AWS tutorial #1171

kennyweiss · 2023-08-21T05:57:53Z

Summary

This PR adds an axom tutorial building up to a GPU- and spatial index-accelerated application akin to our mesh_tester utility (in <axom>/src/tools/mesh_tester)
The tutorial currently has lessons on
- building/configuring an application against an installed axom
- reading in an STL mesh
- developing a naive self-intersection algorithm
The following lessons will be added in short order
- extending the naive algorithm using RAJA and Umpire via axom::forall
- developing a RAJA-based algorithm using spatial indexes
I will also add a top-level README outlining the structure of the tutorial

Misc changes:

Fixes some warnings in Release configs
Optimizes primal::intersect(BoundingBox, BoundingBox)
Fixes a bug with axom::utilities::locale() when the user's default locale is missing
Fixes Component graph is missing #1109 -- we can once again generate graphs in our readthedocs builds

src/examples/radiuss_tutorial/lesson_00/README.md

…le against axom

…hm to RAJA

Provides about 30% improvement in AWS tutorial for self-intersection query on blueos.

Some systems through an error on `std::locale("")` if there is no user-defined locale. Use `std::locale("C")` instead. We encountered this inside a docker image.

white238 · 2023-08-24T03:00:56Z

src/axom/primal/geometry/BoundingBox.hpp

-                                          otherBB.m_min[i],
-                                          otherBB.m_max[i]);
-  }  // END for all dimensions
+    if(!detail::intersect_bbox_bbox(m_min[i],


👍

Nice optimization

Thanks! For the "naive" self-intersection algorithm in the tutorial, the intersect(BoundingBox,BoundingBox) test used something like half the cycles on a test that ran for a few seconds. This optimization improved the runtime by something like 30% on our blueos Power9s.

I still need to benchmark this before merging to ensure that it didn't give up performance on Intel runs.

Tag: @publixsubfan

src/axom/primal/operators/detail/intersect_bounding_box_impl.hpp

white238 · 2023-08-24T03:07:13Z

src/examples/CMakeLists.txt

+# configure and install 'radiuss_tutorial' example
+#------------------------------------------------------------------------------
+configure_file(
+    radiuss_tutorial/host-config.cmake.in


I think I would just call this the tutorial... but we can debate/fix that later.

white238 · 2023-08-24T03:08:20Z

src/examples/radiuss_tutorial/CMakeLists.txt

+#------------------------------------------------------------------------------
+
+set(tutorial_deps axom axom::fmt axom::cli11)
+blt_list_append(TO tutorial_deps ELEMENTS cuda IF CUDA_FOUND)


Suggested change

blt_list_append(TO tutorial_deps ELEMENTS cuda IF CUDA_FOUND)

blt_list_append(TO tutorial_deps ELEMENTS cuda IF ENABLE_CUDA)

white238 · 2023-08-24T03:09:14Z

src/examples/radiuss_tutorial/host-config.cmake.in

+# Config related to compiler
+set(CMAKE_C_COMPILER              "@CMAKE_C_COMPILER@"       CACHE PATH "")
+set(CMAKE_CXX_COMPILER            "@CMAKE_CXX_COMPILER@"     CACHE PATH "")
+set(CMAKE_Fortran_COMPILER        "@CMAKE_Fortran_COMPILER@" CACHE PATH "")


Is fortran being used in this tutorial?

No -- I adapted this from the using_with_blt one. I'm pretty sure our TPLs were also built w/ fortran in the docker image

src/examples/radiuss_tutorial/lesson_00/README.md

src/examples/radiuss_tutorial/lesson_00/check_axom_configuration.cpp

src/examples/radiuss_tutorial/lesson_01/README.md

white238 · 2023-08-24T03:19:04Z

src/examples/radiuss_tutorial/lesson_01/README.md

+};
+```
+
+The constructor calls ``slic::initialize()``, sets the logging level to ``slic::message::Debug`` and then creates log streams for the different message levels. The destructor finalizes the slic component with `slic::finalize()`.


Suggested change

The constructor calls ``slic::initialize()``, sets the logging level to ``slic::message::Debug`` and then creates log streams for the different message levels. The destructor finalizes the slic component with `slic::finalize()`.

The constructor calls ``slic::initialize()``, sets the logging level to ``slic::message::Debug`` and then creates log streams for the different message levels. The destructor finalizes the SLIC component with `slic::finalize()`.

Is component the right word here in the last sentence?

src/examples/radiuss_tutorial/lesson_02/README.md

kennyweiss · 2023-08-24T03:29:44Z

src/axom/core/utilities/System.cpp

@@ -97,7 +97,7 @@ std::locale locale(const std::string& name)
  }
  catch(std::runtime_error&)
  {
-    loc = std::locale(loc, "", std::locale::ctype);
+    loc = std::locale(loc, "C", std::locale::ctype);


Locales are the gift that keep on giving!

The standard appears to require std::locale("C") and std::locale(""), but apparently the latter cannot always be relied upon. See: https://stackoverflow.com/a/46364980
Specifically -- one of the comments there says:

Note that even though "" is in the set of valid string arguments, I've seen exceptions thrown on std::locale("") (from a plugin run under LibreOffice on Mac)

The original was failing in our AWS docker image (but passing in our docker-based CI, and everywhere else I've run it).

See also: #1128

src/examples/radiuss_tutorial/lesson_03/README.md

src/examples/radiuss_tutorial/lesson_04/device_spatial_indexes.cpp

white238

Thanks for the hard work Kenny! This looks great and I look forward for us to continue to build on it.

@white238

Thanks @white238! Co-authored-by: Chris White <white238@llnl.gov>

kennyweiss · 2023-08-24T05:14:13Z

Docs build for this branch w/ working graphviz: https://axom.readthedocs.io/en/feature-kweiss-aws-tutorial/

rhornung67

Thanks @kennyweiss This looks like a great foundation to build on for a more comprehensive tutorial

bmhan12 · 2023-08-24T18:11:51Z

src/examples/radiuss_tutorial/lesson_03/device_self_intersections.cpp

+    IndexArray intersections_d(axom::ArrayOptions::Uninitialized {},
+                               numIndices,
+                               kernel_allocator);


Suggested change

IndexArray intersections_d(axom::ArrayOptions::Uninitialized {},

numIndices,

kernel_allocator);

IndexArray intersections_d(axom::ArrayOptions::Uninitialized {},

numIndices,

numIndices,

kernel_allocator);

Bugfix for CUDA policy. Lesson 4 also has a few instances of this constructor call as well. Looks like the uninitialized constructor does work, just needs a different overload. @kennyweiss reported this works on rzansel as-is, maybe it's the Automatic Translatation Service covering for us?

Thanks @bmhan12

My solution was to use the initializing constructor -- e,g,

IndexArray intersections_d(numIndices,numIndices,kernel_allocator);

Yours is better!

I'll update the code for lesson_03 and lesson_04.

kennyweiss self-assigned this Aug 21, 2023

kennyweiss commented Aug 21, 2023

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rhornung67 approved these changes Aug 21, 2023

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kennyweiss force-pushed the feature/kweiss/aws-tutorial branch from dc714e3 to e9e466c Compare August 23, 2023 04:48

kennyweiss and others added 14 commits August 23, 2023 19:20

Bootstrap tutorial starting from axom's using-with-blt example

fc0c9f7

Adds a lesson to the radiuss tutorial related to configuring an examp…

017da11

…le against axom

Adds a tutorial lesson that loads an STL mesh using slic and CLI11

9751901

Applies formatting to axom examples

3f6649e

Adds a tutorial lesson w/ a naive sequential self-intersection algorithm

5cd2195

Minor corrections

20169e4

Fixes clang warnings for release configs

a684a34

Adds a tutorial lesson that ports the naive self-intersection algorit…

18d45c1

…hm to RAJA

Adds missing guards to a mint structured_exec

73dc9a9

Adds optimizations for BoundingBox intersections

560b8d1

Provides about 30% improvement in AWS tutorial for self-intersection query on blueos.

Adds code for lesson 4 -- device-based spatial indexes

4988ea2

Bugfix for axom::utilities::locale

512bf60

Some systems through an error on `std::locale("")` if there is no user-defined locale. Use `std::locale("C")` instead. We encountered this inside a docker image.

Use github-style markdown alert annotations for tutorial

8829c99

Adds README for lesson_04 of the tutorial

64afd97

kennyweiss force-pushed the feature/kweiss/aws-tutorial branch from a8bc7a0 to 64afd97 Compare August 24, 2023 02:20

kennyweiss changed the title ~~[WIP] aws tutorial~~ [WIP] AWS tutorial Aug 24, 2023

Light editing pass through the tutorial

7d99da4

kennyweiss force-pushed the feature/kweiss/aws-tutorial branch from c5fe052 to 7d99da4 Compare August 24, 2023 02:45

kennyweiss changed the title ~~[WIP] AWS tutorial~~ AWS tutorial Aug 24, 2023

kennyweiss marked this pull request as ready for review August 24, 2023 02:51

kennyweiss requested review from davidbeckingsale, white238, cyrush, BradWhitlock, rhornung67 and nselliott August 24, 2023 02:52

kennyweiss requested review from publixsubfan, ltaylor16, gunney1, agcapps and bmhan12 August 24, 2023 02:52