[BUG] Segmentation fault in Mojo when using Mojmelo's GBDT with Python-imported data

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#4,188 opened on Mar 25, 2025 0 comments 0 reactions 0 assignees View on GitHub

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auto_priority_triaged bug modular-repo mojo

Dominant language: Mojo
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Description

Bug description

Actual Behavior

When running the mojo run GBDTC_test.mojo command with a script that imports a Python module (load_breast_cancer.py) to load data from sklearn.datasets.load_breast_cancer and converts NumPy arrays to Matrix objects for use with the GBDT class, the program crashes with a segmentation fault. The error log includes a symbolized stack trace pointing to Signals.cpp in the LLVM runtime, along with repeated [ERROR elf_dynamic_array_reader.h:64] tag not found messages and ensure you have llvm-symbolizer in your PATH or set the environment var LLVM_SYMBOLIZER_PATH to point to it. Solved that by running sudo apt install llvm. This occurs even after installing llvm, please check the Logs for detailed error message.

Expected Behavior

The GBDTC_test.mojo script should successfully:

Import the Python module load_breast_cancer.
Retrieve NumPy arrays from get_data() and convert them to Matrix objects using Matrix.from_numpy.
Train a GBDT model on the training data and predict on the test data without crashing.
Output the classification accuracy to the console.

The program should run to completion without a segmentation fault or errors related to elf_dynamic_array_reader.h.

Detailed Initial Error Log

(Mojmelo) (base) snape@slytherin:~/projects/Mojmelo/tests$ mojo run GBDTC_test.mojo
[38260:38260:20250326,005148.213697:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.213816:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.213884:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.213960:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.214043:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.214120:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.214195:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.214502:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.214578:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.214655:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.214723:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.214803:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.214888:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215052:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215132:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215208:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215285:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215358:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215438:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215590:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215748:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215824:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215896:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.215970:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.216049:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.216133:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.216208:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.216280:ERROR elf_dynamic_array_reader.h:64] tag not found
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[38260:38260:20250326,005148.216580:ERROR elf_dynamic_array_reader.h:64] tag not found
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[38260:38260:20250326,005148.216887:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.216965:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.217050:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.217125:ERROR elf_dynamic_array_reader.h:64] tag not found
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[38260:38260:20250326,005148.217502:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.217651:ERROR elf_dynamic_array_reader.h:64] tag not found
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[38260:38260:20250326,005148.217877:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.217949:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218027:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218109:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218181:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218255:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218327:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218420:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218506:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218595:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218686:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218786:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218878:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.218968:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219073:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219163:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219260:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219366:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219466:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219565:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219645:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219729:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219808:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219899:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.219998:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.220086:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.220175:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.220272:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.220443:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.220538:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.220628:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.220718:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.220803:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.220905:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221009:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221090:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221176:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221258:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221345:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221428:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221518:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221600:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221690:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221780:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221870:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.221954:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.222045:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.222131:ERROR elf_dynamic_array_reader.h:64] tag not found
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[38260:38260:20250326,005148.222666:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.222754:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.222851:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223020:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223101:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223223:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223315:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223416:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223518:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223606:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223703:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223788:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223883:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.223966:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.224065:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.224152:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.224239:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.224326:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.224420:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.224502:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.224587:ERROR elf_dynamic_array_reader.h:64] tag not found
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[38260:38260:20250326,005148.226995:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227093:ERROR elf_dynamic_array_reader.h:64] tag not found
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[38260:38260:20250326,005148.227419:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227483:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227545:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227619:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227680:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227743:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227804:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227866:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227930:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.227998:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.228074:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.228146:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.228227:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.228310:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.228395:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.228479:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.228552:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.228632:ERROR elf_dynamic_array_reader.h:64] tag not found
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[38260:38260:20250326,005148.229035:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.229115:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.229195:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.229270:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.229353:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.229429:ERROR elf_dynamic_array_reader.h:64] tag not found
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[38260:38260:20250326,005148.230125:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230217:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230299:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230381:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230452:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230531:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230607:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230679:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230762:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230832:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230913:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.230989:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231070:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231145:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231218:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231369:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231443:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231519:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231595:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231671:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231742:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231828:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231901:ERROR elf_dynamic_array_reader.h:64] tag not found
[38260:38260:20250326,005148.231987:ERROR elf_dynamic_array_reader.h:64] tag not found
Please submit a bug report to https://github.com/modular/mojo/issues and include the crash backtrace along with all the relevant source codes.
Stack dump:
0. Program arguments: mojo run GBDTC_test.mojo
Stack dump without symbol names (ensure you have llvm-symbolizer in your PATH or set the environment var LLVM_SYMBOLIZER_PATH to point to it):
0 mojo 0x000059bb807e3c0b
1 mojo 0x000059bb807e1a79
2 mojo 0x000059bb807e427d
3 libc.so.6 0x000077c09b642520
4 libc.so.6 0x000077c01007ef62
mojo crashed!
Please file a bug report.
Segmentation fault (core dumped)

Detailed Final Error Log

(mojo-tutorial) (base) snape@slytherin:~/projects/mojo-tutorial$ mojo run GBDTC_test.mojo
[43966:43966:20250326,011259.850213:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.850380:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.850471:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.850566:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.850669:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.850768:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.850860:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.851271:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.851359:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.851447:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.851531:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.851627:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.851729:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.851917:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.852019:ERROR elf_dynamic_array_reader.h:64] tag not found
[43966:43966:20250326,011259.852120:ERROR elf_dynamic_array_reader.h:64] tag not found
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Please submit a bug report to https://github.com/modular/mojo/issues and include the crash backtrace along with all the relevant source codes.
Stack dump:
0. Program arguments: mojo run GBTC_test.mojo
#0 0x00005b96926f4c0b llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) Signals.cpp:0:0
#1 0x00005b96926f2a79 llvm::sys::RunSignalHandlers() Signals.cpp:0:0
#2 0x00005b96926f527d SignalHandler(int) Signals.cpp:0:0
#3 0x00007da5a0842520 (/lib/x86_64-linux-gnu/libc.so.6+0x42520)
#4 0x00007da50407eea2
mojo crashed!
Please file a bug report.
Segmentation fault (core dumped)

Steps to reproduce

Install Mojmelo and other requirements to Mojo v25.1.1:

magic add "max==25.1.1"
magic run mojo --version
exit
magic shell
magic add mojmelo
bash ./.magic/envs/default/etc/conda/test-files/mojmelo/0/tests/setup.sh
magic add scikit-learn

Run GBDTC_test.mojo:

mojo run GBDTC_test.mojo

This initially returns a segmentation fault and says Stack dump without symbol names (ensure you have llvm-symbolizer in your PATH or set the environment var `LLVM_SYMBOLIZER_PATH` to point to it), I solved this by running: sudo apt install llvm
And re-ran:

mojo run GBDTC_test.mojo

Files:

GBDTC_test.mojo:

from mojmelo.GBDT import GBDT
from mojmelo.utils.Matrix import Matrix
from mojmelo.preprocessing import train_test_split
from mojmelo.utils.utils import accuracy_score
from python import Python

fn main() raises:
    gbdtc_test = Python.import_module("load_breast_cancer")
    data = gbdtc_test.get_data() # X, y
    X_train, X_test, y_train, y_test = train_test_split(Matrix.from_numpy(data[0]), Matrix.from_numpy(data[1]).T(), test_size=0.2, random_state=1234)
    gbdtc = GBDT(criterion='log', n_trees = 5, max_depth = 6, learning_rate = 0.3, reg_lambda = 0.2, gamma = 0.01)
    gbdtc.fit(X_train, y_train)
    y_pred = gbdtc.predict(X_test)
    print("GBDT classification accuracy:", accuracy_score(y_test, y_pred))

load_breast_cancer.py:

from sklearn import datasets

def get_data():
    data = datasets.load_breast_cancer()

    return [data.data, data.target]

System information

magic info:

     Magic version: 0.7.2
System
------------
       Pixi version: 0.41.4
           Platform: linux-64
   Virtual packages: __unix=0=0
                   : __linux=6.8.0=0
                   : __glibc=2.35=0
                   : __cuda=12.2=0
                   : __archspec=1=zen
          Cache dir: /home/snape/.cache/rattler/cache
       Auth storage: /home/snape/.rattler/credentials.json
   Config locations: No config files found

Global
------------
            Bin dir: /home/snape/.modular/bin
    Environment dir: /home/snape/.modular/envs
       Manifest dir: /home/snape/.modular/manifests/pixi-global.toml

Project
------------
               Name: Mojmelo
            Version: 0.1.0
      Manifest file: /home/snape/projects/Mojmelo/mojoproject.toml
       Last updated: 26-03-2025 00:15:52

Environments
------------
        Environment: default
           Features: default
           Channels: https://conda.modular.com/max-nightly, https://conda.modular.com/max, https://repo.prefix.dev/modular-community, conda-forge
   Dependency count: 5
       Dependencies: max, mojmelo, pandas, scikit-learn, matplotlib
   Target platforms: linux-64
              Tasks: setup

magic list max:

Package     Version  Build    Size       Kind   Source
max         25.1.1   release  9.6 KiB    conda  max
max-core    25.1.1   release  233.4 MiB  conda  max-core
max-python  25.1.1   release  115.1 MiB  conda  max-python

Contributor guide

Open the contributing guide

First steps

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

Research direction

Start by running mojo run GBDTC_test.mojo with the Python data loader in load_breast_cancer.py, using the reported stack trace and Signals.cpp reference to locate the failure path. Confirm the crash occurs while converting or using the imported NumPy data with Matrix and GBDT; done means the script trains, predicts, and prints accuracy without a segmentation fault or repeated ELF errors.

Written by the indexing model from the issue text.

Assessment

Tech stack: numpy, python, scikit-learn
Domain: machine-learning
Issue type: Bug
Difficulty: 4/5
Estimated time: 3-5 days
Activity status: Stale
Clarity: Mostly clear
Newbie friendliness: 35/100