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Automatically fixing persistency bugs in PM applications. ASPLOS '21.

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Hippocrates (ASPLOS '21)

This repository contains the artifact for our ASPLOS '21 paper on Hippocrates, an automated tool for fixing PM durability bugs.

ASPLOS '21 Artifact Evaluation

The Artifact Evaluation README contains the README from the original ASPLOS'21 artifact evaluation process. That README will remain relatively static for legacy purposes, while we will keep the following README more up-to-date.

If you are curious:

  • The artifact evaluation results are presented here.
  • The ASPLOS'21 Artifact Evaluation page is available at ctuning.org.

Requirements

This has been tested on a server configured with Ubuntu 20.04.1 LTS on a CPU that supports the clwb instruction (to check if your CPU has this feature enabled, run lscpu and look for the clwb flag, e.g. lscpu | grep clwb).

Other requirements can be installed via the ./install-deps.sh script. Python requirements can be found in requirements.txt.

Compilation

We now provide an overview of how to build and run Hippocrates. We provide pre-built binaries in artifact/prebuilt as an alternative to the following compilation instructions.

Building Hippocrates

Installing Requirements (optional)

This step is only needed if setting up Hippocrates on a new machine.

# Requires root priviledges (sudo)
./install-deps.sh

[GitHub] Setting up the repository (once)

Use the instructions in this section if you are cloning the repository from GitHub. If you are using the Zenodo archive, skip to the Zenodo instructions below.

After cloning the repository, you need to set up the submodules, which Hippocrates depends on for both the LLVM pass and for running tests.

git clone https://github.com/efeslab/hippocrates.git
cd hippocrates

git submodule init
git submodule update --recursive

If you need to re-initialize the submodules for any reason, try:

git submodule deinit --all -f
git submodule init
git submodule update --recursive

[Zenodo] Setting up the repository (once)

Only use these instructions if you are using the Zenodo archive.

unzip <download>
cd efeslab-hippocrates-<revision#>
./zenodo-setup.sh

The zenodo-setup.sh script clones the requires submodules without using the git submodule commands.

Compiling Hippocrates

Starting in the root of the repository:

source build.env

mkdir build
cd build
cmake ..

make PMFIXER -j$(nproc)
make FLUSHREMOVER -j$(nproc)
make PMTEST
# Must build PMEMCHECK before PMINTRINSICS
make PMEMCHECK
make PMINTRINSICS

Updating the repository

When updating the repository, to update any of the files generated in the build directory, you must rerun the compilation steps to rebuild these files. If any of the dependencies are updated, you must rerun the steps listed in "Building Dependencies" section (below).

Note that this also includes updates to scripts in the tools directory, as they are only copied/configured when the above make or cmake commands are rerun. Just running git pull will not automatically apply changes to any files in the build directory.

Building Dependencies

  • wllvm (optional, only if installing on a new machine):
cd deps/whole-program-llvm
sudo -H pip3 install -e .
  • pmemcheck:

This should already be built, however if you need to rebuild:

source build.env
cd build
make -C $REPO_ROOT/deps/valgrind-pmem clean
make PMEMCHECK
  • PMDK:
source build.env
cd build
make PMDK

cd $REPO_ROOT/build/deps/pmdk/lib/pmdk_debug
extract-bc libpmem.so
extract-bc libpmemobj.so
  • memcached-pmem (requires PMDK to be built first)
source build.env
cd $REPO_ROOT/deps/memcached-pmem
git checkout master
git pull

cd $REPO_ROOT/build
make MEMCACHED_PMEM

cd $REPO_ROOT/build/deps/memcached-pmem/bin/
llvm-link-8 memcached.bc -o memcached.linked.bc $REPO_ROOT/build/deps/pmdk/lib/pmdk_debug/libpmem.so.bc
  • RECIPE (P-CLHT)
source build.env
cd build
make p-clht_example

cd ./deps/RECIPE/P-CLHT/
extract-bc p-clht_example
llvm-link-8 p-clht_example.bc --override=../../pmdk/lib/pmdk_debug/libpmem.so.bc \
        --override=../../pmdk/lib/pmdk_debug/libpmemobj.so.bc -o p-clht_example.linked.bc
  • Redis-pmem:
# Note: build.env will define the REPO_ROOT variable
source build.env
cd build

make REDIS -j$(nproc)
# do this if it hasn't been done already
make FLUSHREMOVER -j$(nproc)
make PMEMCHECK -j$(nproc)
make PMTEST -j$(nproc)

cd $REPO_ROOT/deps/redis/src
extract-bc redis-server
llvm-link-8 redis-server.bc --override=$REPO_ROOT/build/deps/pmdk/lib/pmdk_debug/libpmem.so.bc \
        --override=$REPO_ROOT/build/deps/pmdk/lib/pmdk_debug/libpmemobj.so.bc -o redis-server.linked.bc

Evaluation

There are three main results from Hippocrates:

  1. Fixing all previously reported bugs (§6.1)
  2. The Redis performance experiment (§6.3) (Note: this requires access to real PM.)
  3. Hippocrates's overhead (§6.4)

1. Fixing previously reported bugs.

PMDK bugs

We provide a script, build/verify, which does the following:

  1. Gathers the list of all reproducible bugs listed
  2. Patches PMDK to the correct version for each test
  3. Builds the tests
  4. Runs each test, generating a pmemcheck trace
  5. Fixes each test based on the pmemcheck trace
  6. Reruns each test and confirms that the bugs are no longer present.

Note: It is expected that the full test suite takes several hours to run.

To run this script, do the following:

cd build
./verify

The output should look like:

...
11 issues resolved:
[447, 452, 458, 459, 460, 461, 585, 940, 942, 943, 945]

If you instead want to run each issue individually, run the following:

# Issue 447
./verify --target obj_toid_TEST0_8bbb0af9c

# Issue 452
./verify --target obj_constructor_TEST0_8bbb0af9c
./verify --target obj_constructor_TEST2_8bbb0af9c

# Issue 458
./verify --target pmemspoil_TEST0_8bbb0af9c

# Issue 459
./verify --target pmem_memcpy_TEST0_8bbb0af9c
./verify --target pmem_memcpy_TEST1_8bbb0af9c
./verify --target pmem_memcpy_TEST2_8bbb0af9c
./verify --target pmem_memcpy_TEST3_8bbb0af9c

# Issue 460
./verify --target pmem_memmove_TEST0_0fd509d73
./verify --target pmem_memmove_TEST1_0fd509d73
./verify --target pmem_memmove_TEST2_0fd509d73
./verify --target pmem_memmove_TEST3_0fd509d73
./verify --target pmem_memmove_TEST4_0fd509d73
./verify --target pmem_memmove_TEST5_0fd509d73
./verify --target pmem_memmove_TEST6_0fd509d73
./verify --target pmem_memmove_TEST7_0fd509d73
./verify --target pmem_memmove_TEST8_0fd509d73
./verify --target pmem_memmove_TEST9_0fd509d73
./verify --target pmem_memmove_TEST10_0fd509d73
./verify --target pmem_memmove_TEST11_0fd509d73

# Issue 461
./verify --target pmem_memset_TEST1_0fd509d73

# Issue 585
./verify --target rpmemd_db_TEST0_60e24d2

# Issue 940
./verify --target obj_first_next_TEST0_e71dfa41b
./verify --target obj_first_next_TEST1_e71dfa41b

# Issue 942
./verify --target obj_mem_TEST0_e71dfa41b

# Issue 943
./verify --target obj_memops_TEST0_e71dfa41b

# Issue 945
./verify --target pmem_memset_TEST0_e71dfa41b

RECIPE bugs

To reproduce the RECIPE bugs, do the following:

  1. First, generate the bug report using pmemcheck:
source build.env
cd build

rm /mnt/pmem/pool
./deps/valgrind-pmem/bin/valgrind --tool=pmemcheck --log-file=recipe.log ./deps/RECIPE/P-CLHT/p-clht_example 100 1
./parse-trace pmemcheck recipe.log -o recipe.trace
  1. Apply Hippocrates to fix the bugs:
source build.env
cd build

./apply-fixer ./deps/RECIPE/P-CLHT/p-clht_example.linked.bc recipe.trace -o ./deps/RECIPE/P-CLHT/fixed \
        --cxx --extra-opt-args="-fix-summary-file=recipe_summary.txt -heuristic-raising -trace-aa"
  1. Rerun pmemcheck and generate a new bug report:
rm -f /mnt/pmem/pool
./deps/valgrind-pmem/bin/valgrind --tool=pmemcheck --log-file=recipe_fixed.log ./deps/RECIPE/P-CLHT/fixed 100 1
  1. Confirm the bug report is empty, thus confirming the bugs are fixed:
./parse-trace pmemcheck recipe_fixed.log -o recipe_fixed.trace

This should produce output similar to the following:

Identified trace start


Identified trace end
...
Prepare to dump.
        Num items: 1
Prepare to write.
Report written to recipe_fixed.trace

memcached-pmem bugs

This assumes you have run the instructions for building memcached-pmem and pmemcheck, which you can find above.

After building memcached, the bug-fixing process can be automated as follows:

source build.env
cd $REPO_ROOT/build

./verify-memcached --help
./verify-memcached

The verify-memcached can also run over the prebuilt files present in artifact/prebuilt if you run using the --use-prebuilt flag.

For example:

source build.env
cd $REPO_ROOT/build

./verify-memcached --use-prebuilt

To reproduce the memcached-pmem bugs manually, do the following:

  1. First, find the bugs and generate a pmemcheck trace:
source build.env
cd $REPO_ROOT/build/deps/memcached-pmem/bin

LD_LIBRARY_PATH=$(realpath $REPO_ROOT/build/deps/pmdk/lib/pmdk_debug) \
        $REPO_ROOT/build/deps/valgrind-pmem/bin/valgrind --tool=pmemcheck \
        --log-file=memcached.log ./memcached -m 0 -U 0 -t 1 -A -o \
        pslab_file=/mnt/pmem/pool-$(whoami),pslab_size=8,pslab_force

In a second terminal:

source build.env

telnet localhost 11211
# Commands prefixed with ">" are entered inside of telnet
> set foo 1 0 3
> bar
> shutdown

Then parse the trace:

# This can be run in either terminal 1 or 2, but assumes you have run
# `source build.env` already.
cd $REPO_ROOT/build

./parse-trace pmemcheck ./deps/memcached-pmem/bin/memcached.log -o ./deps/memcached-pmem/bin/memcached.trace
  1. Then, apply Hippocrates:
source build.env
cd $REPO_ROOT/build

./apply-fixer ./deps/memcached-pmem/bin/memcached.linked.bc ./deps/memcached-pmem/bin/memcached.trace \
        -o ./deps/memcached-pmem/bin/memcached-fixed --keep-files \
        --extra-opt-args="-fix-summary-file=memcached_summary_time.txt -heuristic-raising -trace-aa"
  1. Repeat steps 1, except using the fixed binary. Then confirm the new binary does not have any bugs:
# In terminal 1
source build.env
cd $REPO_ROOT/build/deps/memcached-pmem/bin

LD_LIBRARY_PATH=$(realpath $REPO_ROOT/build/pmdk/lib/pmdk_debug) $REPO_ROOT/build/deps/valgrind-pmem/bin/valgrind \
        --tool=pmemcheck --log-file=memcached_fixed.log ./memcached-fixed -m 0 -U 0 -t 1 -A -o \
        pslab_file=/mnt/pmem/pool-$(whoami),pslab_size=8,pslab_force
# In terminal 2
source build.env
cd $REPO_ROOT/build

./parse-trace pmemcheck ./deps/memcached-pmem/bin/memcached_fixed.log -o ./deps/memcached-pmem/bin/memcached_fixed.trace

The output should be like the following:

Identified trace start


Identified trace end
...
Prepare to dump.
        Num items: 1
Prepare to write.
Report written to memcached_fixed.trace

2. Performing the Redis experiment

  1. First, we need to generate the baseline and the log.
# Start in the root of the repository, e.g. /home/your_username/hippocrates_repo
# --- Note: build.env will define the REPO_ROOT variable
source build.env
cd $REPO_ROOT/build

# This creates the baseline for the redis experiment
./remove-flushes $REPO_ROOT/deps/redis/src/redis-server.linked.bc -o $REPO_ROOT/deps/redis/src/redis-server-noflush -s
  • The following will be run in two terminals (to collect the trace):
# TERMINAL 1
# --- Start in the root of the repository, e.g. /home/your_username/hippocrates_repo
source build.env
cd $REPO_ROOT/deps/redis/src/

rm -f /mnt/pmem/redis-$(whoami).pmem
$REPO_ROOT/build/deps/valgrind-pmem/bin/valgrind --tool=pmemcheck \
        --log-file=redis.log ./redis-server-noflush ../../redis-pmem.conf --pmfile /mnt/pmem/redis-$(whoami).pmem 1gb
# Wait until Redis displays the following:
> ... * The server is now ready to accept connections on port 6380
# TERMINAL 2
# --- Start in the root of the repository, e.g. /home/your_username/hippocrates_repo
source build.env

telnet localhost 6380
> set foo bar
# ... (repeat set commands as much as you want)
> shutdown

  • This creates a pmemcheck log, $REPO_ROOT/deps/redis/src/redis.log

  • After collecting the trace, run the following in either terminal:

# --- "source build.env" should have already been run
cd $REPO_ROOT/build

# This creates a trace file from the pmemcheck log, which is what Hippocrates uses to locate where to insert bug fixes
./parse-trace pmemcheck $REPO_ROOT/deps/redis/src/redis.log -o $REPO_ROOT/deps/redis/src/redis.trace

# This creates Redis-H-full
./apply-fixer $REPO_ROOT/deps/redis/src/redis-server-noflush.bc $REPO_ROOT/deps/redis/src/redis.trace \
        -o $REPO_ROOT/deps/redis/src/redis-server-trace --keep-files --cxx \
        --extra-opt-args="-fix-summary-file=redis_summary.txt -heuristic-raising"

# This creates Redis-H-intra
./apply-fixer $REPO_ROOT/deps/redis/src/redis-server-noflush.bc $REPO_ROOT/deps/redis/src/redis.trace \
        -o $REPO_ROOT/deps/redis/src/redis-server-dumb --keep-files --cxx \
        --extra-opt-args="-fix-summary-file=redis_intra_summary.txt -disable-raising -intra-only"

Now, run the performance evaluation:

# --- "source build.env" should have already been run

cd $REPO_ROOT/build
./run-redis -t 10 --output-file $REPO_ROOT/results/test.csv
# if using prebuilt:
./run-redis -t 10 --output-file $REPO_ROOT/results/test.csv -r $REPO_ROOT/artifact/prebuilt

cd $REPO_ROOT/results
./graph.py test.csv --output test.pdf

This should create a graph similar to Figure 4 in the paper, and should also produce textual output similar to the following:

          Redis$_{H-intra}$  Redis-pmem  Redis$_{H-full}$
Workload
Load               0.215850         1.0          1.003542
A                  0.797220         1.0          1.009079
B                  0.721691         1.0          1.029106
C                  0.728584         1.0          1.034976
D                  0.682358         1.0          1.004612
E                  0.167548         1.0          1.027780
F                  0.680404         1.0          0.997616

Your results may vary, however the trend in the data (i.e., RedisH-intra is up to 5-10X worse than either Redis-pmem or RedisH-full and RedisH-full has around the same or slightly better performance than Redis-pmem) should still hold.

3. Hippocrates's overhead

This information is gathered from examining ./build/apply_fixer.log. This is a log which is appended to for every invocation of the apply-fixer script.

The format of entries in this log is the following:

Fixer stats for {command line string}
INFO:root:Fixer time: {time in seconds}
INFO:root:Fixer mem: {memory usage in MB}

Example for PMDK:

Fixer stats for "/usr/lib/llvm-8/bin/opt -load /home/iangneal/workspace/pm-bug-fixing/build/src/PMFIXER.so -pm-bug-fixer -trace-file /home/iangneal/workspace/pm-bug-fixing/build/tests/validation/obj_toid_TEST0_8bbb0af9c/pmemcheck0.trace -fix-summary-file=obj_toid_TEST0_8bbb0af9c_summary.txt -heuristic-raising /tmp/tmp9r8nsj59/obj_toid.static-debug_linked.bc":
INFO:root:Fixer time: 00:00:05 (5.251097 seconds)
INFO:root:Fixer mem: 86.9296875 MB

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Automatically fixing persistency bugs in PM applications. ASPLOS '21.

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