<html><head><style type='text/css'>p { margin: 0; }</style></head><body><div style='font-family: times new roman,new york,times,serif; font-size: 12pt; color: #000000'>Hi Ilya,<br><br>One problems is that the meshes do not cover the same domain. Is this intentional?<br><br>Also, you need to use the utility addfield, to add the vertextag and element tags used by default. <br><br>After using the addfield utility, you can check your tags with <br>mbsize -t geom1_p.h5m<br><br>So the idea is to transfer one field from one mesh (source) to the other (target). The result will be saved in a new file, which should contain the transferred field.<br><br>The files used in the test are something like this (source)<br>mbsize -t ../../../moab/MeshFiles/unittest/64bricks_1khex.h5m<br>File ../../../moab/MeshFiles/unittest/64bricks_1khex.h5m:<br> Tag Name Vertex Edge Quad Hex EntitySet<br>------------------ -------- -------- -------- -------- ---------<br> MATERIAL_SET 0 0 0 0 64<br> NEUMANN_SET 0 0 0 0 3<br> DIRICHLET_SET 0 0 0 0 3<br> GEOM_DIMENSION 0 0 0 0 729<br> GLOBAL_ID 2197 3780 2160 1728 1056<br> ATTRIB_VECTOR 0 0 0 0 721<br> CATEGORY 0 0 0 0 799<br>PARALLEL_PARTITION 0 0 0 0 256<br> UNIQUE_ID 0 0 0 0 729<br> element_field 0 0 0 1728 0<br> vertex_field 2197 0 0 0 0<br><br>You can check the test in parallel (on 2 processors) in the test/parallel/par_coupler_test <br><br><br>Best Regards,<br>Iulian<br><br><hr id="zwchr"><blockquote style="border-left:2px solid #1010FF;margin-left:5px;padding-left:5px;color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;">
I found some information about iZoltan <br><a href="http://lists.mcs.anl.gov/pipermail/moab-dev/2012/004439.html" target="_blank">http://lists.mcs.anl.gov/pipermail/moab-dev/2012/004439.html</a><br><br>Maybe I should use this way for loading vtk files? <br><br>_______________________________<br>Best regards, Ilya Romero<br><span style="font-weight: bold; color: rgb(68, 68, 68); font-family: arial, sans-serif; font-size: small; line-height: 16px;">Nuclear</span><span style="color: rgb(68, 68, 68); font-family: arial, sans-serif; font-size: small; line-height: 16px;"> Safety Institute<br></span>Russian Academy of Sciences<br><br>-------- Пересылаемое сообщение --------<br>
От кого: Иля <ilacai@mail.ru><br>
Кому: MOAB-dev@mcs.anl.gov<br>
Дата: Пятница, 6 сентября 2013, 8:53 +04:00<br>
Тема: About reading vtk in parallel mode.<br>
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<br>I am new in MOAB and don't have enough experience in your program product. And I'm sorry for my maybe silly questions.<br><br>Could you please help me with the following situation. The main idea is using solution coupling in my research. I found workable example in MOAB package: {$MOAB_dir}/tools/mbcoupler/mbcoupler_test.cpp. So at the first, I decided just to change meshes in this example. And I tryed to understand how to use meshes in parallel mode.<br><br>1) I had the geometry of both new meshes in vtk format: geom1.vtk, geom2.vtk. Using MBConverter I converted them into vtk format, supporting by MOAB<br><span style="font-family: 'courier new', courier;">./mbconvert -f vtk geom1.vtk geom1_c.vtk</span><br>2)Using MBZoltan I converted new vtk files into h5m format, dividing in 4 parts<br><span style="font-size: 12px;"><span style="line-height: 107%;font-family: 'Courier New';">./</span><span style="line-height: 107%;font-family: 'Courier New';" lang="EN-US">mbpart</span><span style="line-height: 107%;font-family: 'Courier New';"> 4 -</span><span style="line-height: 107%;font-family: 'Courier New';" lang="EN-US">T </span><span style="line-height: 107%;font-family: 'Courier New';" lang="EN-US">geom</span><span style="line-height: 107%;font-family: 'Courier New';">1_c.</span><span style="line-height: 107%;font-family: 'Courier New';" lang="EN-US">vtk </span><span style="line-height: 107%;font-family: 'Courier New';" lang="EN-US">geom</span><span style="line-height: 107%;font-family: 'Courier New';">1_</span><span style="line-height: 107%;font-family: 'Courier New';" lang="EN-US">p</span><span style="line-height: 107%;font-family: 'Courier New';">.</span><span style="line-height: 107%;font-family: 'Courier New';" lang="EN-US">h</span><span style="line-height: 107%;font-family: 'Courier New';">5</span><span style="line-height: 107%;font-family: 'Courier New';" lang="EN-US">m<br></span></span>3) I read geom1_p.h5m with Tecplot and checked PARALLEL_PARTITION tag existance (according MOAB_UG.doc). There are values: 0,1,2,3, that is correct. So I tryed to use 2 variants of reading parameters:<br><span style="font-size: 12px;line-height: 107%;font-family: 'Courier New';" lang="EN-US">«PARALLEL=READ_PART; PARTITION=PARALLEL_PARTITION; PARTITION_DISTRIBUTE;CPUTIME»</span><br>and<br><span style="font-size: 12px;line-height: 107%;font-family: 'Courier New';" lang="EN-US">«PARALLEL=READ_PART; PARTITION=PARALLEL_PARTITION; PARTITION_VAL=0,1,2,3;CPUTIME»</span><br>4) Then I used these meshes with mbcoupler_test <br><span style="font-size: 12px;font-family: 'courier new', courier;">mpirun -as intel -np 2 -q test ./mbcoupler_test -meshes geom1_p.h5m geom2_p.h5m -itag vertex_field -outfile test.h5m</span><br>But these meshes weren't read with program. The listing file has the following information:<br><br><p><span style="font-family: 'courier new', courier;">Parallel Read times: </span><br><span style="font-family: 'courier new', courier;"> 0.030983 PARALLEL READ PART</span><br><span style="font-family: 'courier new', courier;"> 0.030983 PARALLEL TOTAL</span><br><span style="font-family: 'courier new', courier;">Parallel Read times: </span><br><span style="font-family: 'courier new', courier;"> 0.00436592 PARALLEL READ PART</span><br><span style="font-family: 'courier new', courier;"> 0.00436592 PARALLEL TOTAL</span><br><span style="font-family: 'courier new', courier;">Proc 0 iface entities: </span><br><span style="font-family: 'courier new', courier;"> 0 0d iface entities.</span><br><span style="font-family: 'courier new', courier;"> 0 1d iface entities.</span><br><span style="font-family: 'courier new', courier;"> 0 2d iface entities.</span><br><span style="font-family: 'courier new', courier;"> 0 3d iface entities.</span><br><span style="font-family: 'courier new', courier;"> (0 verts adj to other iface ents)</span><br><span style="font-family: 'courier new', courier;">Proc 1 iface entities: </span><br><span style="font-family: 'courier new', courier;"> 0 0d iface entities.</span><br><span style="font-family: 'courier new', courier;"> 0 1d iface entities.</span><br><span style="font-family: 'courier new', courier;"> 0 2d iface entities.</span><br><span style="font-family: 'courier new', courier;"> 0 3d iface entities.</span><br><span style="font-family: 'courier new', courier;"> (0 verts adj to other iface ents)</span><br><span style="font-family: 'courier new', courier;">Failure; message:</span><br><span style="font-family: 'courier new', courier;">No tag value for root set</span><br><span style="font-family: 'courier new', courier;">Failure; message:</span><br><span style="font-family: 'courier new', courier;">No tag value for root set</span><br><span style="font-family: 'courier new', courier;">application called MPI_Abort(MPI_COMM_WORLD, 6) - process 0</span><br><span style="font-family: 'courier new', courier;">application called MPI_Abort(MPI_COMM_WORLD, 6) - process 1</span><br><span style="font-family: 'courier new', courier;">rank 1 in job 1 t60-2.parallel.ru_43452 caused collective abort of all ranks</span><br><span style="font-family: 'courier new', courier;"> exit status of rank 1: return code 6</span> <br></p>5) If I set readOpts = "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARTITION_DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=3.0.1;CPUTIME"; the meshes are read, but option PARALLEL_RESOLVE_SHARED_ENTS gives errror<br><br><p><span style="font-size: 12px;font-family: 'courier new', courier;">Parallel Read times:</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0.198586 PARALLEL READ PART</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0.026906 PARALLEL RESOLVE_SHARED_ENTS</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0.00115585 PARALLEL EXCHANGE_GHOSTS</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 9.60827e-05 PARALLEL RESOLVE_SHARED_SETS</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0.226157 PARALLEL TOTAL</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">Parallel Read times:</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0.00666714 PARALLEL READ PART</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0.00862002 PARALLEL RESOLVE_SHARED_ENTS</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0.00228691 PARALLEL EXCHANGE_GHOSTS</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 4.41074e-05 PARALLEL RESOLVE_SHARED_SETS</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0.0157781 PARALLEL TOTAL</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">Proc 0 iface entities:</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 96 0d iface entities.</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 154 1d iface entities.</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 60 2d iface entities.</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0 3d iface entities.</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> (96 verts adj to other iface ents)</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">Proc 1 iface entities:</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 96 0d iface entities.</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 154 1d iface entities.</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 60 2d iface entities.</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> 0 3d iface entities.</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> (96 verts adj to other iface ents)</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">application called MPI_Abort(MPI_COMM_WORLD, 6) - process 0</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">application called MPI_Abort(MPI_COMM_WORLD, 6) - process 1</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">Failure; message:</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">No sparse tag __PARALLEL_SHARED_PROCS value for Vertex 969</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">Failure; message:</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">No sparse tag __PARALLEL_SHARED_PROCS value for Vertex 800</span><br><span style="font-size: 12px;font-family: 'courier new', courier;">rank 1 in job 1 t60-2.parallel.ru_41693 caused collective abort of all ranks</span><br><span style="font-size: 12px;font-family: 'courier new', courier;"> exit status of rank 1: return code 6</span><br></p><br>5) Using <a href="https://trac.mcs.anl.gov/projects/ITAPS/wiki/ParallelRead" target="_blank">this information</a> I checked my h5m files with MBconverter<br><span style="font-size: 12px;font-family: 'courier new', courier;">mpirun -np 2 -q test -as intel ./mbconvert -O PARALLEL=READ_PART -O PARTITION=PARALLEL_PARTITION -O PARALLEL_RESOLVE_SHARED_ENTS -O PARALLEL_GHOSTS=3.0.1 -o PARALLEL=WRITE_PART geom1_p.h5m geom1_last.h5m</span><br>The result is successful:<br><p>Read "geom1_p.h5m"<br>Wrote "geom1_last.h5m"</p>6) So could you please explain how I should correct read meshes in parallel? Form vtk to h5m parallel mesh (I would like to use <span style="font-family: 'courier new', courier;">READ_PART method</span>). What do I do wrong? (All using files are applied with this letter)<br><br>Thank you.<br><br>_______________________________<br>Best regards, Ilya Romero<br><span style="font-weight: bold;color: rgb(68, 68, 68);font-family: arial, sans-serif;font-size: small;line-height: 16px;">Nuclear</span><span style="color: rgb(68, 68, 68);font-family: arial, sans-serif;font-size: small;line-height: 16px;"> Safety Institute<br></span>Russian Academy of Sciences<br>
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