scylladb/docs/debugging.md

Debugging with GDB

Introduction

GDB is a source level debugger for C, C++ and more languages. It allows inspecting the internal state of a program as it is running as well the post-mortem inspection of chrashed programs.

You can attach GDB to a running process, run a process inside GDB or examine a coredump.

Starting GDB

The two most common usages of GDB for scylla is running a process inside it (e.g. a unit test):

gdb /path/to/executable

You can specify command-line arguments that gdb will forward to the executable:

gdb /path/to/executable --args arg1 arg2 arg3

Another prevalent usage is to examine coredumps:

gdb --core=/path/to/coredump /path/to/executable

You can also attach it to an already running process:

gdb -p $pid

Where $pid is the PID of the running process you wish to attach GDB to.

Using GDB

GDB has excellent online documentation that you can find here.

Some of the more important topics:

• Starting GDB
• Setting breakpoints
• Setting catchpoints
• Stepping through the code
• Examining the stack
• Examining data

Debugging Scylla with GDB

In general Scylla is quite hard to debug in GDB due to its asynchronous nature. You will soon find that backtraces always lead to the reactor's event loop and stepping through the code will not work as you expect as soon as you leave or enter an asynchronous function. That said GDB is an indispensable tool in debugging coredumps and when used right can be of great help.

Over the years we have collected a set of tools for helping with debugging scylla. These are collected in scylla-gdb.py and are in the form of commands, conveninence functions and pretty printers. To load the file issue the following command (inside gdb):

(gdb) source /path/to/scylla-gdb.py

You should be now ready to use all of the tools contained therein. To list all available commands do:

(gdb) help scylla

To read the documentation of an individual command do:

(gdb) help scylla $commandname

Some commands have self explanatory names, some have documentation, and some have neither :( (contributions are welcome).

To get the list of the available convenience functions do:

(gdb) help function

Note that this will list GDB internal functions as well as those added by scylla-gdb.py. Again, just like before, to see the documentation of an individual function do:

(gdb) help function $functionname

Tips and tricks

Tell GDB to not stop on signals used by seastar

When running scylla (or any seastar application for that matter) inside GDB it will get interrupted often due to catching some signals used by seastar internally. This makes debugging almost impossible. To avoid this, instruct GDB to not stop on these signals:

(gdb) handle SIG34 SIG35 SIGUSR1 nostop noprint pass

Avoid (some) symbol parsing related crashes

GDB is known to crash when parsing some of scylla's symbols (especially those related to futures). Usually telling it to not print static members of classes and structs helps:

(gdb) set print static-members no

Enable extended python diagnostics

When using the facilities from scylla-gdb.py it is very useful to know the full stack of a failure in some of the provided tools, so that you can fix it or report it. To enable this run:

(gdb) set python print-stack full

Helping GDB find the source code for the executable

Often you find yourself debugging an executable, whose internal source paths don't match those where they can be found on your machine. There is an easy workaround for this:

(gdb) set substitute-path /path/to/src/in/executable /path/to/src/on/your/machine

Note that the pattern that you supply to set substitute-path just has to be a common prefix of the paths. Example: if the source location inside the executable to some file is /opt/src/scylla/database.hh and on your machine it is /home/joe/work/scylla/database.hh, you can make GDB find the sources on your machine via:

(gdb) set substitute-path /opt/src/scylla /home/joe/work/scylla

This method might not work if the sources do not have a prefix, e.g. they are relative to the source tree root directory. In this case you can use the set directories command to set the search path of sources for gdb:

(gdb) set directories /path/to/scylla/source/tree

Multiple directories can be listed, separated with :.

.gdbinit

GDB supports writing arbitrary GDB commands in any file and sourcing it. One can use this to place commands that one would have to issue every time when debugging in a file, instead of typing them each time GDB is started. Conventionally this file is called .gdbinit and GDB in fact will look for it in you current directory, in your $HOME directory and some other places. You can always load it by hand if GDB refuses or fails to load it:

(gdb) source /path/to/your/.gdbinit

TUI

GDB has a terminal based GUI called TUI. This is extremely useful when you wish to see the source code while you are debugging. The TUI mode can be activated by passing -tui to GDB on the command line, or any time by executing the tui enable to activate it and tui disable to deactivate it respectively.

Debugging coredumps

Up until release 3.0 we used to build and package Scylla separately for each supported distribution. Starting with 3.1 we moved to relocatable binaries. These are built with a common frozen toolchain and packages are bundled with all dependencies. This means that post 3.1 there is just one build across all supported distros and that the exact environment the binaries were built with is available in the form of a Docker image. This makes debugging cores generated from relocatable binaries much easier. As of now, all releases except 2019.1 ship via relocatable packages, so in this chapter we will focus on how to debug cores generated from relocatable binaries, with a subsection later explaining how to debug cores generated by 2019.1 binaries.

Relocatable binaries

Cores produced by relocatable binaries can be simply opened in the dbuild container they were built with. To do that, two things (apart from the core itself of course) are needed:

1. The exact frozen toolchain (dbuild container).
2. The exact relocatable package the binary was part of.

Obtaining the frozen toolchain

The frozen toolchain is obtained based on the commit id of the version of the scylla executable the core was produced with. The exact commit hash can be obtained by running:

$ scylla --version
666.development-0.20200630.28c3d4f8e

The version can be divided into 4 parts:

• The version identifier, in this case: 666; in case of a release this will be something like 4.2.
• The build identifier, in this case: development-0.
• The date, in this case: 20200630.
• The commit hash, in this case: 28c3d4f8e.

Based on the latter, you can obtain the right frozen toolchain:

$ cd /path/to/scylla
$ git checkout $commit_hash

Obtaining the relocatable-package

Once we have the right toolchain, we have to obtain the relocatable package. This is obtained based on the build-id, which can be obtained from the coredump like this:

$ eu-unstrip -n --core $corefile

Or from the executable like this:

$ eu-unstrip -n --exec $executable

With the build-id you can find the relocatable using the scylla-pkg.git/scripts/scylla-s3-reloc (private repo) script.

Loading the core

Move the coredump and the unpackaged relocatable package into some dir $dir on your system, then:

(host)$ cd /path/to/scylla # with the right commit checked out
(host)$ ./tools/toolchain/dbuild -it -v $dir:/workdir:z -- bash -l
(dbuild)$ cd /workdir
(dbuild)$ cd unpackaged-relocatable-package && ./install.sh && cd ..
(dbuild)$ gdb --core=$corefile /opt/scylladb/libexec/scylla

You might need to add

-ex 'set auto-load safe-path /opt/scylladb/libreloc'

to the command line, see No thread debugging.

Non-relocatable binaries (2019.1)

The first step in opening any core is (after obtaining the core itself) obtaining the exact executable and library versions it was produced with. This is very important, it is not enough to get a binary with the same version, or to build one with the same commit, the binaries and libraries have to be the very same ones the core was produced with. This is because neither distros nor use use reproducible builds, which means that each build will produce a slightly different binary, which might be enough to make debugging hard or downright impossible. A foolproof method to match cores to their matching executables and libraries is the build-id. This is automatically assigned to each binary when it is built and it uniquely identifies it.

Collecting libraries

As stated above, just installing Scylla on another machine with the same OS version is not enough to obtain the correct environment to load the core. Packages might have newer versions, or the customer might be using different packages. It is important that we obtain the exact packages installed on the system where the core was produced on.

A method that should work regardless of the used distro is zipping all libs:

eu-unstrip -n --core corefile | awk '{print $3}' | grep -v '[-.]$' | zip scylla-libs -@

This might however produce a rather large zip or zip might not be available on the node and it can't be installed (yes really). So below we are going to look at methods that doesn't involve copying a huge zip from the node, nor installing any new software.

CentOS/Redhat

CentOS and Redhat has means to obtain the binaries given a certain build-id. TODO: document how that works.

Ubuntu/Debian

Run the following script to collect the version of each library used by Scylla:

function file_uri() {
    dpkg -S $1 | cut -d" " -f1 | cut -d: -f1,2 | xargs apt-get download --print-uris
}

for lib in $(ldd `which scylla` | cut -d'(' -f1 | awk '{print $3}'); do
    if [ -n "$lib" ]; then
        echo "${lib}: $(file_uri $lib)"
    fi
done

This will produce an output like:

/opt/scylladb/lib/libstdc++.so.6: 'http://some.mirror.example/mirrors/scylla/versioned/2019100201/ubuntu/pool/main/s/scylla-gcc73/scylla-gcc73-libstdc++6_7.3.0-3ubuntu2~xenialppa1_amd64.deb' scylla-gcc73-libstdc++6_7.3.0-3ubuntu2~xenialppa1_amd64.deb 368128 SHA256:7aa085e85c2a6bbd5b1517985e84cf280b74839d7ccb313f823f201ad162fccc
/usr/lib/libcrypto++.so.9: 'http://some.mirror.example/mirrors/debian/versioned/2018060600/ubuntu/pool/universe/libc/libcrypto++/libcrypto++9v5_5.6.1-9_amd64.deb' libcrypto++9v5_5.6.1-9_amd64.deb 885184 SHA256:888ce5da554200dac297d97b376d27607515689a79df944295e0e43cd0d94d31
/lib/x86_64-linux-gnu/librt.so.1: 'http://some.mirror.example/mirrors/debian/versioned/2018060600/ubuntu/pool/main/g/glibc/libc6_2.23-0ubuntu10_amd64.deb' libc6_2.23-0ubuntu10_amd64.deb 2580230 SHA256:bd05c3487325a4386dee6abb02ad904e1f2d8d3d0adc0df8e8f29168fbe2b5bb

Usually the URLs are accessible and the packages can be simply downloaded. In some case however they are on some internal mirror that is only accessible from within the internal network of the cluster. In this case one has to obtain the exact name and version of the packages then download it themselves with apt-get. Given the file with the output of the above script containing the package versions (packages.txt from now on), you can use the below script to parse the package name and version from it and download the appropriate .deb package files:

while read l
do
    deb=$(echo $l | cut -f3 -d' ')
    pkg_name=$(echo $deb | cut -f1 -d_)
    pkg_version=$(echo $deb | cut -f2 -d_)
    apt-get download ${pkg_name}=${pkg_version}
done < /path/to/packages.txt

Note that in some cases the names of packages or their versions in packages.txt will contain encoded characters, like %3a. This will make apt-get fail to download the package. Be sure to decode any of these before attempting the run the downloading script. Also in some cases the exact version will not be available anymore. In this case try to locate the closest version to the desired one and download that one. You can use apt-cache to query available versions:

apt-cache show package-name | grep Version:

Opening the core on the same OS

The packages obtained can be installed on the system, and the core can be simply opened with GDB, which should find the libraries without issues. One thing to note is that usually these distros will have older GDB:s available, which might have problems handling Scylla symbols. For this reason we also build and package GDB for all supported distros. This can be installed via the scylla-gdb package, after adding the Scylla repositories. Run GDB via /opt/scylladb/bin/gdb.

Opening the core on another OS

If you don't feel like struggling to get recent enough tools on a potentially very old distro, a viable alternative is to just debug on your development box. The first step is unpacking (not installing!) all the packages. This can be easily done with a docker image, e.g. for ubuntu:

$ docker run -it --privileged -v .:/workspace ubuntu:16.04 bash -l
(docker) $ for pkg in $(ls *.deb); do dpkg -x $pkg .; done

After running the above snippet the current directory will contain a linux / directory structure. To load the core in GDB:

$ gdb -q
(gdb) set sysroot .
(gdb) set solib-search-path ./lib64:./lib/x86_64-linux-gnu
(gdb) core /path/to/core
(gdb) file ./usr/bin/scylla
(gdb) set solib-search-path ./lib64:./lib/x86_64-linux-gnu

Note that although relative paths should work for set sysroot and set solib-search-path, sometimes I could only get this working with absolute path. If opening the core wasn't successful (thread debugging doesn't work) try using absolute paths. Also note that issuing the set solib-search-path command has to be done once before and once after the file command. Don't ask me why. Another thing to keep in mind is that set solib-search-path has to contain all directories that contain libraries. In the case of ubuntu:16.04 this is /lib64 and /lib/x86_64-linux-gnu. Other distros could have less or more such paths. Multiple paths can be added separated with :.

You can check that GDB correctly loaded the libraries by using info sharedlibrary and ensuring all libraries are loaded from the directory where the packages were extracted to, and not from the host.

Troubleshooting

Namespace issues

GDB complaints that it can't find namespace seastar or some other Scylla or Seastar symbol that you know exists. This usually happens when GDB is in the wrong context i.e. a frame is selected which is not in the Scylla executable but in some other library. A typical situation is opening a coredump and attempting to access Scylla symbols when the initial frame is in libc. Move up the stack, or select a frame which is a Scylla or Seastar function to fix.

No thread debugging

Unable to access thread-local variables. Example:

(gdb) p seastar::local_engine
Cannot find thread-local storage for LWP 22604, executable file /usr/lib/debug/usr/bin/scylla.debug:
Cannot find thread-local variables on this target

The first step in finding out why thread debugging doesn't work is enabling additional information about why thread debugging is not working:

(gdb) set debug libthread 1

This has to be done right after starting GDB, before the core and the executable are loaded.

The usual cause is that GDB failed to find some libraries or that the library versions of those libraries GDB loaded don't match those the core was generated with.

Of special note is the libthread_db.so library, which is crucial for thread debugging to work. This library will not appear in any library listing (see below) and GDB requires the path it can be found at to be declared safe to load from. You might see a message like this:

warning: File "/opt/scylladb/libreloc/libthread_db.so.1" auto-loading has been declined by your `auto-load safe-path' set to "$debugdir:$datadir/auto-load"
thread_db_load_search returning 0

To declare the directory this library is found at as safe to load from, do:

set auto-load safe-path /opt/scylladb/libreloc

Use the path that is appropriate for your setup. Alternatively you can use / as the path to declare your entire file-system as safe to load stuff from. Note that libthread_db.so is packaged together with libc. So if you have the build-id appropriate libc package, you can be sure you have the correct libthread_db.so too.

If you ensured libthread_db.so is present and is successfully loaded by GDB but thread debugging still doesn't work, inspect the other libraries loaded by GDB:

(gdb) info sharedlibrary

The listing will contain the path of the loaded libraries. If a library wasn't found by GDB that will also be visible in the listing. You can then use the file utility to obtain the build-id of the libraries:

file /path/to/libsomething.so

This build-id must match the one obtained from the core. The library build-ids from the core can be obtained with:

eu-unstrip -n --core=/path/to/core

In general you can get away some non-core libraries missing or having the wrong version, but the core libraries like libc.so, libgcc_s.so, librt.so and ld.so (often called something like ld-linux-x86-64.so.2) etc. must have the correct version. Best to ensure all libraries are correct to minimize the chance of something not working. Also, make sure the build-id of the executable matches that the core was generated with. Again, you can use file to obtain the build-id of the executable, then compare it with the build-id obtained from the eu-unstrip listing. For more information on how to obtain the correct version of libraries and how to override the path GDB loads them from, see Collecting libraries and Opening the core on another OS.

GDB crashes when priting the backtrace or some variable

See Avoid (some) symbol parsing related crashes.

GDB keeps stopping on some signals

See Tell GDB to not stop on signals used by seastar.

Advanced guides

TODO: write guides for typical flows for debugging an OOM situation and any other situation that contains typical steps.