Merge pull request 'Jepsen testing (NLnet task 3 subtask 1)' (#544) from jepsen into main

Reviewed-on: #544

script/jepsen.garage/.envrc

@@ -0,0 +1 @@
+use nix

script/jepsen.garage/.gitignore

@@ -0,0 +1,17 @@
+/target
+/classes
+/checkouts
+profiles.clj
+pom.xml
+pom.xml.asc
+*.jar
+*.class
+/.lein-*
+/.nrepl-port
+/.prepl-port
+.hgignore
+.hg/
+.direnv
+/store
+/store.*
+.vagrant

script/jepsen.garage/README.md

@@ -0,0 +1,166 @@
+# jepsen.garage
+
+Jepsen checking of Garage consistency properties.
+
+## Usage
+
+Requirements:
+
+- vagrant
+- VirtualBox, configured so that nodes can take an IP in a private network `192.168.56.0/24` (it's the default)
+- a user that can create VirtualBox VMs
+- leiningen
+- gnuplot
+
+Set up VMs before running tests:
+
+```
+vagrant up
+```
+
+Run tests: see commands below.
+
+
+## Results
+
+### Register linear, without timestamp patch
+
+Command: `lein run test --nodes-file nodes.vagrant --time-limit 60 --rate 100  --concurrency 20 --workload reg1 --ops-per-key 100`
+
+Results without timestamp patch:
+
+- Fails with a simple clock-scramble nemesis (`--scenario c`).
+  Explanation: without the timestamp patch, nodes will create objects using their
+  local clock only as a timestamp, so the ordering will be all over the place if
+  clocks are scrambled.
+
+Results with timestamp patch (`--patch tsfix2`):
+
+- No failure with clock-scramble nemesis
+
+- Fails with clock-scramble nemesis + partition nemesis (`--scenario cp`).
+
+**This test is expected to fail.**
+Indeed, S3 objects are not meant to behave like linearizable registers.
+TODO explain using a counter-example
+
+
+### Read-after-write CRDT register model
+
+Command: `lein run test --nodes-file nodes.vagrant --time-limit 60 --rate 100  --concurrency 100 --workload reg2 --ops-per-key 100`
+
+Results without timestamp patch:
+
+- Fails with a simple clock-scramble nemesis (`--scenario c`).
+  Explanation: old values are not overwritten correctly when their timestamps are in the future.
+
+Results with timestamp patch (`--patch tsfix2`):
+
+- No failures with clock-scramble nemesis + partition nemesis (`--scenario cp`).
+  This proves that `tsfix2` (PR#543) does improve consistency.
+
+- **Fails with layout reconfiguration nemesis** (`--scenario r`).
+  Example of a failed run: `garage reg2/20231024T120806.899+0200`.
+  This is the failure mode we are looking for and trying to fix for NLnet task 3.
+
+Results with NLnet task 3 code (commit 707442f5de, `--patch task3a`):
+
+- No failures with `--scenario r` (0 of 10 runs), `--scenario pr` (0 of 10 runs),
+  `--scenario cpr` (0 of 10 runs) and `--scenario dpr` (0 of 10 runs).
+
+- Same with `--patch task3c` (commit `0041b013`, the final version).
+
+
+### Set, basic test (write some items, then read)
+
+Command: `lein run test --nodes-file nodes.vagrant --time-limit 60 --rate 200  --concurrency 200 --workload set1 --ops-per-key 100`
+
+Results without NLnet task3 code (`--patch tsfix2`):
+
+- For now, no failures with clock-scramble nemesis + partition nemesis -> TODO long test run
+
+- Does not seem to fail with only the layout reconfiguation nemesis (<10 runs), although theoretically it could
+
+- **Fails with the partition + layout reconfiguration nemesis** (`--scenario pr`).
+  Example of a failed run: `garage set1/20231024T172214.488+0200` (1 failure in 4 runs).
+  This is the failure mode we are looking for and trying to fix for NLnet task 3.
+
+Results with NLnet task 3 code (commit 707442f5de, `--patch task3a`):
+
+- The tests are buggy and often result in an "unknown" validity status, which
+  is caused by some requests not returning results during network partitions or
+  other nemesis-induced broken cluster states.  However, when the tests were
+  able to finish, there were no failures with scenarios `r`, `pr`, `cpr`,
+  `dpr`.
+
+
+### Set, continuous test (interspersed reads and writes)
+
+Command: `lein run test --nodes-file nodes.vagrant --time-limit 60 --rate 100  --concurrency 100 --workload set2 --ops-per-key 100`
+
+Results without NLnet task3 code (`--patch tsfix2`):
+
+- No failures with clock-scramble nemesis + db nemesis + partition nemesis (`--scenario cdp`) (0 failures in 10 runs).
+
+- **Fails with just layout reconfiguration nemesis** (`--scenario r`).
+  Example of a failed run: `garage set2/20231025T141940.198+0200` (10 failures in 10 runs).
+  This is the failure mode we are looking for and trying to fix for NLnet task 3.
+
+Results with NLnet task3 code (commit 707442f5de, `--patch task3a`):
+
+- No failures with `--scenario r` (0 of 10 runs), `--scenario pr` (0 of 10 runs),
+  `--scenario cpr` (0 of 10 runs) and `--scenario dpr` (0 of 10 runs).
+
+- Same with `--patch task3c` (commit `0041b013`, the final version).
+
+
+## NLnet task 3 final results
+
+- With code from task3 (`--patch task3c`): [reg2 and set2](results/Results-2023-12-13-task3c.png), [set1](results/Results-2023-12-14-task3-set1.png).
+- Without (`--patch tsfix2`): [reg2 and set2](results/Results-2023-12-13-tsfix2.png), set1 TBD.
+
+## Investigating (and fixing) errors
+
+### Segfaults
+
+They are due to the download being interrupted in the middle (^C during first launch on clean VMs), the `garage` binary is truncated.
+Add `:force?` to the `cached-wget!` call in `daemon.clj` to re-download the binary,
+or restar the VMs to clear temporary files.
+
+### In `jepsen.garage`: prefix wierdness
+
+In `store/garage set1/20231019T163358.615+0200`:
+
+```
+INFO [2023-10-19 16:35:20,977] clojure-agent-send-off-pool-207 - jepsen.garage.set list results for prefix set20/ : (set13/0 set13/1 set13/10 set13/11 set13/12 set13/13 set13/14 set13/15 set13/16 set13/17 set13/18 set13/19 set13/2 set13/20 set13/21 set13/22 set13/23 set13/24 set13/25 set13/26 set13/27 set13/28 set13/29 set13/3 set13/30 set13/31 set13/32 set13/33 set13/34 set13/35 set13/36 set13/37 set13/38 set13/39 set13/4 set13/40 set13/41 set13/42 set13/43 set13/44 set13/45 set13/46 set13/47 set13/48 set13/49 set13/5 set13/50 set13/51 set13/52 set13/53 set13/54 set13/55 set13/56 set13/57 set13/58 set13/59 set13/6 set13/60 set13/61 set13/62 set13/63 set13/64 set13/65 set13/66 set13/67 set13/68 set13/69 set13/7 set13/70 set13/71 set13/72 set13/73 set13/74 set13/75 set13/76 set13/77 set13/78 set13/79 set13/8 set13/80 set13/81 set13/82 set13/83 set13/84 set13/85 set13/86 set13/87 set13/88 set13/89 set13/9 set13/90 set13/91 set13/92 set13/93 set13/94 set13/95 set13/96 set13/97 set13/98 set13/99)  (node: http://192.168.56.25:3900 )
+```
+
+After inspecting, the actual S3 call made was with prefix "set13/", so at least this is not an error in Garage itself but in the jepsen code.
+
+Finally found out that this was due to closures not correctly capturing their context in the list function in s3api.clj (wtf clojure?)
+Not sure exactly where it came from but it seems to have been fixed by making list-inner a separate function and not a sub-function,
+and passing all values that were previously in the context (creds and prefix) as additional arguments.
+
+### `reg2` test inconsistency, even with timestamp fix
+
+The reg2 test is our custom checker for CRDT read-after-write on individual object keys, acting as registers which can be updated.
+The test fails without the timestamp fix, which is expected as the clock scrambler will prevent nodes from having a correct ordering of objects.
+
+With the timestamp fix (`--patch tsfix1`), the happenned-before relationship should at least be respected, meaning that when a PutObject call starts
+after another PutObject call has ended, the second call should overwrite the value of the first call, and that value should not be
+readable by future GetObject calls.
+However, we observed inconsistencies even with the timestamp fix.
+
+The inconsistencies seemed to always happenned after writing a nil value, which translates to a DeleteObject call
+instead of a PutObject. By removing the possibility of writing nil values, therefore only doing
+PutObject calls, the issue disappears. There is therefore an issue to fix in DeleteObject.
+
+The issue in DeleteObject seems to have been fixed by commit `c82d91c6bccf307186332b6c5c6fc0b128b1b2b1`, which can be used using `--patch tsfix2`.
+
+
+## License
+
+Copyright © 2023 Alex Auvolat
+
+This program and the accompanying materials are made available under the
+terms of the GNU Affero General Public License v3.0.

script/jepsen.garage/Vagrantfile

@@ -0,0 +1,40 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+#
+
+def vm(config, hostname, ip)
+  config.vm.hostname = hostname
+  config.vm.network "private_network", ip: ip
+end
+
+Vagrant.configure("2") do |config|
+  config.vm.box = "generic/debian10"
+
+  config.vm.provider "virtualbox" do |vb|
+    vb.gui = false
+    vb.memory = "512"
+    vb.customize ["modifyvm", :id, "--vram=12"]
+  end
+
+  config.vm.provision "shell", inline: <<-SHELL
+    echo "root:root" | chpasswd
+    mkdir -p /root/.ssh
+    echo "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIJpaBZdYxHqMxhv2RExAOa7nkKhPBOHupMP3mYaZ73w9 lx@lindy" >> /root/.ssh/authorized_keys
+  SHELL
+
+  config.vm.define "n1" do |config| vm(config, "n1", "192.168.56.21") end
+  config.vm.define "n2" do |config| vm(config, "n2", "192.168.56.22") end
+  config.vm.define "n3" do |config| vm(config, "n3", "192.168.56.23") end
+  config.vm.define "n4" do |config| vm(config, "n4", "192.168.56.24") end
+  config.vm.define "n5" do |config| vm(config, "n5", "192.168.56.25") end
+  config.vm.define "n6" do |config| vm(config, "n6", "192.168.56.26") end
+  config.vm.define "n7" do |config| vm(config, "n7", "192.168.56.27") end
+
+  config.vm.define "n8" do |config| vm(config, "n8", "192.168.56.28") end
+  config.vm.define "n9" do |config| vm(config, "n9", "192.168.56.29") end
+  config.vm.define "n10" do |config| vm(config, "n10", "192.168.56.30") end
+  config.vm.define "n11" do |config| vm(config, "n11", "192.168.56.31") end
+  config.vm.define "n12" do |config| vm(config, "n12", "192.168.56.32") end
+  config.vm.define "n13" do |config| vm(config, "n13", "192.168.56.33") end
+  config.vm.define "n14" do |config| vm(config, "n14", "192.168.56.34") end
+end

script/jepsen.garage/all_tests_1.sh

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+#!/usr/bin/env bash
+
+set -x
+
+#for ppatch in task3c task3a tsfix2; do
+for ppatch in tsfix2; do
+	#for psc in c cp cdp r pr cpr dpr; do
+	for psc in cdp r pr cpr dpr; do
+		#for ptsk in reg2 set1 set2; do
+		for ptsk in set1; do
+			for irun in $(seq 10); do
+				lein run test --nodes-file nodes.vagrant \
+					--time-limit 60 --rate 100  --concurrency 100 --ops-per-key 100 \
+					--workload $ptsk --patch $ppatch --scenario $psc
+			done
+		done
+	done
+done

script/jepsen.garage/all_tests_2.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+set -x
+
+#for ppatch in task3c tsfix2; do
+for ppatch in tsfix2; do
+	for psc in cdp r pr cpr dpr; do
+		for ptsk in set1; do
+			for irun in $(seq 10); do
+				lein run test --nodes-file nodes2.vagrant \
+					--time-limit 60 --rate 100  --concurrency 100 --ops-per-key 100 \
+					--workload $ptsk --patch $ppatch --scenario $psc
+			done
+		done
+	done
+done

script/jepsen.garage/jaeger.sh

@@ -0,0 +1,13 @@
+docker stop jaeger
+docker rm jaeger
+
+# UI is on localhost:16686
+# otel-grpc collector is on localhost:4317
+# otel-http collector is on localhost:4318
+
+docker run -d --name jaeger \
+  -e COLLECTOR_OTLP_ENABLED=true \
+  -p 4317:4317 \
+  -p 4318:4318 \
+  -p 16686:16686 \
+  jaegertracing/all-in-one:1.50

script/jepsen.garage/nodes.vagrant

@@ -0,0 +1,7 @@
+192.168.56.21
+192.168.56.22
+192.168.56.23
+192.168.56.24
+192.168.56.25
+192.168.56.26
+192.168.56.27

script/jepsen.garage/nodes2.vagrant

@@ -0,0 +1,7 @@
+192.168.56.28
+192.168.56.29
+192.168.56.30
+192.168.56.31
+192.168.56.32
+192.168.56.33
+192.168.56.34

script/jepsen.garage/project.clj

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+(defproject jepsen.garage "0.1.0-SNAPSHOT"
+  :description "Jepsen testing for Garage"
+  :url "https://git.deuxfleurs.fr/Deuxfleurs/garage"
+  :license {:name "AGPLv3"
+            :url "https://www.gnu.org/licenses/agpl-3.0.en.html"}
+  :main jepsen.garage
+  :dependencies [[org.clojure/clojure "1.11.1"]
+                 [jepsen "0.3.3-SNAPSHOT"]
+                 [amazonica "0.3.163"]]
+  :repl-options {:init-ns jepsen.garage})

script/jepsen.garage/shell.nix

@@ -0,0 +1,18 @@
+{ pkgs ? import <nixpkgs> {
+  overlays = [
+    (self: super: {
+      jdk = super.jdk11;
+      jre = super.jre11;
+    })
+  ];
+} }:
+pkgs.mkShell {
+  nativeBuildInputs = with pkgs; [
+    leiningen
+    jdk
+    jna
+    vagrant
+    gnuplot
+    graphviz
+  ];
+}

script/jepsen.garage/src/jepsen/garage.clj

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+(ns jepsen.garage
+  (:require
+    [clojure.string :as str]
+    [jepsen
+     [checker :as checker]
+     [cli :as cli]
+     [generator :as gen]
+     [nemesis :as nemesis]
+     [tests :as tests]]
+    [jepsen.os.debian :as debian]
+    [jepsen.garage
+     [daemon :as grg]
+     [nemesis :as grgNemesis]
+     [reg :as reg]
+     [set :as set]]))
+
+(def workloads
+  "A map of workload names to functions that construct workloads, given opts."
+  {"reg1" reg/workload1
+   "reg2" reg/workload2
+   "set1" set/workload1
+   "set2" set/workload2})
+
+(def scenari
+  "A map of scenari to the associated nemesis"
+  {"c" grgNemesis/scenario-c
+   "cp" grgNemesis/scenario-cp
+   "r"  grgNemesis/scenario-r
+   "pr"  grgNemesis/scenario-pr
+   "cpr"  grgNemesis/scenario-cpr
+   "cdp"  grgNemesis/scenario-cdp
+   "dpr"  grgNemesis/scenario-dpr})
+
+(def patches
+  "A map of patch names to Garage builds"
+  {"default" "v0.9.0"
+   "tsfix1" "d146cdd5b66ca1d3ed65ce93ca42c6db22defc09"
+   "tsfix2" "c82d91c6bccf307186332b6c5c6fc0b128b1b2b1"
+   "task3a" "707442f5de416fdbed4681a33b739f0a787b7834"
+   "task3b" "431b28e0cfdc9cac6c649193cf602108a8b02997"
+   "task3c" "0041b013a473e3ae72f50209d8f79db75a72848b"})
+
+(def cli-opts
+  "Additional command line options."
+  [["-p" "--patch NAME" "Garage patch to use"
+    :default "default"
+    :validate [patches (cli/one-of patches)]]
+   ["-s" "--scenario NAME" "Nemesis scenario to run"
+    :default "cp"
+    :validate [scenari (cli/one-of scenari)]]
+   ["-r" "--rate HZ" "Approximate number of requests per second, per thread."
+    :default  10
+    :parse-fn read-string
+    :validate [#(and (number? %) (pos? %)) "Must be a positive number"]]
+   [nil "--ops-per-key NUM" "Maximum number of operations on any given key."
+    :default  100
+    :parse-fn parse-long
+    :validate [pos? "Must be a positive integer."]]
+   ["-w" "--workload NAME" "Workload of test to run"
+    :default "reg1"
+    :validate [workloads (cli/one-of workloads)]]])
+
+(defn garage-test
+  "Given an options map from the command line runner (e.g. :nodes, :ssh,
+  :concurrency, ...), constructs a test map."
+  [opts]
+  (let [garage-version (get patches (:patch opts))
+        db (grg/db garage-version)
+        workload ((get workloads (:workload opts)) opts)
+        scenario ((get scenari (:scenario opts)) (assoc opts :db db))]
+    (merge tests/noop-test
+           opts
+           {:pure-generators  true
+            :name             (str "garage-" (name (:patch opts)) " " (name (:workload opts)) " " (name (:scenario opts)))
+            :os               debian/os
+            :db               db
+            :client           (:client workload)
+            :generator        (gen/phases
+                                (->>
+                                  (:generator workload)
+                                  (gen/stagger (/ (:rate opts)))
+                                  (gen/nemesis (:generator scenario))
+                                  (gen/time-limit (:time-limit opts)))
+                                (gen/log "Healing cluster")
+                                (gen/nemesis (:final-generator scenario))
+                                (gen/log "Waiting for recovery")
+                                (gen/sleep 10)
+                                (gen/log "Running final generator")
+                                (gen/clients (:final-generator workload))
+                                (gen/log "Generators all done"))
+            :nemesis          (:nemesis scenario)
+            :checker          (checker/compose
+                                {:perf (checker/perf (:perf scenario))
+                                 :workload (:checker workload)})
+            })))
+
+
+(defn -main
+  "Handles command line arguments. Can either run a test, or a web server for
+  browsing results."
+  [& args]
+  (cli/run! (merge (cli/single-test-cmd {:test-fn garage-test
+                                         :opt-spec cli-opts})
+                   (cli/serve-cmd))
+            args))

script/jepsen.garage/src/jepsen/garage/daemon.clj

@@ -0,0 +1,152 @@
+(ns jepsen.garage.daemon
+  (:require [clojure.tools.logging :refer :all]
+            [jepsen [control :as c]
+             [core :as jepsen]
+             [db :as db]]
+            [jepsen.control.util :as cu]))
+
+; CONSTANTS -- HOW GARAGE IS SET UP
+
+(def base-dir "/opt/garage")
+(def data-dir (str base-dir "/data"))
+(def meta-dir (str base-dir "/meta"))
+(def binary (str base-dir "/garage"))
+(def logfile (str base-dir "/garage.log"))
+(def pidfile (str base-dir "/garage.pid"))
+
+(def admin-token "icanhazadmin")
+(def access-key-id "GK8bfb6a51286071c6c9cd8bc3")
+(def secret-access-key "b0be95f71c1c6f16858a9edf395078b75c12ecb6b1c03385c4ae92076e4994a3")
+(def bucket-name "jepsen")
+
+; THE GARAGE DB
+
+(defn install!
+  "Download and install Garage"
+  [node version]
+  (c/su
+    (c/trace
+      (info node "installing garage" version)
+      (c/exec :mkdir :-p base-dir)
+      (let [url (str "https://garagehq.deuxfleurs.fr/_releases/" version "/x86_64-unknown-linux-musl/garage")
+            cache (cu/cached-wget! url)]
+        (c/exec :cp cache binary))
+      (c/exec :chmod :+x binary))))
+
+(defn configure!
+  "Configure Garage"
+  [node]
+  (c/su
+    (c/trace
+      (cu/write-file!
+        (str "rpc_secret = \"0fffabe52542c2b89a56b2efb7dfd477e9dafb285c9025cbdf1de7ca21a6b372\"\n"
+             "rpc_bind_addr = \"0.0.0.0:3901\"\n"
+             "rpc_public_addr = \"" node ":3901\"\n"
+             "db_engine = \"lmdb\"\n"
+             "replication_mode = \"2\"\n"
+             "data_dir = \"" data-dir "\"\n"
+             "metadata_dir = \"" meta-dir "\"\n"
+             "[s3_api]\n"
+             "s3_region = \"us-east-1\"\n"
+             "api_bind_addr = \"0.0.0.0:3900\"\n"
+             "[k2v_api]\n"
+             "api_bind_addr = \"0.0.0.0:3902\"\n"
+             "[admin]\n"
+             "api_bind_addr = \"0.0.0.0:3903\"\n"
+             "admin_token = \"" admin-token "\"\n"
+             "trace_sink = \"http://192.168.56.1:4317\"\n")
+        "/etc/garage.toml"))))
+
+(defn connect-node!
+  "Connect a Garage node to the rest of the cluster"
+  [test node]
+  (c/trace
+    (let [node-id (c/exec binary :node :id :-q)]
+      (info node "node id:" node-id)
+      (c/on-many (:nodes test)
+                 (c/exec binary :node :connect node-id)))))
+
+(defn configure-node!
+  "Configure a Garage node to be part of a cluster layout"
+  [test node]
+  (c/trace
+    (let [node-id (c/exec binary :node :id :-q)]
+      (c/on (jepsen/primary test)
+          (c/exec binary :layout :assign (subs node-id 0 16) :-c :1G :-z :dc1 :-t node)))))
+
+(defn finalize-config!
+  "Apply the layout and create a key/bucket pair in the cluster"
+  [node]
+  (c/trace
+    (c/exec binary :layout :apply :--version 1)
+    (info node "garage status:" (c/exec binary :status))
+    (c/exec binary :key :import access-key-id secret-access-key :--yes)
+    (c/exec binary :bucket :create bucket-name)
+    (c/exec binary :bucket :allow :--read :--write bucket-name :--key access-key-id)
+    (info node "key info: " (c/exec binary :key :info access-key-id))))
+
+(defn db
+  "Garage DB for a particular version"
+  [version]
+  (reify db/DB
+    (setup! [_ test node]
+      (install! node version)
+      (configure! node)
+      (cu/start-daemon!
+        {:logfile logfile
+         :pidfile pidfile
+         :chdir base-dir
+         :env {:RUST_LOG "garage=debug,garage_api=trace"}}
+        binary
+        :server)
+      (c/exec :sleep 3)
+
+      (jepsen/synchronize test)
+      (connect-node! test node)
+
+      (jepsen/synchronize test)
+      (configure-node! test node)
+
+      (jepsen/synchronize test)
+      (when (= node (jepsen/primary test))
+        (finalize-config! node)))
+
+    (teardown! [_ test node]
+      (info node "tearing down garage" version)
+      (c/su
+        (cu/stop-daemon! binary pidfile)
+        (c/exec :rm :-rf logfile)
+        (c/exec :rm :-rf data-dir)
+        (c/exec :rm :-rf meta-dir)))
+
+    db/Pause
+    (pause! [_ test node]
+      (cu/grepkill! :stop binary))
+    (resume! [_ test node]
+      (cu/grepkill! :cont binary))
+
+    db/Kill
+    (kill! [_ test node]
+      (cu/stop-daemon! binary pidfile))
+    (start! [_ test node]
+      (cu/start-daemon!
+        {:logfile logfile
+         :pidfile pidfile
+         :chdir base-dir
+         :env {:RUST_LOG "garage=debug,garage_api=trace"}}
+        binary
+        :server))
+
+    db/LogFiles
+    (log-files [_ test node]
+      [logfile])))
+
+(defn creds
+  "Obtain Garage credentials for node"
+  [node]
+  {:access-key access-key-id
+   :secret-key secret-access-key
+   :endpoint (str "http://" node ":3900")
+   :bucket bucket-name
+   :client-config {:path-style-access-enabled true}})
+

script/jepsen.garage/src/jepsen/garage/nemesis.clj

@@ -0,0 +1,142 @@
+(ns jepsen.garage.nemesis
+  (:require [clojure.tools.logging :refer :all]
+            [jepsen [control :as c]
+             [core :as jepsen]
+             [generator :as gen]
+             [nemesis :as nemesis]]
+            [jepsen.nemesis.combined :as combined]
+            [jepsen.garage.daemon :as grg]
+            [jepsen.control.util :as cu]))
+
+; ---- reconfiguration nemesis ----
+
+(defn configure-present!
+  "Configure node to be active in new cluster layout"
+  [test nodes]
+  (info "configure-present!" nodes)
+  (let [node-ids (c/on-many nodes (c/exec grg/binary :node :id :-q))
+        node-id-strs (map (fn [[_ v]] (subs v  0 16)) node-ids)]
+    (c/on
+      (jepsen/primary test)
+      (apply c/exec (concat [grg/binary :layout :assign :-c :1G] node-id-strs)))))
+
+(defn configure-absent!
+  "Configure nodes to be active in new cluster layout"
+  [test nodes]
+  (info "configure-absent!" nodes)
+  (let [node-ids (c/on-many nodes (c/exec grg/binary :node :id :-q))
+        node-id-strs (map (fn [[_ v]] (subs v  0 16)) node-ids)]
+    (c/on
+      (jepsen/primary test)
+      (apply c/exec (concat [grg/binary :layout :assign :-g] node-id-strs)))))
+
+(defn finalize-config!
+  "Apply the proposed cluster layout"
+  [test]
+  (let [layout-show (c/on (jepsen/primary test) (c/exec grg/binary :layout :show))
+        [_ layout-next-version] (re-find #"apply --version (\d+)\n" layout-show)]
+    (if layout-next-version
+      (do
+        (info "layout show: " layout-show "; next-version: " layout-next-version)
+        (c/on (jepsen/primary test)
+              (c/exec grg/binary :layout :apply :--version layout-next-version)))
+      (info "no layout changes to apply"))))
+
+(defn reconfigure-subset
+  "Reconfigure cluster with only a subset of nodes"
+  [cnt]
+  (reify nemesis/Nemesis
+    (setup! [this test] this)
+
+    (invoke! [this test op] op
+      (case (:f op)
+        :start
+          (let [[keep-nodes remove-nodes]
+                (->> (:nodes test)
+                     shuffle
+                     (split-at cnt))]
+            (info "layout split: keep " keep-nodes ", remove " remove-nodes)
+            (configure-present! test keep-nodes)
+            (configure-absent! test remove-nodes)
+            (finalize-config! test)
+            (assoc op :value keep-nodes))
+        :stop
+          (do
+            (info "layout un-split: all nodes=" (:nodes test))
+            (configure-present! test (:nodes test))
+            (finalize-config! test)
+            (assoc op :value (:nodes test)))))
+
+    (teardown! [this test] this)))
+
+; ---- nemesis scenari ----
+
+(defn nemesis-op
+  "A generator for a single nemesis operation"
+  [op]
+  (fn [_ _] {:type :info, :f op}))
+
+(defn reconfiguration-package
+  "Cluster reconfiguration nemesis package"
+  [opts]
+  {:generator        (->>
+                       (gen/mix [(nemesis-op :reconfigure-start)
+                                 (nemesis-op :reconfigure-stop)])
+                       (gen/stagger (:interval opts 5)))
+   :final-generator  {:type :info, :f :reconfigure-stop}
+   :nemesis          (nemesis/compose
+                       {{:reconfigure-start :start
+                         :reconfigure-stop :stop} (reconfigure-subset 3)})
+   :perf              #{{:name  "reconfigure"
+                         :start #{:reconfigure-start}
+                         :stop  #{:reconfigur-stop}
+                         :color "#A197E9"}}})
+
+(defn scenario-c
+  "Clock modifying scenario"
+  [opts]
+  (combined/clock-package {:db (:db opts), :interval 1, :faults #{:clock}}))
+
+(defn scenario-cp
+  "Clock modifying + partition scenario"
+  [opts]
+  (combined/compose-packages
+    [(combined/clock-package {:db (:db opts), :interval 1, :faults #{:clock}})
+     (combined/partition-package {:db (:db opts), :interval 1, :faults #{:partition}})]))
+
+(defn scenario-r
+  "Cluster reconfiguration scenario"
+  [opts]
+  (reconfiguration-package {:interval 1}))
+
+(defn scenario-pr
+  "Partition + cluster reconfiguration scenario"
+  [opts]
+  (combined/compose-packages
+    [(combined/partition-package {:db (:db opts), :interval 1, :faults #{:partition}})
+     (reconfiguration-package {:interval 1})]))
+
+(defn scenario-cpr
+  "Clock scramble + partition + cluster reconfiguration scenario"
+  [opts]
+  (combined/compose-packages
+    [(combined/clock-package {:db (:db opts), :interval 1, :faults #{:clock}})
+     (combined/partition-package {:db (:db opts), :interval 1, :faults #{:partition}})
+     (reconfiguration-package {:interval 1})]))
+
+(defn scenario-cdp
+  "Clock modifying + db + partition scenario"
+  [opts]
+  (combined/compose-packages
+    [(combined/clock-package {:db (:db opts), :interval 1, :faults #{:clock}})
+     (combined/db-package {:db (:db opts), :interval 1, :faults #{:db :pause :kill}})
+     (combined/partition-package {:db (:db opts), :interval 1, :faults #{:partition}})]))
+
+(defn scenario-dpr
+  "Db + partition + cluster reconfiguration scenario"
+  [opts]
+  (combined/compose-packages
+    [(combined/db-package {:db (:db opts), :interval 1, :faults #{:db :pause :kill}})
+     (combined/partition-package {:db (:db opts), :interval 1, :faults #{:partition}})
+     (reconfiguration-package {:interval 1})]))
+

script/jepsen.garage/src/jepsen/garage/reg.clj

@@ -0,0 +1,143 @@
+(ns jepsen.garage.reg
+  (:require [clojure.tools.logging :refer :all]
+            [clojure.string :as str]
+            [clojure.set :as set]
+            [jepsen [checker :as checker]
+             [cli :as cli]
+             [client :as client]
+             [control :as c]
+             [db :as db]
+             [generator :as gen]
+             [independent :as independent]
+             [nemesis :as nemesis]
+             [util :as util]
+             [tests :as tests]]
+            [jepsen.checker.timeline :as timeline]
+            [jepsen.control.util :as cu]
+            [jepsen.os.debian :as debian]
+            [jepsen.garage.daemon :as grg]
+            [jepsen.garage.s3api :as s3]
+            [knossos.model :as model]
+            [slingshot.slingshot :refer [try+]]))
+
+(defn op-get [_ _] {:type :invoke, :f :read, :value nil})
+(defn op-put [_ _] {:type :invoke, :f :write, :value (str (rand-int 99))})
+(defn op-del [_ _] {:type :invoke, :f :write, :value nil})
+
+(defrecord RegClient [creds]
+  client/Client
+  (open! [this test node]
+    (assoc this :creds (grg/creds node)))
+  (setup! [this test])
+  (invoke! [this test op]
+    (try+
+      (let [[k v] (:value op)]
+        (case (:f op)
+          :read
+            (util/timeout
+              10000
+              (assoc op :type :fail, :error ::timeout)
+              (let [value (s3/get (:creds this) k)]
+                (assoc op :type :ok, :value (independent/tuple k value))))
+          :write
+            (util/timeout
+              10000
+              (assoc op :type :info, :error ::timeout)
+              (do
+                (s3/put (:creds this) k v)
+                (assoc op :type :ok)))))
+      (catch (re-find #"Unavailable" (.getMessage %)) ex
+        (assoc op :type :info, :error ::unavailable))
+      (catch (re-find #"Broken pipe" (.getMessage %)) ex
+        (assoc op :type :info, :error ::broken-pipe))
+      (catch (re-find #"Connection refused" (.getMessage %)) ex
+        (assoc op :type :info, :error ::connection-refused))))
+  (teardown! [this test])
+  (close! [this test]))
+
+(defn reg-read-after-write
+  "Read-after-Write checker for register operations"
+  []
+  (reify checker/Checker
+    (check [this test history opts]
+      (let [init {:put-values {-1 nil}
+                  :put-done #{-1}
+                  :put-in-progress {}
+                  :read-can-contain {}
+                  :bad-reads #{}}
+            final (reduce
+                    (fn [state op]
+                      (let [current-values (set/union
+                                             (set (map (fn [idx] (get (:put-values state) idx)) (:put-done state)))
+                                             (set (map (fn [[_ [idx _]]] (get (:put-values state) idx)) (:put-in-progress state))))
+                            read-can-contain (reduce
+                                               (fn [rcc [idx v]] (assoc rcc idx (set/union current-values v)))
+                                               {} (:read-can-contain state))]
+                      (info "--------")
+                      (info "state: " state)
+                      (info "current-values: " current-values)
+                      (info "read-can-contain: " read-can-contain)
+                      (info "op: " op)
+                      (case [(:type op) (:f op)]
+                        ([:invoke :write])
+                          (assoc state
+                                 :read-can-contain read-can-contain
+                                 :put-values (assoc (:put-values state) (:index op) (:value op))
+                                 :put-in-progress (assoc (:put-in-progress state) (:process op) [(:index op) (:put-done state)]))
+                        ([:ok :write])
+                          (let [[index overwrites] (get (:put-in-progress state) (:process op))]
+                            (assoc state
+                                   :read-can-contain read-can-contain
+                                   :put-in-progress (dissoc (:put-in-progress state) (:process op))
+                                   :put-done
+                                     (conj
+                                       (set/difference (:put-done state) overwrites)
+                                       index)))
+                        ([:invoke :read])
+                         (assoc state
+                                :read-can-contain (assoc read-can-contain (:process op) current-values))
+                        ([:ok :read])
+                         (let [this-read-can-contain (get read-can-contain (:process op))
+                               bad-reads (if (contains? this-read-can-contain (:value op))
+                                           (:bad-reads state)
+                                           (conj (:bad-reads state) [(:process op) (:index op) (:value op) this-read-can-contain]))]
+                           (info "this-read-can-contain: " this-read-can-contain)
+                           (assoc state
+                                  :read-can-contain (dissoc read-can-contain (:process op))
+                                  :bad-reads bad-reads))
+                        state)))
+                    init history)
+            valid? (empty? (:bad-reads final))]
+        (assoc final :valid? valid?)))))
+
+(defn workload-common
+  "Common parts of workload"
+  [opts]
+  {:client           (RegClient. nil)
+   :generator        (independent/concurrent-generator
+                       10
+                       (range)
+                       (fn [k]
+                         (->>
+                           (gen/mix [op-get op-put op-del])
+                           (gen/limit (:ops-per-key opts)))))})
+
+(defn workload1
+  "Tests linearizable reads and writes"
+  [opts]
+  (assoc (workload-common opts)
+         :checker (independent/checker
+                    (checker/compose
+                      {:linear (checker/linearizable
+                                 {:model     (model/register)
+                                  :algorithm :linear})
+                       :timeline (timeline/html)}))))
+
+(defn workload2
+  "Tests CRDT reads and writes"
+  [opts]
+  (assoc (workload-common opts)
+         :checker (independent/checker
+                    (checker/compose
+                      {:reg-read-after-write (reg-read-after-write)
+                       :timeline (timeline/html)}))))

script/jepsen.garage/src/jepsen/garage/s3api.clj

@@ -0,0 +1,48 @@
+(ns jepsen.garage.s3api
+  (:require [clojure.tools.logging :refer :all]
+            [jepsen [control :as c]]
+            [amazonica.aws.s3 :as s3]
+            [slingshot.slingshot :refer [try+]]))
+
+; GARAGE S3 HELPER FUNCTIONS
+
+(defn get
+  "Helper for GetObject"
+  [creds k]
+  (try+
+    (-> (s3/get-object creds (:bucket creds) k)
+        :input-stream
+        slurp)
+    (catch (re-find #"Key not found" (.getMessage %)) ex
+      nil)))
+
+(defn put
+  "Helper for PutObject or DeleteObject (is a delete if value is nil)"
+  [creds k v]
+  (if (= v nil)
+    (s3/delete-object creds
+                      :bucket-name (:bucket creds)
+                      :key k)
+    (let [some-bytes (.getBytes v "UTF-8")
+          bytes-stream (java.io.ByteArrayInputStream. some-bytes)]
+      (s3/put-object creds
+                     :bucket-name (:bucket creds)
+                     :key k
+                     :input-stream bytes-stream
+                     :metadata {:content-length (count some-bytes)}))))
+
+(defn list-inner [creds prefix ct accum]
+  (let [list-result (s3/list-objects-v2 creds
+                                        {:bucket-name (:bucket creds)
+                                         :prefix prefix
+                                         :continuation-token ct})
+        new-object-summaries (:object-summaries list-result)
+        new-objects (map (fn [d] (:key d)) new-object-summaries)
+        objects (concat new-objects accum)]
+    (if (:truncated? list-result)
+      (list-inner creds prefix (:next-continuation-token list-result) objects)
+      objects)))
+(defn list
+  "Helper for ListObjects -- just lists everything in the bucket"
+  [creds prefix]
+  (list-inner creds prefix nil []))

script/jepsen.garage/src/jepsen/garage/set.clj

@@ -0,0 +1,135 @@
+(ns jepsen.garage.set
+  (:require [clojure.tools.logging :refer :all]
+            [clojure.string :as str]
+            [clojure.set :as set]
+            [jepsen [checker :as checker]
+             [cli :as cli]
+             [client :as client]
+             [control :as c]
+             [checker :as checker]
+             [db :as db]
+             [generator :as gen]
+             [independent :as independent]
+             [nemesis :as nemesis]
+             [util :as util]
+             [tests :as tests]]
+            [jepsen.checker.timeline :as timeline]
+            [jepsen.control.util :as cu]
+            [jepsen.os.debian :as debian]
+            [jepsen.garage.daemon :as grg]
+            [jepsen.garage.s3api :as s3]
+            [knossos.model :as model]
+            [slingshot.slingshot :refer [try+]]))
+
+(defn op-add-rand100 [_ _] {:type :invoke, :f :add, :value (rand-int 100)})
+(defn op-read [_ _] {:type :invoke, :f :read, :value nil})
+
+(defrecord SetClient [creds]
+  client/Client
+  (open! [this test node]
+    (assoc this :creds (grg/creds node)))
+  (setup! [this test])
+  (invoke! [this test op]
+    (try+
+      (let [[k v] (:value op)
+            prefix (str "set" k "/")]
+        (case (:f op)
+          :add
+            (util/timeout
+              10000
+              (assoc op :type :info, :error ::timeout)
+              (do
+                (s3/put (:creds this) (str prefix v) "present")
+                (assoc op :type :ok)))
+          :read
+            (util/timeout
+              10000
+              (assoc op :type :fail, :error ::timeout)
+              (do
+                (let [items (s3/list (:creds this) prefix)]
+                  (let [items-stripped (map (fn [o]
+                                            (assert (str/starts-with? o prefix))
+                                            (str/replace-first o prefix "")) items)
+                        items-set (set (map parse-long items-stripped))]
+                    (assoc op :type :ok, :value (independent/tuple k items-set))))))))
+      (catch (re-find #"Unavailable" (.getMessage %)) ex
+        (assoc op :type :info, :error ::unavailable))
+      (catch (re-find #"Broken pipe" (.getMessage %)) ex
+        (assoc op :type :info, :error ::broken-pipe))
+      (catch (re-find #"Connection refused" (.getMessage %)) ex
+        (assoc op :type :info, :error ::connection-refused))))
+  (teardown! [this test])
+  (close! [this test]))
+
+(defn set-read-after-write
+  "Read-after-Write checker for set operations"
+  []
+  (reify checker/Checker
+    (check [this test history opts]
+      (let [init {:add-started #{}
+                  :add-done #{}
+                  :read-must-contain {}
+                  :missed #{}
+                  :unexpected #{}}
+            final (reduce
+                    (fn [state op]
+                      (case [(:type op) (:f op)]
+                        ([:invoke :add])
+                          (assoc state :add-started (conj (:add-started state) (:value op)))
+                        ([:ok :add])
+                          (assoc state :add-done (conj (:add-done state) (:value op)))
+                        ([:invoke :read])
+                          (assoc-in state [:read-must-contain (:process op)] (:add-done state))
+                        ([:ok :read])
+                          (let [read-must-contain (get (:read-must-contain state) (:process op))
+                                new-missed (set/difference read-must-contain (:value op))
+                                new-unexpected (set/difference (:value op) (:add-started state))]
+                            (assoc state
+                                   :read-must-contain (dissoc (:read-must-contain state) (:process op))
+                                   :missed (set/union (:missed state) new-missed),
+                                   :unexpected (set/union (:unexpected state) new-unexpected)))
+                         state))
+                    init history)
+            valid? (and (empty? (:missed final)) (empty? (:unexpected final)))]
+        (assoc final :valid? valid?)))))
+
+(defn workload1
+  "Tests insertions and deletions"
+  [opts]
+  {:client            (SetClient. nil)
+   :checker           (independent/checker
+                        (checker/compose
+                          {:set (checker/set)
+                           :timeline (timeline/html)}))
+   :generator         (independent/concurrent-generator
+                        10
+                        (range 100)
+                        (fn [k]
+                          (->> (range)
+                           (map (fn [x] {:type :invoke, :f :add, :value x}))
+                           (gen/limit (:ops-per-key opts)))))
+   :final-generator   (independent/concurrent-generator
+                        10
+                        (range 100)
+                        (fn [k]
+                          (gen/phases
+                            (gen/once op-read)
+                            (gen/sleep 5))))})
+
+(defn workload2
+  "Tests insertions and deletions"
+  [opts]
+  {:client            (SetClient. nil)
+   :checker           (independent/checker
+                        (checker/compose
+                          {:set-read-after-write (set-read-after-write)
+                           ; :set-full (checker/set-full {:linearizable? false})
+                           :timeline (timeline/html)}))
+   :generator         (independent/concurrent-generator
+                        10
+                        (range)
+                        (fn [k]
+                          (->> (gen/mix [op-add-rand100 op-read])
+                               (gen/limit (:ops-per-key opts)))))})
+
+

script/jepsen.garage/test/jepsen/garage_test.clj

@@ -0,0 +1,7 @@
+(ns jepsen.garage-test
+  (:require [clojure.test :refer :all]
+            [jepsen.garage :refer :all]))
+
+(deftest a-test
+  (testing "FIXME, I fail."
+    (is (= 0 1))))