oracle / oracle/graalpython

double free or corruption when enable python.IsolateNativeModules

Open
#563 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
1.6k
Forks
155
Avg merge
9h 42m
Merged PRs (30d)
36

Description

How to reproduce?

> environment

container image: ghcr.io/graalvm/graalpy-community:25
jdk: graalvm-jdk-25_linux-x64_bin.tar.gz

> python venv deps installed

pip install torch transformers patchelf

> multi context in maven repo(not packaged as native-image)
// Create a new GraalVM Python context and managed by org.apache.commons.pool2.impl.GenericObjectPool
Context context = GraalPyResources
        .contextBuilder(Path.of("python-resources"))
        .option("python.IsolateNativeModules", "true")
        .allowExperimentalOptions(true)
        .allowIO(IOAccess.ALL)
        .allowCreateThread(true)
        .allowCreateProcess(true)
        .allowHostAccess(HostAccess.ALL)
        .allowAllAccess(true)
        .build();

// use contexts in parallel, scriptPool has 3 context above
String scriptText = ""
        + "import torch\n"
        + "import transformers\n"
        + "\n"
        + "def main():\n"
        + "    print(f'Torch version: {torch.__version__}, Transformers version: {transformers.__version__}')\n";
PythonScriptPool scriptPool = new PythonScriptPool("testScript", scriptText, 3);
java.util.stream.Stream.iterate(0, n -> n + 1).limit(10).parallel().forEach(n -> {
    try {
        scriptPool.executeMethod("main", new Object[] {});
    } catch (Throwable e) {
        e.printStackTrace();
        System.exit(1);
    }
});
> error log
18:18:13  #14 0.761 WARNING: A restricted method in java.lang.System has been called
18:18:13  #14 0.761 WARNING: java.lang.System::load has been called by com.oracle.truffle.polyglot.JDKSupport in an unnamed module (file:/app/repo/target/bb-1.0-SNAPSHOT.jar)
18:18:13  #14 0.761 WARNING: Use --enable-native-access=ALL-UNNAMED to avoid a warning for callers in this module
18:18:13  #14 0.761 WARNING: Restricted methods will be blocked in a future release unless native access is enabled
18:18:13  #14 0.761 
18:18:13  #14 1.081 WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
18:18:13  #14 1.081 WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.runtime.hotspot.HotSpotTruffleRuntime (file:/app/repo/target/bb-1.0-SNAPSHOT.jar)
18:18:13  #14 1.081 WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.runtime.hotspot.HotSpotTruffleRuntime
18:18:13  #14 1.081 WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
18:18:21  #14 8.482 [To redirect Truffle log output to a file use one of the following options:
18:18:21  #14 8.482 * '--log.file=<path>' if the option is passed using a guest language launcher.
18:18:21  #14 8.482 * '-Dpolyglot.log.file=<path>' if the option is passed using the host Java launcher.
18:18:21  #14 8.482 * Configure logging using the polyglot embedding API.]
18:18:21  #14 8.482 [To redirect Truffle log output to a file use one of the following options:
18:18:21  #14 8.482 * '--log.file=<path>' if the option is passed using a guest language launcher.
18:18:21  #14 8.482 * '-Dpolyglot.log.file=<path>' if the option is passed using the host Java launcher.
18:18:21  #14 8.482 * Configure logging using the polyglot embedding API.]
18:18:21  #14 8.482 [To redirect Truffle log output to a file use one of the following options:
18:18:21  #14 8.482 * '--log.file=<path>' if the option is passed using a guest language launcher.
18:18:21  #14 8.482 * '-Dpolyglot.log.file=<path>' if the option is passed using the host Java launcher.
18:18:21  #14 8.482 * Configure logging using the polyglot embedding API.]
18:18:21  #14 8.482 [python::CApiContext] WARNING: Loading C extension module torch._C from '/app/repo/python-resources/venv/lib/python3.12/site-packages/torch/_C.graalpy250-312-native-x86_64-linux.so'. Support for the Python C API is considered experimental. See https://www.graalvm.org/latest/reference-manual/python/Native-Extensions/#embedding-limitations for the limitations. You can suppress this warning by setting the context option 'python.WarnExperimentalFeatures' to 'false'.
18:18:21  #14 8.482 [python::CApiContext] WARNING: Loading C extension module torch._C from '/app/repo/python-resources/venv/lib/python3.12/site-packages/torch/_C.graalpy250-312-native-x86_64-linux.so'. Support for the Python C API is considered experimental. See https://www.graalvm.org/latest/reference-manual/python/Native-Extensions/#embedding-limitations for the limitations. You can suppress this warning by setting the context option 'python.WarnExperimentalFeatures' to 'false'.
18:18:21  #14 8.482 [python::CApiContext] WARNING: Loading C extension module torch._C from '/app/repo/python-resources/venv/lib/python3.12/site-packages/torch/_C.graalpy250-312-native-x86_64-linux.so'. Support for the Python C API is considered experimental. See https://www.graalvm.org/latest/reference-manual/python/Native-Extensions/#embedding-limitations for the limitations. You can suppress this warning by setting the context option 'python.WarnExperimentalFeatures' to 'false'.
18:18:21  #14 8.806 double free or corruption (out)
18:18:21  #14 8.806 double free or corruption (!prev)
18:18:21  #14 8.806 #
18:18:21  #14 8.806 # A fatal error has been detected by the Java Runtime Environment:
18:18:21  #14 8.806 #
18:18:21  #14 8.806 #  SIGSEGV (0xb) at pc=0x00007f24b9d9a997, pid=1, tid=52
18:18:21  #14 8.806 #
18:18:21  #14 8.806 # JRE version: Java(TM) SE Runtime Environment Oracle GraalVM 25.0.1+8.1 (25.0.1+8) (build 25.0.1+8-LTS-jvmci-b01)
18:18:21  #14 8.806 # Java VM: Java HotSpot(TM) 64-Bit Server VM Oracle GraalVM 25.0.1+8.1 (25.0.1+8-LTS-jvmci-b01, mixed mode, sharing, tiered, jvmci, jvmci compiler, compressed oops, compressed class ptrs, g1 gc, linux-amd64)
18:18:21  #14 8.806 # Problematic frame:
18:18:21  #14 8.806 # C  [libc.so.6+0x28997]  abort+0x174
18:18:21  #14 8.806 #
18:18:21  #14 8.806 # Core dump will be written. Default location: /app/repo/core.1
18:18:21  #14 8.806 #
18:18:21  #14 8.807 # An error report file with more information is saved as:
18:18:21  #14 8.807 # /app/repo/hs_err_pid1.log
18:18:21  #14 8.835 [8.718s][warning][os] Loading hsdis library failed
18:18:53  #14 39.29 #
18:18:53  #14 39.29 # If you would like to submit a bug report, please visit:
18:18:53  #14 39.29 #   https://bugreport.java.com/bugreport/crash.jsp
18:18:53  #14 39.29 # The crash happened outside the Java Virtual Machine in native code.
18:18:53  #14 39.29 # See problematic frame for where to report the bug.
18:18:53  #14 39.29 #

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the Maven embedding example with three parallel contexts, python.IsolateNativeModules enabled, and torch plus transformers installed. Compare the crash output around C extension loading and native memory handling; done means identifying the concurrency or isolation failure and demonstrating a stable run with a focused regression test or reproduction.

Written by the indexing model from the issue text.

Assessment

Tech stack
java, python, pytorch
Domain
backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.