Ken's PRs

GMSH v4 support - Kj/gmsh4 #374
Extrusion tags - PR for extrusion tags only #375
matchedNodeElementReader and serial mesh support for > 2B entities #380 - in master @ 229f849
merge CGNS reader/writer - Parallel Cgns reader/writer #296
- this is needed for CEEDPhasta
chef support for part count reductions - add part count reduction to chef #384 - in develop @ 31ddc29
CGNS writer with a single 'base' - Prepare and write CGNS boundary connectivity and ZoneBC in one base #395
convert with option to skip verify(...)
chef support for matched/periodic faces - Chef makes boundary elements on periodic/matched faces #377 - needs testing
topo model closure - add topo model support for gmi_is_in_closure #369
write 'face type' tags for boundary layer entities only - chef: geombc boundary element 'face type' string shouldn't be in the interior block tag #381
check for high numbers of upward adjacencies and fail early - https://github.com/SCOREC/core/tree/cws/failUpwardAdjLimit - verify: fail if the upward adjacency limit is exceeded #529

meeting notes 11/4/2022

for a (partial) summary of how parallel mesh construction works see Construct a distributed parallel PUMI mesh from own file format #245

the current HEAD of develop has added multi-topology support via repeated calls to assemble followed by finalize (see

core/apf/apfConvert.h

Lines 34 to 67 in 8311337

    
           /** \brief assemble a mixed-cell-type mesh from just a connectivity array 
        
             \details construct is now split into two functions,  
        
             assemble and finalise. The premise of assemble being  
        
             that it is called multiple times for a given cell type, 
        
             across several different cell types in the input mesh. */ 
        
           void assemble(Mesh2* m, const int* conn, int nelem, int etype, 
        
               GlobalToVert& globalToVert); 
        
           /** \brief finalise construction of a mixed-cell-type mesh from just a connectivity array 
        
             \details construct is now split into two functions,  
        
             assemble and finalise. Once the mixed cell type mesh  
        
             is assembled finalise should be called.  Doing it this  
        
             way provides non-breaking changes for current users of  
        
             construct, which now just calls assemble and finalise. */ 
        
           void finalise(Mesh2* m, GlobalToVert& globalToVert); 
        
           /** \brief construct a mesh from just a connectivity array 
        
             \details this function is here to interface with very 
        
             simple mesh formats. Given a set of elements described 
        
             only in terms of the ordered global ids of their vertices, 
        
             this function builds a reasonable apf::Mesh2 structure 
        
             and as a side effect returns a map from global ids 
        
             to local vertices.  This functions assumes a uniform  
        
             cell type.  Use a combination of assemble and finalise for  
        
             meshes loaded with mixed cell types. 
        
             This is a fully scalable parallel mesh construction 
        
             algorithm, no processor incurs memory or runtime costs 
        
             proportional to the global mesh size. 
        
             Note that all vertices will have zero coordinates, so 
        
             it is often good to use apf::setCoords after this. */ 
        
           void construct(Mesh2* m, const int* conn, int nelem, int etype, 
        
               GlobalToVert& globalToVert);

)

the branch that exists for matchedNodeElementReader has one call to the construct api which takes in a numElements*maxDownwardVerts array for element-to-vertex connectivity (where vertices are defined by their global vertex id)
the mesh generator that feeds matchedNodeElementReader already produces elements in groups by topological type and can/will be changed to create files that have one array (numElements(elmType)*numDownwardVerts(elmType))
- a test input for this will be created for the next meeting on 11/11
with the mesh generator change the modifications to construct will be abandoned and assemble will be called instead
- the MeshInfo struct that handles these arrays in the matchedNodeElementReader.cpp driver will have to be modified to support split topology arrays

meeting notes 11/18/2022

multi topo file format
- coordinate file does not change
- element file
  - header per block/topology:
    - num verts per element
    - num elements
source of matching info
- if the mesh generator does not provide per-entity matching info (remote copies), then a serial code (ideally in PUMI) should derive the entity level matching info from model attributes specified on model edges/faces
matching support in chef
- ideally, a model attribute per face/edge pair defines whether matching is enabled on that pair
  - if a specific pair is enabled, then the mesh entities that are matched must have remote copy information for their matches
  - currently in chef matching is on (for all model face/edge pairs) if the mesh contains matching info and has to be disabled explicitly (which again, turns all model face/edge pair matching off)
  - in the current code, changing the default to 'off' would be helpful
extrusion mesh generation with matching
- two cases, info is the same, but mesh generation and structure differs
  - perfect matching in a simple extrusion across one pair of geometric model faces
  - 2d root plane, any number of points along z, with each layer having varying z depths

meeting notes 12/2/2022

CWS will assume the files exist for reading in the multi-topo format discussed last time and write a draft of the reading logic for it
KJ will prepare an example multi-topo formatted file

meeting notes 12/9/2022

matchedNodeElementReader and serial mesh support for > 2B entities #380 created, compiles, multi-topo reader is a WIP
proposed file format for element-to-vertex multi-topology meshes
- vertex coordinate file reading does not change
- part ids start at 0
- each part gets a file that contains a rectangular array, one for each topology present on that part, that provides element to vertexGlobalId connectivity in the order listed in the section of the header file for that part
- one header file with:

1 1  No idea why we write this
3    also not sure what this is used for
<numelTotal>  <maxNodesPerElement>
Part1
    <numel_topo_1>   <NodesInElementTopo1>
    <numel_topo_2>   <NodesInElementTopo2>
    …. for as many topos as are in  Part 1
Repeat the above bock for  each part.

meeting notes 1/6/2022

found latest branch for chef reduction (across ALCF, NASA, colorado viz nodes) and added the branch to the OP list
added 4 part test case for matchedNodeElementReader to pumi-meshes SCOREC/pumi-meshes@7733c3e
- mixed topo
- in new file format
- 4 parts: 0,1 - all hex, 2 - mixed, 3 - all wedges

meeting notes 1/13/2022

as of b46f2c8 the header and the conn arrays are being read for multi-topo
there is one hack in the code for setting the dimension here:

core/test/matchedNodeElmReader.cc

Line 776 in b46f2c8

mesh.dim = 3; //FIXME

I didn't see it in the header:
SCOREC/pumi-meshes@7733c3e#diff-93a634d03353fa0e6384bb7a8842220b948f1ec18a25e1082afd200cb4c32aa6
running the SCOREC/pumi-meshes@7733c3e test case fails with a floating point exception and the output pasted below

$ mpirun -np 4 ./test/matchedNodeElmReader   \
  /space/cwsmith/core/pumi-meshes/matchedNodeElementReader/geom3D.cnndt \
  /space/cwsmith/core/pumi-meshes/matchedNodeElementReader/geom3D.coord \
  NULL \
  /space/cwsmith/core/pumi-meshes/matchedNodeElementReader/geom3D.class \
  NULL \
  NULL \
  /space/cwsmith/core/pumi-meshes/matchedNodeElementReader/geom3DHead.cnn  \
  foo.dmg foo.smb

numVerts 352068
2 46941 8
2 18222 6
1 65037 8
3 153102 6
0 64704 8
isMatched 0
CR1 mysize=0 
CR5: self=3,myOffset=0,quotient=0 
0 after residence 
2 after residence 
3 after residence 
1 after residence 
0 done inside remotes 
1 done inside remotes 
2 done inside remotes 
3 done inside remotes 

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 28879 RUNNING AT cranium.scorec.rpi.edu
=   EXIT CODE: 136
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Floating point exception (signal 8)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
cwsmith@cranium: /space/cwsmith/buildPumiOptonSimonOmegaoff $

@KennethEJansen

meeting notes 1/20/2022

Fixed the FPE bug with cacacac
The run now fails in mesh verification ('verify'). See the output below.
@KennethEJansen Does the setCoords int overflow of: output mean we are overflowing?

cwsmith@cranium: /space/cwsmith/buildPumiOptonSimonOmegaoff $ ../runMner.sh 
numVerts 352068
3 153102 6
1 65037 8
0 64704 8
2 46941 8
2 18222 6
isMatched 0
constructResidence: self=0,gid=0,ifirst=0  
constructResidence: self=1,gid=0,ifirst=0  
constructResidence: self=2,gid=91452,ifirst=0  
constructResidence: self=3,gid=488,ifirst=0  
constructResidence: self=0,gid=0,ifirst=0,max=352067  
constructResidence: self=1,gid=0,ifirst=0,max=352067  
constructResidence: self=2,gid=91452,ifirst=0,max=352067  
constructResidence: self=3,gid=488,ifirst=0,max=352067  
CR1 mysize=88017 
CR5: self=3,myOffset=264051,quotient=88017 
2 after residence 
0 after residence 
1 after residence 
3 after residence 
0 done inside remotes 
1 done inside remotes 
2 done inside remotes 
3 done inside remotes 
setCoords int overflow of: self=0,mySize=88017,total=352068, n=88017,to=0, quotient=88017, remainder=0 start=0, peers=4, sizeToSend=2112408, nverts=88017 
setCoords int overflow of: self=1,mySize=88017,total=352068, n=88017,to=1, quotient=88017, remainder=0 start=88017, peers=4, sizeToSend=2112408, nverts=88017 
setCoords int overflow of: self=2,mySize=88017,total=352068, n=88017,to=2, quotient=88017, remainder=0 start=176034, peers=4, sizeToSend=2112408, nverts=88017 
setCoords int overflow of: self=3,mySize=88017,total=352068, n=88017,to=3, quotient=88017, remainder=0 start=264051, peers=4, sizeToSend=2112408, nverts=88017 
fathers2D not requested 
seconds to create mesh 1.044
APF FAILED: apf::Verify: edge with 2 adjacent faces
centroid: (0.684542, 0.00348426, 0.0833333)
based on the following:
 - edge is classified on a model region
we would expect the adjacent face count to be at least 3

APF FAILED: apf::Verify: edge with 2 adjacent faces
centroid: (0.53322, -0.00227891, 0.0833333)
based on the following:
 - edge is classified on a model region
we would expect the adjacent face count to be at least 3

APF FAILED: apf::Verify: edge with 2 adjacent faces
centroid: (0.684311, 0.000954821, 0.0833333)
based on the following:
 - edge is classified on a model region
we would expect the adjacent face count to be at least 3

APF FAILED: apf::Verify: edge with 2 adjacent faces
centroid: (0.538636, -0.0196729, 0.0833333)
based on the following:
 - edge is classified on a model region
we would expect the adjacent face count to be at least 3


===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 32670 RUNNING AT cranium.scorec.rpi.edu
=   EXIT CODE: 134
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

meeting notes 2/3/2023

all tests passing in the PRmatch2B PR
fixed broken github CI tests by adding pumi.h to phCook.cc for the memory query function ...
update 2/4/2023 which in-turn breaks builds with simmetrix. See building develop with Simmetrix SimModSuite fails with pMesh symbol conflict #382

meeting notes 2/17/2023

cgns merged - there is one CI failure that needs to be resolved
moved chef part count reduction up to the next PR
ken will provide a test that doesn't exit cleanly
- on colorado: /projects/tools/SCOREC-core/core/pumi-meshes/phasta/4-1-Chef-Tet-Part/4-4-Chef-Part-ts20/run
- changed split factor from 1 to -2 in adapt.inp
- fails on free (double free we assume)
cws will rebase off develop and take a look at the failure

meeting notes 2/24/2023

see add part count reduction to chef #384

meeting notes 3/17/2023

debugged leak in chef reduction and fixed it
see add part count reduction to chef #384 (comment)

meeting notes 6/30/2023

merged chef reduction branch - see add part count reduction to chef #384

meeting notes 6/13/2024

added CGNS writer with a single 'base' - Prepare and write CGNS boundary connectivity and ZoneBC in one base #395 to list
resuming weekly meetings starting on 6/21

meeting notes 6/21/2024

rebased CGNS_oneBase on develop e765832 and pushed to https://github.com/SCOREC/core/tree/CGNS_OneBaseRB2Dev
need to merge the changes from the pumi-meshes branch (https://github.com/SCOREC/pumi-meshes/tree/CGNS_tests) into the master branch - this showed up as a conflict during the rebase onto develop
issues accessing spack installed compilers on viz003 - spack load gcc@11.2.0 reports 'invalid version specifier'
need to decide if we are going to keep the current PR or start a new one

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Ken's PRs #376

meeting notes 11/4/2022

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	/** \brief assemble a mixed-cell-type mesh from just a connectivity array
	\details construct is now split into two functions,
	assemble and finalise. The premise of assemble being
	that it is called multiple times for a given cell type,
	across several different cell types in the input mesh. */
	void assemble(Mesh2* m, const int* conn, int nelem, int etype,
	GlobalToVert& globalToVert);

	/** \brief finalise construction of a mixed-cell-type mesh from just a connectivity array
	\details construct is now split into two functions,
	assemble and finalise. Once the mixed cell type mesh
	is assembled finalise should be called. Doing it this
	way provides non-breaking changes for current users of
	construct, which now just calls assemble and finalise. */
	void finalise(Mesh2* m, GlobalToVert& globalToVert);

	/** \brief construct a mesh from just a connectivity array
	\details this function is here to interface with very
	simple mesh formats. Given a set of elements described
	only in terms of the ordered global ids of their vertices,
	this function builds a reasonable apf::Mesh2 structure
	and as a side effect returns a map from global ids
	to local vertices. This functions assumes a uniform
	cell type. Use a combination of assemble and finalise for
	meshes loaded with mixed cell types.

	This is a fully scalable parallel mesh construction
	algorithm, no processor incurs memory or runtime costs
	proportional to the global mesh size.

	Note that all vertices will have zero coordinates, so
	it is often good to use apf::setCoords after this. */
	void construct(Mesh2* m, const int* conn, int nelem, int etype,
	GlobalToVert& globalToVert);

Ken's PRs #376

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cwsmith commented on Nov 4, 2022

meeting notes 11/4/2022

cwsmith commented on Nov 18, 2022

meeting notes 11/18/2022

cwsmith commented on Dec 2, 2022

meeting notes 12/2/2022

cwsmith commented on Dec 9, 2022

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cwsmith commented on Jan 6, 2023

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cwsmith commented on Jan 13, 2023

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cwsmith commented on Jan 20, 2023

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cwsmith commented on Feb 4, 2023

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cwsmith commented on Feb 17, 2023

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cwsmith commented on Feb 24, 2023

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cwsmith commented on Jun 30, 2023

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cwsmith commented on Jun 13, 2024

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cwsmith commented on Jun 21, 2024

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