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Dear Matthew, I came up with a workaround for the problem. I duplicate the vector and use the duplicated copy to read the information from the hdf5 file. Then I swap both vectors and delete the copy. If I invoke VecView outside of the function,
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<div>Dear Matthew, </div>
<div><br>
</div>
<div>I came up with a workaround for the problem. I duplicate the vector and use the duplicated copy to read the information from the hdf5 file. Then I swap both vectors and delete the copy. If I invoke VecView outside of the function, the value has been modified
properly. However, this solution seems a little bit “ugly”. I share it just in case someone is facing a similar problem or it can help to understand what is going wrong with my previous implementation.</div>
<div><br>
</div>
<div>Best,</div>
<div>Miguel</div>
<div><br>
</div>
<div>
<div style="color: rgb(212, 212, 212); background-color: rgb(30, 30, 30); font-family: Menlo, Monaco, "Courier New", monospace; line-height: 18px; white-space: pre;">
<div><span style="color: rgb(78, 201, 176);">Vec</span> <span style="color: rgb(156, 220, 254);">
stdv_q</span>;</div>
<div style="line-height: 18px;">
<div><span style="color: rgb(86, 156, 214);">PetscCall</span>(<span style="color: rgb(220, 220, 170);">DMSwarmCreateGlobalVectorFromField</span>(<span style="color: rgb(156, 220, 254);">Simulation</span>-><span style="color: rgb(156, 220, 254);">atomistic_data</span>,</div>
<div><span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
<br>
<div><span style="color: rgb(78, 201, 176);">Vec</span> <span style="color: rgb(156, 220, 254);">
stdv_q_hdf5</span>;</div>
<div><span style="color: rgb(86, 156, 214);">PetscCall</span>(<span style="color: rgb(220, 220, 170);">VecDuplicate</span>(<span style="color: rgb(156, 220, 254);">stdv_q</span>, &<span style="color: rgb(156, 220, 254);">stdv_q_hdf5</span>));</div>
<div><span style="color: rgb(86, 156, 214);">PetscCall</span>(<span style="color: rgb(220, 220, 170);">PetscObjectSetName</span>((<span style="color: rgb(78, 201, 176);">PetscObject</span>)<span style="color: rgb(156, 220, 254);">stdv_q_hdf5</span>,</div>
<div><span style="color: rgb(206, 145, 120);">"DMSwarmSharedField_stdv-q"</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">PetscCall</span>(<span style="color: rgb(220, 220, 170);">VecLoad</span>(<span style="color: rgb(156, 220, 254);">stdv_q_hdf5</span>,
<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">PetscCall</span>(<span style="color: rgb(220, 220, 170);">VecSwap</span>(<span style="color: rgb(156, 220, 254);">stdv_q</span>,
<span style="color: rgb(156, 220, 254);">stdv_q_hdf5</span>));</div>
<div><span style="color: rgb(86, 156, 214);">PetscCall</span>(<span style="color: rgb(220, 220, 170);">VecDestroy</span>(&<span style="color: rgb(156, 220, 254);">stdv_q_hdf5</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">PetscCall</span>(<span style="color: rgb(220, 220, 170);">DMSwarmDestroyGlobalVectorFromField</span>(<span style="color: rgb(156, 220, 254);">Simulation</span>-><span style="color: rgb(156, 220, 254);">atomistic_data</span>,</div>
<div><span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
</div>
</div>
</div>
<div><br>
<blockquote type="cite">
<div>On 1 Apr 2024, at 17:13, Miguel Molinos <mmolinos@us.es> wrote:</div>
<br class="Apple-interchange-newline">
<div>
<div style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">
Dear Matthew,
<div><br>
</div>
<div>Thank you for your suggestion. I tried to update the vector with the information coming from the hdf5 file inside the main function. Then I print the vector two times (see the lines below), the first time it has the correct data. However, the second time,
it has the same values like I never updated it with VecLoad. </div>
<div><br>
</div>
<div>It is an alternative way of initialise a vector coming from DMSWarm with previously stored information (keeping the parallel structure)? </div>
<div><br>
</div>
<div>Miguel</div>
<div><br>
</div>
<div>
<div style="color: rgb(212, 212, 212); background-color: rgb(30, 30, 30); font-family: Menlo, Monaco, "Courier New", monospace; line-height: 18px; white-space: pre;">
<div><span style="color: rgb(106, 153, 85);">//! Load Hdf5 viewer</span></div>
<div><span style="color: rgb(78, 201, 176);">PetscViewer</span> <span style="color: rgb(156, 220, 254);">
viewer_hdf5</span>;</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerHDF5Open</span>(MPI_COMM_WORLD, Output_hdf5_file,</div>
<div>FILE_MODE_READ, &viewer_hdf5));</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerHDF5PushTimestepping</span>(<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>));</div>
<br>
<div><span style="color: rgb(106, 153, 85);">//! Load the vector and fill it with the information from the .hdf5 file</span></div>
<div><span style="color: rgb(78, 201, 176);">Vec</span> <span style="color: rgb(156, 220, 254);">
stdv_q</span>;</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">DMSwarmCreateGlobalVectorFromField</span>(</div>
<div><span style="color: rgb(156, 220, 254);">Simulation</span>.<span style="color: rgb(156, 220, 254);">atomistic_data</span>,
<span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerHDF5PushGroup</span>(<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>,
<span style="color: rgb(206, 145, 120);">"/particle_fields"</span>));</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">VecLoad</span>(<span style="color: rgb(156, 220, 254);">stdv_q</span>,
<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>));</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">VecView</span>(stdv_q,
<span style="color: rgb(86, 156, 214);">PETSC_VIEWER_STDOUT_WORLD</span>));</div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerHDF5PopGroup</span>(<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">DMSwarmDestroyGlobalVectorFromField</span>(</div>
<div><span style="color: rgb(156, 220, 254);">Simulation</span>.<span style="color: rgb(156, 220, 254);">atomistic_data</span>,
<span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
<br>
<div><span style="color: rgb(106, 153, 85);">//! Destoy HDF5 context</span></div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">PetscViewerDestroy</span>(&<span style="color: rgb(156, 220, 254);">viewer_hdf5</span>));</div>
<br>
<div><span style="color: rgb(106, 153, 85);">//! Load the vector again and print</span></div>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">DMSwarmCreateGlobalVectorFromField</span>(</div>
<div><span style="color: rgb(156, 220, 254);">Simulation</span>.<span style="color: rgb(156, 220, 254);">atomistic_data</span>,
<span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">VecView</span>(stdv_q,
<span style="color: rgb(86, 156, 214);">PETSC_VIEWER_STDOUT_WORLD</span>));</div>
<br>
<div><span style="color: rgb(86, 156, 214);">REQUIRE_NOTHROW</span>(<span style="color: rgb(220, 220, 170);">DMSwarmDestroyGlobalVectorFromField</span>(</div>
<div><span style="color: rgb(156, 220, 254);">Simulation</span>.<span style="color: rgb(156, 220, 254);">atomistic_data</span>,
<span style="color: rgb(206, 145, 120);">"stdv-q"</span>, &<span style="color: rgb(156, 220, 254);">stdv_q</span>));</div>
</div>
</div>
<div><br>
</div>
<div>Best,</div>
<div>Miguel</div>
<div><br id="lineBreakAtBeginningOfMessage">
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Miguel Molinos<br>
Investigador postdoctoral <br>
Juan de la Cierva<br>
Dpto. Mecánica de Medios Continuos y Teoría de Estructuras - ETSI<br>
Universidad de Sevilla<br>
Camino de los descubrimientos, s/n<br>
41092 Sevilla</div>
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<blockquote type="cite">
<div>On 1 Apr 2024, at 16:28, Matthew Knepley <knepley@gmail.com> wrote:</div>
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>From the description, my guess is that this is pointer confusion. The vector inside the function is different from the vector outside the function.</div>
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