization. And as you can see the number of particles per rank is not evenly distributed:
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210 420 366 732 420 840 732 1464<br>
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Am I missing something?<br>
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Thanks,<br>
Miguel<br>
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<span id="cid:416E729B516F0E4586D649C85120D0F7@eurprd01.prod.exchangelabs.com"><atoms-3D.cpp></span><span id="cid:03059E64AC33EC40A54CB28898885CB4@eurprd01.prod.exchangelabs.com"><Mg-hcp-cube-x17-x10-x10.dump></span></div>
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