From ecae4f8b9d18f6fd5fa77714418acde8d4d393f4 Mon Sep 17 00:00:00 2001
From: smoehrle <26185187+smoehrle@users.noreply.github.com>
Date: Wed, 31 Aug 2022 13:52:48 +0200
Subject: [PATCH] Add some documentation

---
 README.md                               | 33 ++++++++++++++++++++++---
 galaxy_benchmarker/benchmarks/fio.py    | 16 +++++++++---
 galaxy_benchmarker/benchmarks/galaxy.py |  9 ++++---
 3 files changed, 48 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 696901eb..b0037128 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,8 @@
 # Galaxy Benchmarker
 
-TODO...
+A tool for benchmarking different storage types individually or in more complex setups like Galaxy in combination with iRODS.
+
+Link to the [original version](https://github.com/usegalaxy-eu/GalaxyBenchmarker/tree/668b9a5125541f686d00950a0e862a260ca4b787) of the GalaxyBenchmarker.
 
 ## Basic architecture
 
@@ -14,6 +16,7 @@ state after benchmarking.
 ```
 .
 ├── ansible            -- Ansible playbooks and inventory
+├── evaluation         -- Example plot code in jupiter notebooks
 ├── examples           -- Example configurations
 ├── galaxy_benchmarker -- Source code
 ├── logs               -- Generated logs
@@ -28,7 +31,9 @@ environment or as a local project. For the container env it automatically maps
 SSH (config, agent, ...) inside the container. With this you can use your local
 SSH config and keys within the inventory.
 
-### Inside container
+[Example usage described here](#example-usage)
+
+### Run with container
 
 
 ```bash
@@ -52,7 +57,7 @@ make stop
 make stop_sudo
 ```
 
-### Local
+### Run locally
 
 This project requires [Poetry](https://python-poetry.org/docs/).
 
@@ -72,3 +77,25 @@ The targets/hosts are defined in [ansible/inventory/](./ansible/inventory/) as
 Here, you can also set host specific variables, if necessary.
 
 The defined hosts can then be used throughout the various benchmarker configs.
+
+## Example usage
+
+1. All examples use `irods_client` and `irods_server` as aliases for the hosts. These hosts have to be configured in [the inventory](./ansible/inventory/example.yml)
+1. Run the GalaxyBenchmarker with `--cfg examples/01_verify_setup.yml` to verify the setup.
+
+
+## Debugging
+
+1. Change the configuration for more detailed logging
+    ```
+    log_ansible_output: true
+    results_save_raw_results: true
+    ```
+
+1. Run GalaxyBenchmarker with the flags `--only-pre-task`, `--only-benchmark`, and `--only-post-task` to check the individual stages
+
+1. Have a look into the logs of the container:
+    ```
+    irods-fuse -> /tmp
+    irods -> /var/lib/irods/log/
+    ```
diff --git a/galaxy_benchmarker/benchmarks/fio.py b/galaxy_benchmarker/benchmarks/fio.py
index 64f3eadc..2e450e2b 100644
--- a/galaxy_benchmarker/benchmarks/fio.py
+++ b/galaxy_benchmarker/benchmarks/fio.py
@@ -255,8 +255,16 @@ def _parse_job_result(result: dict, prefix: str) -> dict[str, Any]:
         f"{prefix}_iops_max": result["iops_max"],
         f"{prefix}_iops_mean": result["iops_mean"],
         f"{prefix}_iops_stddev": result["iops_stddev"],
-        f"{prefix}_lat_min_in_ms": result["lat_ns"]["min"] / 1_000_000 if result["bw_mean"] > 0 else 0.0,
-        f"{prefix}_lat_max_in_ms": result["lat_ns"]["max"] / 1_000_000 if result["bw_mean"] > 0 else 0.0,
-        f"{prefix}_lat_mean_in_ms": result["lat_ns"]["mean"] / 1_000_000 if result["bw_mean"] > 0 else 0.0,
-        f"{prefix}_lat_stddev_in_ms": result["lat_ns"]["stddev"] / 1_000_000 if result["bw_mean"] > 0 else 0.0,
+        f"{prefix}_lat_min_in_ms": result["lat_ns"]["min"] / 1_000_000
+        if result["bw_mean"] > 0
+        else 0.0,
+        f"{prefix}_lat_max_in_ms": result["lat_ns"]["max"] / 1_000_000
+        if result["bw_mean"] > 0
+        else 0.0,
+        f"{prefix}_lat_mean_in_ms": result["lat_ns"]["mean"] / 1_000_000
+        if result["bw_mean"] > 0
+        else 0.0,
+        f"{prefix}_lat_stddev_in_ms": result["lat_ns"]["stddev"] / 1_000_000
+        if result["bw_mean"] > 0
+        else 0.0,
     }
diff --git a/galaxy_benchmarker/benchmarks/galaxy.py b/galaxy_benchmarker/benchmarks/galaxy.py
index df041287..0f39199b 100644
--- a/galaxy_benchmarker/benchmarks/galaxy.py
+++ b/galaxy_benchmarker/benchmarks/galaxy.py
@@ -187,7 +187,8 @@ def __init__(self, name: str, config: dict, benchmarker: Benchmarker):
         )
         self._post_tasks.append(
             ansible.AnsibleTask(
-                playbook="cleanup_galaxy_server.yml", host=self.destination.host,
+                playbook="cleanup_galaxy_server.yml",
+                host=self.destination.host,
                 extra_vars={
                     "galaxy_export_volume": self.config.export_volume,
                 },
@@ -254,7 +255,8 @@ def __init__(self, name: str, config: dict, benchmarker: Benchmarker):
         )
         self._post_tasks.append(
             ansible.AnsibleTask(
-                playbook="cleanup_galaxy_server.yml", host=self.destination.host,
+                playbook="cleanup_galaxy_server.yml",
+                host=self.destination.host,
                 extra_vars={
                     "galaxy_export_volume": self.config.export_volume,
                 },
@@ -288,7 +290,8 @@ def __init__(self, name: str, config: dict, benchmarker: Benchmarker):
         )
         self._post_tasks.append(
             ansible.AnsibleTask(
-                playbook="cleanup_galaxy_server.yml", host=self.destination.host,
+                playbook="cleanup_galaxy_server.yml",
+                host=self.destination.host,
                 extra_vars={
                     "galaxy_export_volume": self.config.export_volume,
                 },