add basic support for kripke (#39)

* add basic support for kripke

I can add log parsing when it is needed.

Signed-off-by: vsoch <[email protected]>

Author: vsoch

.github/workflows/main.yaml

@@ -70,6 +70,7 @@ jobs:
                ["io-host-volume", "ghcr.io/converged-computing/metric-sysstat:latest", 60],                 # storage test
                ["io-fio", "ghcr.io/converged-computing/metric-fio:latest", 120],                            # storage test
                ["app-amg", "ghcr.io/converged-computing/metric-amg:latest", 120],                           # standalone app test
+               ["app-kripke", "ghcr.io/converged-computing/metric-amg:latest", 120],                        # standalone app test
                ["app-lammps", "ghcr.io/converged-computing/metric-lammps:latest", 120]]                     # standalone app test
 
     steps:

README.md

@@ -20,6 +20,7 @@ To learn more:
 - Add assertions checking for python tests
 - Plotting examples needed for
   - io-sysstat
+  - app-kripke
 
 ## License
 

docs/_static/data/metrics.json

@@ -6,6 +6,13 @@
   "image": "ghcr.io/converged-computing/metric-amg:latest",
   "url": "https://github.com/LLNL/AMG"
  },
+ {
+  "name": "app-kripke",
+  "description": "parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids",
+  "type": "standalone",
+  "image": "ghcr.io/converged-computing/metric-kripke:latest",
+  "url": "https://github.com/LLNL/Kripke"
+ },
  {
   "name": "app-lammps",
   "description": "LAMMPS molecular dynamic simulation",

docs/getting_started/metrics.md

@@ -7,7 +7,7 @@ The following metrics are under development (or being planned).
  - [Application Metrics](https://converged-computing.github.io/metrics-operator/getting_started/metrics.html#application)
  - [Standalone Metrics](https://converged-computing.github.io/metrics-operator/getting_started/metrics.html#standalone)
 
-<iframe src="../_static/data/table.html" style="width:100%; height:600px;" frameBorder="0"></iframe>
+<iframe src="../_static/data/table.html" style="width:100%; height:650px;" frameBorder="0"></iframe>
 
 All metrics can be customized with the following variables
 
@@ -18,16 +18,21 @@ All metrics can be customized with the following variables
 
 ## Implemented Metrics
 
+Each metric has a link to the type, along with (optionally) examples.
+
 ### Performance
 
 These metrics are intended to assess application performance.
 
 #### perf-sysstat
 
  - [Application Metric Set](user-guide.md#application-metric-set)
+ - *[perf-hello-world](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/perf-hello-world)*
+ - *[perf-lammps](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/perf-lammps)*
 
 This metric provides the "pidstat" executable of the sysstat library. The following options are available:
 
+
 |Name | Description | Type | Default |
 |-----|-------------|------------|------|
 | color | Set to turn on color parsing | Anything set | unset |
@@ -62,7 +67,10 @@ for how we use them.  If there is an option or command that is not exposed that
 
 These metrics are intended to assess storage volumes.
 
-#### fio
+#### io-sfio
+
+ - [Storage Metric Set](user-guide.md#application-metric-set)
+ - *[io-host-volume](https://github.com/converged-computing/metrics-operator/tree/main/examples/storage/google/io-fusion)*
 
 This is a nice tool that you can simply point at a path, and it measures IO stats by way of writing a file there! 
 Options you can set include:
@@ -81,6 +89,7 @@ This allows for testing storage mounted from multiple metric pods without worryi
 #### io-sysstat
 
  - [Storage Metric Set](user-guide.md#application-metric-set)
+ - *[io-host-volume](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/io-host-volume)*
 
 This is the "iostat" executable of the sysstat library.
 
@@ -96,6 +105,7 @@ This is good for mounted storage that can be seen by the operating system, but m
 #### network-netmark
 
  - [Standalone Metric Set](user-guide.md#application-metric-set)
+ - *[network-netmark](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/network-netmark)* (code still private)
 
 This is currently a private container/software, but we have support for it when it's ready to be made public (networking)
 Variables to customize include:
@@ -111,6 +121,9 @@ Variables to customize include:
 
 #### network-osu-benchmark
 
+ - [Standalone Metric Set](user-guide.md#application-metric-set)
+ - *[network-osu-benchmark](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/network-osu-benchmark)*
+
 Point to point benchmarks for MPI (networking). If listOptions->commands not set, will use all one-point commands.
 Variables to customize include:
 
@@ -200,6 +213,7 @@ Here are some useful resources for the benchmarks:
 #### app-lammps
 
  - [Standalone Metric Set](user-guide.md#application-metric-set)
+ - *[app-lammps](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/app-lammps)*
 
 Since we were using LAMMPS so often as a benchmark (and testing timing of a network) it made sense to add it here
 as a standalone metric! Although we are doing MPI with communication via SSH, this can still serve as a means
@@ -223,6 +237,9 @@ anticipating that you as a user would want total control.
 
 #### app-amg
 
+ - [Standalone Metric Set](user-guide.md#application-metric-set)
+ - *[app-amg](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/app-amg)*
+
 AMG means "algebraic multi-grid" and it's easy to confuse with the company [AMD](https://www.amd.com/en/solutions/supercomputing-and-hpc) "Advanced Micro Devices" ! From [the guide](https://asc.llnl.gov/sites/asc/files/2020-09/AMG_Summary_v1_7.pdf):
 
 > AMG is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. The driver provided for this benchmark builds linear systems for a 3D problem with a 27-point stencil and generates two different problems that are described in section D of the AMG.readme file in the docs directory.
@@ -273,22 +290,48 @@ More likely you want an actual problem size on a specific number of node and tas
 run a larger problem and the parser does not work as expected, please [send us the output](https://github.com/converged-computing/metrics-operator/issues) and we will provide an updated parser.
 See [this guide](https://asc.llnl.gov/sites/asc/files/2020-09/AMG_Summary_v1_7.pdf) for more detail.
 
-## Examples
+#### app-kripke
 
-The following examples are provided alongside the operator. Each directory has a README with complete instructions for usage.
+ - [Standalone Metric Set](user-guide.md#application-metric-set)
+ - *[app-kripke](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/app-kripke)*
 
- - [perf-hello-world](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/perf-hello-world)
- - [perf-lammps](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/perf-lammps)
- - [io-host-volume](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/io-host-volume)
- - [network-netmark](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/network-netmark) (code still private)
- - [network-osu-benchmark](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/network-osu-benchmark)
- - [app-lammps](https://github.com/converged-computing/metrics-operator/tree/main/examples/tests/app-lammps)
+[Kripke](https://github.com/LLNL/Kripke) is (from the README):
 
+> Kripke is a simple, scalable, 3D Sn deterministic particle transport code. Its primary purpose is to research how data layout, programming paradigms and architectures effect the implementation and performance of Sn transport. A main goal of Kripke is investigating how different data-layouts affect instruction, thread and task level parallelism, and what the implications are on overall solver performance. Akin to AMG, we allow you to modify each of the mpirun and kripke commands via:
 
-The following example uses io-fio to measure the Fusion filesystem:
+| Name | Description | Option Key | Type | Default |
+|-----|-------------|------------|------|---------|
+| command | The amg command (without mpirun) | options->command |string | (see below) |
+| mpirun | The mpirun command (and arguments) | options->mpirun | string | (see below) | 
+| workdir | The working directory for the command | options->workdir | string | /opt/AMG |
+
+By default, when not set, you will just run the kripke binary to get a test case run, so mpirun is set to be blank.
+
+```bash
+# mpirun is blank
+""
+# But could be an actual mpirun command
+mpirun --hostfile ./hostlist.txt
+
+# command written to problem.sh
+kripke
 
- - [io-host-volume](https://github.com/converged-computing/metrics-operator/tree/main/examples/storage/google/io-fusion)
+# Assembled into
+mpirun --hostfile ./hostlist.txt ./problem.sh
+```
 
+There is a nice [guide here](https://asc.llnl.gov/sites/asc/files/2020-09/Kripke_Summary_v1.2.2-CORAL2_0.pdf) that can help you to decide
+on your specific command or problem size. Also note that we expose the following executables built with it:
+
+```console
+ex1_vector-addition            ex4_atomic-histogram                ex7_nested-loop-reorder
+ex1_vector-addition_solution   ex4_atomic-histogram_solution       ex7_nested-loop-reorder_solution
+ex2_approx-pi                  ex5_line-of-sight                   ex8_tiled-matrix-transpose
+ex2_approx-pi_solution         ex5_line-of-sight_solution          ex8_tiled-matrix-transpose_solution
+ex3_colored-indexset           ex6_stencil-offset-layout           ex9_matrix-transpose-local-array
+ex3_colored-indexset_solution  ex6_stencil-offset-layout_solution  ex9_matrix-transpose-local-array_solution
+```
+(meaning on the PATH in `/opt/Kripke/build/bin` in the container).
 For apps / metrics to be added, please see [this issue](https://github.com/converged-computing/metrics-operator/issues/30).
 
 ## Containers