HDF5 Library Version Mismatch

Oct 13, 2025 by pynkocean.com 63 views

Introduction

The recent NERSC Feb18 maintenance has brought about several issues with the E3SM project, particularly with the maint-2.0 branch. Initially, it was assumed that maint-2.0 was unaffected by the maintenance, but further testing revealed a runtime error with certain tests. In this article, we will delve into the details of the issue, its causes, and potential solutions.

Background

The E3SM project is a community-driven effort to develop a next-generation Earth system model. The project relies on a robust testing framework to ensure the accuracy and reliability of the model. The maint-2.0 branch is a critical component of the project, as it serves as a testing ground for new features and bug fixes.

Identifying the Issue

Initially, two tests were run on the maint-2.0 branch without any issues:

SMS.ne4pg2_oQU480.F2010.pm-cpu_intel
SMS_D.ne4pg2_oQU480.F2010.pm-cpu_gnu

However, when a third test was attempted, which reads in different input netcdf files, a runtime error occurred:

SMS_Ln5.ne30pg2_EC30to60E2r2.F20TR.pm-cpu_intel

The error was logged in the e3sm.log file, which revealed a warning about a mismatched HDF5 library version.

HDF5 Library Version Mismatch

The warning message indicated that the HDF5 header files used to compile the application did not match the version used by the HDF5 library to which the application was linked. This can lead to data corruption or segmentation faults if the application continues to run.

The warning message provided the following information:

HDF5 header files version: 1.14.3
HDF5 library version: 1.12.2
Installation point: /opt/cray/pe/hdf5-parallel/1.12.2.9/intel/2023.2

Causes of the Issue

The issue is likely caused by a mismatch between the HDF5 header files and the library version used by the application. This can occur when an application is compiled with one version of HDF5 but linked with a different version of the library.

Potential Solutions

To resolve the issue, the following solutions can be considered:

Recompile the application: Recompiling the application with the correct version of HDF5 header files and library can resolve the issue.
Check shared library settings: Verifying the shared library settings, such as LD_LIBRARY_PATH, can help ensure that the correct version of the HDF5 library is used.
Disable the warning: Setting the environment variable HDF5_DISABLE_VERSION_CHECK to a value of 1 can disable the warning message. However, this should be done with caution, as it may mask other issues.

Conclusion

The runtime error with tests on maint-2.0 after NERSC Feb18 maintenance is a critical issue that requires immediate attention. By understanding the causes of the issue and exploring potential solutions, we can ensure the accuracy and reliability of the E3SM project.

Recommendations

To prevent similar issues in the future, the following recommendations can be made:

Regularly update HDF5 header files and library: Keeping the HDF5 header files and library up-to-date can help prevent version mismatches.
Verify shared library settings: Regularly verifying shared library settings can help ensure that the correct version of the HDF5 library is used.
Test applications thoroughly: Thorough testing of applications can help identify potential issues before they become critical.

Introduction

In our previous article, we discussed the runtime error with tests on maint-2.0 after NERSC Feb18 maintenance. In this article, we will provide a Q&A section to address some of the frequently asked questions related to this issue.

Q: What is the cause of the HDF5 library version mismatch?

A: The HDF5 library version mismatch is likely caused by a mismatch between the HDF5 header files and the library version used by the application. This can occur when an application is compiled with one version of HDF5 but linked with a different version of the library.

Q: How can I resolve the HDF5 library version mismatch?

A: To resolve the HDF5 library version mismatch, you can try the following:

Recompiling the application with the correct version of HDF5 header files and library
Checking shared library settings, such as LD_LIBRARY_PATH, to ensure that the correct version of the HDF5 library is used
Disabling the warning message by setting the environment variable HDF5_DISABLE_VERSION_CHECK to a value of 1

Q: What are the potential consequences of ignoring the HDF5 library version mismatch warning?

A: Ignoring the HDF5 library version mismatch warning can lead to data corruption or segmentation faults if the application continues to run. This can result in inaccurate or unreliable results, which can have significant consequences in scientific research and applications.

Q: How can I prevent similar issues in the future?

A: To prevent similar issues in the future, you can:

Regularly update HDF5 header files and library to ensure that they are compatible
Verify shared library settings to ensure that the correct version of the HDF5 library is used
Thoroughly test applications to identify potential issues before they become critical

Q: What is the recommended course of action for resolving the HDF5 library version mismatch?

A: The recommended course of action for resolving the HDF5 library version mismatch is to:

Recompiling the application with the correct version of HDF5 header files and library
Verifying shared library settings to ensure that the correct version of the HDF5 library is used
Disabling the warning message by setting the environment variable HDF5_DISABLE_VERSION_CHECK to a value of 1 (with caution)

Q: Can I disable the HDF5 library version mismatch warning permanently?

A: Yes, you can disable the HDF5 library version mismatch warning permanently by setting the environment variable HDF5_DISABLE_VERSION_CHECK to a value of 2 or higher. However, this should be done with caution, as it may mask other issues.

Q: What is the impact of the HDF5 library version mismatch on the E3SM project?

A: The HDF5 library version mismatch can have a significant impact on the E3SM project, particularly in terms of accuracy and reliability. It is essential to resolve this issue to ensure the continued success of the project.