Error Message and LDD Output

Oct 13, 2025 by thesweetdesigns.com 18 views

Introduction

When working with distributed computing frameworks like Mpi4py, it's essential to ensure that the OpenMPI version is correctly linked to the Mpi4py installation. However, issues can arise when the wrong OpenMPI version is linked, leading to errors and difficulties in resolving the problem. In this article, we'll explore the issue of wrong linked OpenMPI version with Mpi4py and provide suggestions on how to resolve it.

Understanding the Issue

The issue at hand is that the Mpi4py installation is linked to the wrong OpenMPI version, despite the correct version being installed. This can be seen in the error message and the output of the ldd command, which shows that the Mpi4py library is linked to the OpenMPI version 4.1.5, instead of the expected 5.0.6.

Installation Steps

To install Mpi4py, the following commands were used:

export PATH="/usr/local/openmpi-5.0.6/bin:$PATH"
export LD_LIBRARY_PATH="/usr/local/openmpi-5.0.6:$LD_LIBRARY_PATH"
(myenv) [myid@server tmp_save]$ env MPICC=/usr/local/openmpi-5.0.6/mpicc env MPI4PY_BUILD_BACKEND="scikit-build-core" pip install --no-cache-dir mpi4py

However, as seen in the output, the version of Mpi4py installed is 4.0.3, which is not the expected version.

Error Message and LDD Output

The error message and the output of the ldd command are as follows:

(myenv) [myid@server tmp_save]$ python
Python 3.9.21 | packaged by conda-forge | (main, Dec  5 2024, 13:51:40)
[GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import mpi4py
>>> from mpi4py import MPI
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: /home/myid/miniforge3/envs/deinfer/lib/python3.9/site-packages/mpi4py/[MPI.cpython-39-x86_64-linux-gnu.so](http://mpi.cpython-39-x86_64-linux-gnu.so/): undefined symbol: ompi_mpi_errors_abort
(myenv) [myid@server tmp_save]$ ldd /home/myid/miniforge3/envs/deinfer/lib/python3.9/site-packages/mpi4py/[MPI.cpython-39-x86_64-linux-gnu.so](http://mpi.cpython-39-x86_64-linux-gnu.so/)
        linux-vdso.so.1 (0x00007ffe4a1fb000)
        libmpi.so.40 => /usr/local/openmpi-4.1.5/lib/libmpi.so.40 (0x00007fec4aab3000)
        libc.so.6 => /lib64/libc.so.6 (0x00007fec4a898000)
        libopen-rte.so.40 => /usr/local/openmpi-4.1.5/lib/libopen-rte.so.40 (0x00007fec4a7de000)
        libopen-pal.so.40 => /usr/local/openmpi-4.1.5/lib/libopen-pal.so.40 (0x00007fec4a714000)
        libm.so.6 => /lib64/libm.so.6 (0x00007fec4a639000)
        libz.so.1 => /lib64/libz.so.1 (0x00007fec4a61d000)
        libhwloc.so.15 => /lib64/libhwloc.so.15 (0x00007fec4a5c4000)
        /lib64/ld-linux-x86-64.so.2 (0x00007fec4ae4f000)

Resolving the Issue

To resolve the issue, we need to ensure that the Mpi4py installation is linked to the correct OpenMPI version. Here are some suggestions:

1. Reinstall Mpi4py with the Correct OpenMPI Version

Try reinstalling Mpi4py with the correct OpenMPI version using the following commands:

export PATH="/usr/local/openmpi-5.0.6/bin:$PATH"
export LD_LIBRARY_PATH="/usr/local/openmpi-5.0.6:$LD_LIBRARY_PATH"
(myenv) [myid@server tmp_save]$ env MPICC=/usr/local/openmpi-5.0.6/mpicc env MPI4PY_BUILD_BACKEND="scikit-build-core" pip install --no-cache-dir mpi4py

2. Use the `--force-reinstall` Option

Try reinstalling Mpi4py with the --force-reinstall option to force the installation of the correct OpenMPI version:

(myenv) [myid@server tmp_save]$ pip install --no-cache-dir --force-reinstall mpi4py

3. Check the `LD_LIBRARY_PATH` Environment Variable

Ensure that the LD_LIBRARY_PATH environment variable is set correctly to point to the correct OpenMPI version:

(myenv) [myid@server tmp_save]$ echo $LD_LIBRARY_PATH

4. Check the `MPICC` Environment Variable

Ensure that the MPICC environment variable is set correctly to point to the correct OpenMPI version:

(myenv) [myid@server tmp_save]$ echo $MPICC

5. Check the Mpi4py Installation

Check the Mpi4py installation to ensure that it is linked to the correct OpenMPI version:

(myenv) [myid@server tmp_save]$ ldd /home/myid/miniforge3/envs/deinfer/lib/python3.9/site-packages/mpi4py/[MPI.cpython-39-x86_64-linux-gnu.so](http://mpi.cpython-39-x86_64-linux-gnu.so/)

Q: What is the wrong linked OpenMPI version issue with Mpi4py?

A: The wrong linked OpenMPI version issue with Mpi4py occurs when the Mpi4py installation is linked to the wrong OpenMPI version, despite the correct version being installed. This can lead to errors and difficulties in resolving the problem.

Q: What are the common symptoms of the wrong linked OpenMPI version issue?

A: The common symptoms of the wrong linked OpenMPI version issue include:

Error messages indicating that the Mpi4py library is linked to the wrong OpenMPI version
The output of the ldd command showing that the Mpi4py library is linked to the wrong OpenMPI version
Issues with Mpi4py installation and usage

Q: How can I resolve the wrong linked OpenMPI version issue with Mpi4py?

A: To resolve the wrong linked OpenMPI version issue with Mpi4py, you can try the following:

Reinstall Mpi4py with the correct OpenMPI version using the following commands:

export PATH="/usr/local/openmpi-5.0.6/bin: $PATH" export LD_LIBRARY_PATH="/usr/local/openmpi-5.0.6:$ LD_LIBRARY_PATH" (myenv) [myid@server tmp_save]$ env MPICC=/usr/local/openmpi-5.0.6/mpicc env MPI4PY_BUILD_BACKEND="scikit-build-core" pip install --no-cache-dir mpi4py


*   Use the `--force-reinstall` option to force the installation of the correct OpenMPI version:

    ```bash
(myenv) [myid@server tmp_save]$ pip install --no-cache-dir --force-reinstall mpi4py

Check the LD_LIBRARY_PATH environment variable to ensure that it is set correctly to point to the correct OpenMPI version:

(myenv) [myid@server tmp_save]$ echo $LD_LIBRARY_PATH


*   Check the `MPICC` environment variable to ensure that it is set correctly to point to the correct OpenMPI version:

    ```bash
(myenv) [myid@server tmp_save]$ echo $MPICC

Check the Mpi4py installation to ensure that it is linked to the correct OpenMPI version:

(myenv) [myid@server tmp_save]$ ldd /home/myid/miniforge3/envs/deinfer/lib/python3.9/site-packages/mpi4py/MPI.cpython-39-x86_64-linux-gnu.so


**Q: What are the potential causes of the wrong linked OpenMPI version issue with Mpi4py?**
-----------------------------------------------------------------------------------------

A: The potential causes of the wrong linked OpenMPI version issue with Mpi4py include:

*   Incorrect installation of Mpi4py
*   Incorrect configuration of the `LD_LIBRARY_PATH` and `MPICC` environment variables
*   Issues with the OpenMPI version being used
*   Conflicts with other libraries or packages

**Q: How can I prevent the wrong linked OpenMPI version issue with Mpi4py?**
-------------------------------------------------------------------------

A: To prevent the wrong linked OpenMPI version issue with Mpi4py, you can:

*   Ensure that you are using the correct OpenMPI version
*   Verify that the `LD_LIBRARY_PATH` and `MPICC` environment variables are set correctly
*   Use the `--force-reinstall` option when reinstalling Mpi4py
*   Check the Mpi4py installation to ensure that it is linked to the correct OpenMPI version

**Q: What are the best practices for resolving the wrong linked OpenMPI version issue with Mpi4py?**
-----------------------------------------------------------------------------------------

A: The best practices for resolving the wrong linked OpenMPI version issue with Mpi4py include:

*   Thoroughly investigate the issue and identify the root cause
*   Follow the recommended installation and configuration procedures for Mpi4py
*   Use the `--force-reinstall` option when reinstalling Mpi4py
*   Verify that the `LD_LIBRARY_PATH` and `MPICC` environment variables are set correctly
*   Check the Mpi4py installation to ensure that it is linked to the correct OpenMPI version