final commit for bachelor's thesis

.gitignore

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+/debug/
+/target/
+/qemu/
+
+*.lock

Cargo.toml

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+[workspace]
+members = [
+	"permanent_common",
+	"permanent_plugin",
+	"permanent_trace",
+	"permanent_cig",
+	"permanent_tester",
+]
+exclude = [
+	# Needs to be built with musl.
+	"fs-testing/fs-dump",
+]
+
+[profile.release]
+debug = true

README.md

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+# Permanent: Persistent Memory and NVMe Non-Deterministic Tester
+
+This is the source code of Permanent, a tool for automated crash consistency testing for file systems using persistent memory and NVMe.
+It is a combination of [Vinter](https://os.itec.kit.edu/65_3814.php) [(source)](https://github.com/KIT-OSGroup/vinter) and [Revin](https://os.itec.kit.edu/97_3853.php).
+
+## Setup
+
+```sh
+# install dependencies
+# TODO
+
+# Rust via rustup (see https://rustup.rs)
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+rustup target add x86_64-unknown-linux-musl
+
+# get QEMU
+wget https://download.qemu.org/qemu-8.0.4.tar.xz
+tar xvJf qemu-8.0.4.tar.xz && mv qemu-8.0.4 qemu
+# apply patch
+pushd qemu && patch -p1 < ../qemu.patch && popd
+# configure QEMU
+mkdir qemu/build && pushd qemu/build && ../configure --target-list=x86_64-softmmu --enable-debug --enable-plugins && popd
+# build QEMU
+make -C qemu/build -j$(nproc)
+
+# build permanent
+./build.sh
+
+```
+
+## License
+
+Permanent is released under the MIT license, see `LICENSE` for details.

build.sh

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+#!/usr/bin/env bash
+
+set -eux
+
+cargo build --release
+
+# build fs-dump
+(cd fs-testing/fs-dump && cargo build --release --target=x86_64-unknown-linux-musl)
+
+# build checkpoint
+(cd permanent_plugin && ./build_checkpoint.sh)
+
+# build initramfs
+make -C fs-testing/initramfs

fs-testing/fs-dump/.gitignore

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+/target

fs-testing/fs-dump/Cargo.toml

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+[package]
+name = "fs-dump"
+version = "0.1.0"
+edition = "2018"
+
+[dependencies]
+walkdir = "2"
+serde = { version = "1.0", features = ["derive"] }
+serde_json = "1.0"

fs-testing/fs-dump/src/main.rs

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+use serde::Serialize;
+use std::collections::BTreeMap;
+use std::os::unix::fs::MetadataExt;
+use std::fs::File;
+use std::io::Read;
+use walkdir::WalkDir;
+
+#[derive(Serialize)]
+struct FileAttrs {
+    typeflag: String,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    content: Option<String>,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    target: Option<String>,
+    st_ino: u64,
+    st_mode: u32,
+    st_nlink: u64,
+    st_uid: u32,
+    st_gid: u32,
+    st_size: u64,
+    st_blocks: u64,
+    st_atim_sec: i64,
+    st_atim_nsec: i64,
+    st_mtim_sec: i64,
+    st_mtim_nsec: i64,
+    st_ctim_sec: i64,
+    st_ctim_nsec: i64,
+}
+
+fn main() {
+    let args: Vec<String> = std::env::args().collect();
+    let (path, dump_contents) = match args.len() {
+        2 => (&args[1], false),
+        3 if args[1] == "--contents" => (&args[2], true),
+        _ => {
+            println!("usage: {} [--contents] <path>", args[0]);
+            std::process::exit(1);
+        }
+    };
+    let mut result = BTreeMap::new();
+    for entry in WalkDir::new(path) {
+        let entry = entry.expect("could not read dir entry");
+        let metadata = entry.metadata().expect("could not retrieve file metadata");
+        result.insert(
+            entry.path().to_string_lossy().into_owned(),
+            FileAttrs {
+                typeflag: match entry.file_type() {
+                    t if t.is_file() => "F",
+                    t if t.is_dir() => "D",
+                    t if t.is_symlink() => "SL",
+                    _ => panic!("unexpected file type at {}", entry.path().display())
+                }.to_string(),
+                content: if dump_contents && entry.file_type().is_file() {
+                    let mut file = File::open(entry.path()).expect("could not open file");
+                    let mut contents = String::new();
+                    file.read_to_string(&mut contents).expect("could not read file contents");
+                    Some(contents)
+                } else {
+                    None
+                },
+                target: if dump_contents && entry.file_type().is_symlink() {
+                    Some(std::fs::read_link(entry.path()).expect("could not read symlink").to_string_lossy().into_owned())
+                } else {
+                    None}
+                    ,
+                st_ino: metadata.ino(),
+                st_mode: metadata.mode(),
+                st_nlink: metadata.nlink(),
+                st_uid: metadata.uid(),
+                st_gid: metadata.gid(),
+                st_size: metadata.size(),
+                st_blocks: metadata.blocks(),
+                st_atim_sec: metadata.atime(),
+                st_atim_nsec: metadata.atime_nsec(),
+                st_mtim_sec: metadata.mtime(),
+                st_mtim_nsec: metadata.mtime_nsec(),
+                st_ctim_sec: metadata.ctime(),
+                st_ctim_nsec: metadata.ctime_nsec(),
+            },
+        );
+    }
+    print!("PERMANENT START");
+    serde_json::to_writer_pretty(std::io::stdout(), &result).expect("could not serialize JSON");
+    print!("PERMANENT END");
+}

fs-testing/initramfs/.gitignore

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+/initramfs
+/busybox
+/busybox_pmfs
+*.cpio.gz

fs-testing/initramfs/Makefile

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+
+INITRAMFS_DEPS := \
+	create-initramfs.sh \
+	busybox \
+	../../permanent_plugin/checkpoint \
+	../fs-dump/target/x86_64-unknown-linux-musl/release/fs-dump
+
+default: initramfs.cpio.gz
+.PHONY: default
+
+initramfs.cpio.gz: $(INITRAMFS_DEPS)
+	./create-initramfs.sh > $@
+
+initramfs_mainline.cpio.gz: $(INITRAMFS_DEPS)
+	rm -rf initramfs_mainline
+	mkdir -p initramfs_mainline/{bin,lib}
+	ln -s lib initramfs_mainline/lib64
+	./copy-binary.sh `which mkfs.ext4` initramfs_mainline
+	./copy-binary.sh `which fsck.ext4` initramfs_mainline
+	./copy-binary.sh `which mkfs.xfs` initramfs_mainline
+	./copy-binary.sh `which xfs_repair` initramfs_mainline
+	./create-initramfs.sh initramfs_mainline > $@
+
+initramfs_zilpmem.cpio.gz: $(INITRAMFS_DEPS) ../zil-pmem/initramfs_zfs
+	./create-initramfs.sh ../zil-pmem/initramfs_zfs > $@
+
+busybox:
+	curl -o $@ https://busybox.net/downloads/binaries/1.35.0-x86_64-linux-musl/busybox
+	chmod +x $@

fs-testing/initramfs/copy-binary.sh

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+#!/usr/bin/env bash
+
+set -eu
+
+# Usage: copy-binary.sh <binary> <initramfs root>
+
+binary=${1:?need binary}
+initramfs=${2:?need initramfs root}
+
+cp "$binary" "$initramfs/bin/"
+
+# Copy libraries from host system.
+ldd "$binary" | \
+  awk '/ => \// { print $3 } /ld-linux/ { print $1 }' | \
+  xargs cp -t "$initramfs/lib"
+

fs-testing/initramfs/create-initramfs.sh

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+#!/usr/bin/env bash
+set -eu
+
+# Usage: create-initramfs.sh [folder with extra files] > initramfs.cpio.gz
+
+cd "$( dirname "${BASH_SOURCE[0]}" )"
+
+rm -rf initramfs
+
+# put extra stuff in $1
+if [[ -n "${1:-}" ]]; then
+	cp -rH "$1" initramfs
+fi
+
+mkdir -p initramfs/{bin,mnt,proc,sys}
+
+cp init initramfs
+"${BUSYBOX:-./busybox}" --install initramfs/bin
+cp ../../permanent_plugin/checkpoint initramfs/bin
+cp ../fs-dump/target/x86_64-unknown-linux-musl/release/fs-dump initramfs/bin
+
+(cd initramfs && find . -print0 | cpio --owner root:root --null -ov --format=newc | gzip -9)

fs-testing/initramfs/init

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+#!/bin/sh
+
+mount -t proc none /proc
+mount -t sysfs none /sys
+mount -t devtmpfs none /dev
+
+if [ -d /init.d ]; then
+  for f in /init.d/*; do
+    . "$f"
+  done
+fi
+
+exec /bin/sh

fs-testing/tests/test_append.yaml

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+trace_cmd_suffix: "checkpoint 0 && echo -n test > /mnt/myfile && sync && checkpoint 1 && sleep 2 && echo -n appendedalignedtext01234 >> /mnt/myfile && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/myfile && rm -r /mnt/*"

fs-testing/tests/test_atime.yaml

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+# atomically update access time
+# touch with old timestamp first to trick relatime feature
+trace_cmd_suffix: "checkpoint 0 && echo -n test > /mnt/myfile && touch -d '2020-01-01 00:00:00' /mnt/myfile && sync && checkpoint 1 && sleep 2 && cat /mnt/myfile > /dev/null && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/myfile && rm -r /mnt/*"

fs-testing/tests/test_chmod.yaml

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+trace_cmd_suffix: "checkpoint 0 && echo -n test > /mnt/myfile && sync && checkpoint 1 && sleep 2 && chmod 666 /mnt/myfile && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/myfile && rm -r /mnt/*"

fs-testing/tests/test_chown.yaml

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+trace_cmd_suffix: "checkpoint 0 && echo -n test > /mnt/myfile && sync && checkpoint 1 && sleep 2 && chown 321:789 /mnt/myfile && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/myfile && rm -r /mnt/*"

fs-testing/tests/test_ctime-mtime.yaml

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+# touch with old timestamp first to trick relatime feature
+trace_cmd_suffix: "checkpoint 0 && mkdir /mnt/mydir && touch /mnt/mydir/myfile && touch -d '2020-01-01 00:00:00' /mnt/mydir && sync && checkpoint 1 && sleep 2 && rm /mnt/mydir/myfile && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/myfile && if [ -e /mnt/mydir ] ; then echo test >> /mnt/mydir/myfile ; else true ; fi && rm -r /mnt/*"

fs-testing/tests/test_hello-world.yaml

@@ -0,0 +1,3 @@
+trace_cmd_suffix: "checkpoint 0 && sync && checkpoint 1 && echo HelloWorld > /mnt/myfile && checkpoint 2 && sync && checkpoint 3"
+checkpoint_range: [0, 3]
+dump_cmd_suffix: "echo test >> /mnt/myfile && rm /mnt/myfile"

fs-testing/tests/test_link-hard.yaml

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+trace_cmd_suffix: "checkpoint 0 && echo -n test > /mnt/myfile && sync && checkpoint 1 && ln /mnt/myfile /mnt/hardlink && sync && checkpoint 2 && sleep 2 && rm /mnt/myfile && sync && checkpoint 3"
+checkpoint_range: [0, 3]
+dump_cmd_suffix: "echo test > /mnt/myfile && rm -r /mnt/*"

fs-testing/tests/test_link-sym.yaml

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+trace_cmd_suffix: "checkpoint 0 && echo -n test > /mnt/myfile && sync && checkpoint 1 && ln -s /mnt/myfile /mnt/symlink && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/myfile && rm -r /mnt/*"

fs-testing/tests/test_mkdir-rmdir.yaml

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+trace_cmd_suffix: "checkpoint 0 && mkdir /mnt/mydir && sync && checkpoint 1 && sleep 2 && rmdir /mnt/mydir && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "if [ -e /mnt/mydir ] ; then echo -n hoho > /mnt/mydir/file ; else echo -n test > /mnt/mydir ; fi && echo -n test > /mnt/myfile && rm -r /mnt/*"

fs-testing/tests/test_rename-dir.yaml

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+trace_cmd_suffix: "checkpoint 0 && mkdir /mnt/newdir && sync && checkpoint 1 && mkdir /mnt/newdir2 && sync && checkpoint 2 && echo -n test > /mnt/newdir/testfile && sync && checkpoint 3 && mv /mnt/newdir /mnt/newdir2 && sync && checkpoint 4"
+checkpoint_range: [0, 4]
+dump_cmd_suffix: "echo test >> /mnt/myfile && if [ -f /mnt/newdir2/newdir/testfile ] ; then echo test >> /mnt/newdir2/newdir/testfile ; else true ; fi && rm -r /mnt/*"

fs-testing/tests/test_rename-long-name.yaml

@@ -0,0 +1,3 @@
+trace_cmd_suffix: "checkpoint 0 && echo -n test > /mnt/myfile && sync && checkpoint 1 && mv /mnt/myfile /mnt/testfile_renamed_to_a_long_filename2222222222222222222222222222222222222222222222222223200 && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/testfile_renamed_to_a_long_filename2222222222222222222222222222222222222222222222222223200 && rm -r /mnt/*"

fs-testing/tests/test_rename.yaml

@@ -0,0 +1,3 @@
+trace_cmd_suffix: "checkpoint 0 && echo -n tes1 > /mnt/myfile && echo -n tes2 > /mnt/myfile2 && sync && checkpoint 1 && mv /mnt/myfile2 /mnt/myfile && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/myfile && rm /mnt/myfile"

fs-testing/tests/test_touch-long-name.yaml

@@ -0,0 +1,3 @@
+trace_cmd_suffix: "checkpoint 0 && touch /mnt/eizAKifFfyOn72ieKYxbCraXxNonCfH8CargS4xDIbOGGW6BPBCPEc1RYyNyZWZgXXX && sync && checkpoint 1 && sleep 2 && echo -n helo > /mnt/eizAKifFfyOn72ieKYxbCraXxNonCfH8CargS4xDIbOGGW6BPBCPEc1RYyNyZWZgXXX && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/eizAKifFfyOn72ieKYxbCraXxNonCfH8CargS4xDIbOGGW6BPBCPEc1RYyNyZWZgXXX && rm -r /mnt/*"

fs-testing/tests/test_touch.yaml

@@ -0,0 +1,3 @@
+trace_cmd_suffix: "checkpoint 0 && touch /mnt/myfile && sync && checkpoint 1 && sleep 2 && touch /mnt/myfile && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test >> /mnt/myfile && rm -r /mnt/*"

fs-testing/tests/test_unlink.yaml

@@ -0,0 +1,3 @@
+trace_cmd_suffix: "checkpoint 0 && echo -n test > /mnt/myfile && sync && checkpoint 1 && rm /mnt/myfile && sync && checkpoint 2"
+checkpoint_range: [0, 2]
+dump_cmd_suffix: "echo test > /mnt/myfile && rm -r /mnt/*"

fs-testing/tests/test_update-middle.yaml

@@ -0,0 +1,4 @@
+# update part of file
+trace_cmd_suffix: 'checkpoint 0 && for i in `seq 71` ; do printf MjOf1E3x18E3R5EP6hq7WjzALMtjsAXY ; done > /mnt/myfile && sync && checkpoint 1 && echo -n hohoho | dd of=/mnt/myfile seek=171 bs=6 conv=notrunc && checkpoint 2 && sync && checkpoint 3'
+checkpoint_range: [0, 3]
+dump_cmd_suffix: "echo test >> /mnt/myfile && rm -r /mnt/*"

fs-testing/vms/vm_zilpmem.yaml

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+fs_type: "hybrid"
+pmem_start: 536870912 # 512 * 2**20
+pmem_len:   134217728 # 128 * 2**20
+qemu_path: "qemu/build/qemu-system-x86_64"
+kernel_path: "fs-testing/zil-pmem/linux_build/arch/x86/boot/bzImage"
+initrd_path: "fs-testing/initramfs/initramfs_zilpmem.cpio.gz"
+qemu_args: [ "-m", "1G", "-append", "console=ttyS0,115200n8 memmap=128M!512M" ]
+trace_cmd_prefix: 'echo 1 > /proc/sys/kernel/printk && echo 1 > /sys/module/zfs/parameters/zfs_zil_pmem_prb_ncommitters && echo 2 > /sys/module/zfs/parameters/zil_default_kind && zpool create -O mountpoint=legacy testpool /dev/nvme0n1 log dax:/dev/pmem0 && mount -t zfs -o sync=always testpool /mnt'
+# Recovery: Import pool read-write to allow replay, then mount dataset read-only. 
+recovery_cmd: 'echo 1 > /proc/sys/kernel/printk && echo 1 > /sys/module/zfs/parameters/zfs_zil_pmem_prb_ncommitters && zpool import testpool && mount -t zfs -oro testpool /mnt && ls -lah /mnt && fs-dump --contents /mnt > /dev/null'
+# reduce linux console level to prevent garbage in the output
+dump_cmd_prefix: 'echo 1 > /proc/sys/kernel/printk && echo 1 > /sys/module/zfs/parameters/zfs_zil_pmem_prb_ncommitters && zpool import testpool && mount -t zfs -oro testpool /mnt && fs-dump --contents /mnt && umount /mnt && mount -t zfs testpool /mnt'

fs-testing/zil-pmem/README.md

@@ -0,0 +1,34 @@
+# Analyzing ZIL-PMEM
+
+https://github.com/openzfs/zfs/pull/12731
+
+## Building
+
+Clone ZFS (with ZIL-PMEM) into openzfs/ and a suitable Linux version into linux/ (e.g., 5.11).
+
+```sh
+# upstream
+git clone -b zil-pmem/upstreaming https://github.com/problame/zfs/ openzfs
+# with some patches (e.g., smaller chunk size) to ease analysis
+git clone -b zil-pmem/vinter https://github.com/lluchs/zfs/ openzfs
+```
+
+Build the kernel:
+
+```sh
+./build-zfs-builtin.sh
+# builds linux_build/arch/x86/boot/bzImage
+```
+
+Build the ZFS tools:
+
+```sh
+./build-zfs-tools.sh
+# builds initramfs_zfs/
+```
+
+Build the initramfs:
+
+```sh
+make -C../initramfs initramfs_zilpmem.cpio.gz
+```