A critical heap‑based buffer overflow affecting HDF5's cache reconstruction routine — tracked as CVE‑2025‑6269 — was disclosed in mid‑June 2025 and affects HDF5 releases up to and including 1.14.6; the flaw lives in the function H5C__reconstruct_cache_entry inside H5Cimage.c and can be triggered by local manipulation of crafted HDF5 data, producing reliable process crashes and potential memory corruption on unpatched systems.
HDF5 (Hierarchical Data Format version 5) is a widely used binary container and C library for storing large scientific datasets, multidimensional image stacks, and structured metadata. It is commonly embedded into scientific tools, data pipelines, container images, and vendor appliances, making any memory‑safety weakness in its core implementation a high‑value target for attackers and an operational headache for administrators.
CVE‑2025‑6269 specifically targets the cache entry reconstruction codepath in the HDF5 file-handling layer. Public vulnerability records indicate the defect is a heap‑based buffer overflow (CWE‑122 / CWE‑119) in the function H5C__reconstruct_cache_entry within H5Cimage.c. The vulnerability was disclosed on June 19, 2025, and has seen wide indexing in national and vendor trackers (NVD, Ubuntu, SUSE, and others). Multiple advisories and vendor trackers describe the exploitability as local (the attacker must supply crafted HDF5 content that the vulnerable process reads) and note an available proof‑of‑concept in public repositories. The practical impact ranges from reliable denial‑of‑service (process crashes) to potential heap corruption that, under particular allocator and runtime conditions, could be leveraged for privilege escalation or code execution — although confirmed, reliable remote code execution (RCE) claims remain unverified in public advisories.
Source: MSRC Security Update Guide - Microsoft Security Response Center
Background / Overview
HDF5 (Hierarchical Data Format version 5) is a widely used binary container and C library for storing large scientific datasets, multidimensional image stacks, and structured metadata. It is commonly embedded into scientific tools, data pipelines, container images, and vendor appliances, making any memory‑safety weakness in its core implementation a high‑value target for attackers and an operational headache for administrators.CVE‑2025‑6269 specifically targets the cache entry reconstruction codepath in the HDF5 file-handling layer. Public vulnerability records indicate the defect is a heap‑based buffer overflow (CWE‑122 / CWE‑119) in the function H5C__reconstruct_cache_entry within H5Cimage.c. The vulnerability was disclosed on June 19, 2025, and has seen wide indexing in national and vendor trackers (NVD, Ubuntu, SUSE, and others). Multiple advisories and vendor trackers describe the exploitability as local (the attacker must supply crafted HDF5 content that the vulnerable process reads) and note an available proof‑of‑concept in public repositories. The practical impact ranges from reliable denial‑of‑service (process crashes) to potential heap corruption that, under particular allocator and runtime conditions, could be leveraged for privilege escalation or code execution — although confirmed, reliable remote code execution (RCE) claims remain unverified in public advisories.
What the bug is — technical summary
The vulnerable routine and how it is reached
The flaw occurs during cache entry reconstruction: HDF5 reconstructs in‑memory cache structures when reading or reconstituting dataset metadata and image data from a file. The vulnerable function, H5C__reconstruct_cache_entry, lives in H5Cimage.c and is responsible for populating buffers while rebuilding a cache entry from serialized on‑disk (or on‑stream) data. Under certain malformed conditions, the code computes or trusts a length value and performs memory operations that can write past the end of a heap allocation, triggering a heap overflow. Public trackers classify the root cause as unchecked bounds handling during the reconstruction path.Technical classification and CWE mapping
- Primary class: Heap‑based buffer overflow (CWE‑122).
- Related weakness: Improper Restriction of Operations within the Bounds of a Memory Buffer (CWE‑119).
- Typical observable effects: process crash (segmentation fault or abort), heap metadata corruption, and possible memory disclosure depending on downstream behavior.
Typical trigger conditions
The vulnerability is triggered by presenting the vulnerable library with crafted HDF5 metadata or dataset images that exercise the reconstruction path — for example, specially formed file objects or serialized cache entries where length fields or offsets are inconsistent with actual buffer sizes. The code path is reachable when an application (or service) uses HDF5 to open or parse files containing the affected structures; server‑side ingestion pipelines that accept user uploads and automatically parse .h5 files are therefore the highest‑risk deployment model.Affected versions and scope
- Upstream affected release: HDF5 up to and including 1.14.6. Public vulnerability trackers and vendor advisories consistently name 1.14.6 as the release containing the vulnerable code.
- Packaging scope: Many Linux distributions and package ecosystems that shipped HDF5 1.14.6 are potentially impacted; vendor trackers (Ubuntu, Debian, SUSE, and others) listed the issue and began triage and packaging work after disclosure.
- Exposure conditions: Any binary that links (statically or dynamically) against an affected HDF5 build and processes untrusted or adversarial .h5 files is in scope. Containers, HPC modules, Python wheels or conda packages that bundle the vulnerable library also count as exposure vectors.
Exploitability, proof‑of‑concepts and real‑world risk
Public reports and vendor commentary indicate at least one proof‑of‑concept (PoC) exists that reliably causes a crash when a vulnerable HDF5 library parses a crafted file. A public PoC materially reduces the window for attackers to weaponize the issue against unpatched targets; for that reason, defenders should prioritize remediation for high‑exposure services. However, translating a heap overflow into reliable remote code execution depends on several environmental factors:- Address space layout randomization (ASLR) and modern allocator hardening raise the bar for exploitation.
- Whether the process runs with low or elevated privileges affects the blast radius of any successful exploit.
- Static linking and older images (e.g., in scientific HPC environments) can lengthen the time windows during which vulnerable builds remain live.
Vendor and distribution response (timeline & status)
- Disclosure and indexing: The CVE was publicly recorded on June 19, 2025, and rapidly indexed by vulnerability databases (NVD, CVE aggregators) and distribution trackers. Several vendor pages (Ubuntu, SUSE, Debian) created security entries and began triage.
- Upstream commits: HDF Group maintainers and community contributors typically produce small, surgical patches to bounds checks and serialization routines; for CVEs in the 1.14.6 window, upstream issue threads and pull requests were used to record fixes. Administrators are advised to verify that a vendor package explicitly references the upstream commit or release that contains the remediation.
- Distribution packaging: Responses varied by vendor. Some distributions produced patched packages or backports quickly; others placed packages in “needs evaluation” status pending further testing and integration. Enterprise patch managers must confirm the exact package version and changelog entry that contains the fix before marking systems remediated.
- PoC publication and follow‑up: The public PoC was noted in advisories and aggregators; this raised urgency for internet‑facing ingestion services that parse .h5 files.
Detection and hunting guidance
- Inventory: Produce a comprehensive inventory of binaries and container images that include HDF5 (dynamic or static). Focus on:
- Scientific toolchains (Python/R/MATLAB wrappers).
- Container images used by ingestion pipelines, cloud functions, or batch processors.
- Statically linked vendor artifacts and embedded appliances.
- HPC modules and custom builds in research clusters.
- Monitor process crashes: Configure telemetry and crash reporting for processes that use HDF5. Frequent, reproducible crashes when opening .h5 files are a high‑signal indicator of attempted exploitation or PoC testing.
- File ingest controls: Identify endpoints that accept .h5 uploads. Log and quarantine suspicious or malformed files for offline analysis; enforce authentication and size/type checks at the upload boundary to reduce attack surface.
- Fuzzing and regression testing: Where feasible, run targeted fuzzers or corpus tests against the HDF5 reading paths (specifically cache reconstruction and image reconstruction routines) in a sandboxed environment to validate that patched builds no longer crash on previously problematic inputs.
Mitigation, patching and operational playbook
The single correct remediation is to apply a patched HDF5 build that includes the upstream fix, or to install a vendor package that explicitly references the remediation commit. If a vendor package is not yet available, rebuild HDF5 from source including the upstream commit that addresses the H5C__reconstruct_cache_entry overflow and rebuild any downstream artifacts that statically link HDF5. Short‑term compensations and practical steps:- Inventory: Find all binaries and images that include HDF5 (dynamic or static), including Python wheels, conda packages, containers, HPC modules, and vendor appliances.
- Block ingestion: Where possible, prevent untrusted .h5 uploads or require authenticated upload flows. Implement file‑type whitelisting and content‑type checks.
- Sandbox and isolate: Run HDF5 processing in strong sandboxes and with least privilege (containers with seccomp, AppArmor/SELinux, reduced capabilities). Reduce the privileges of services that parse untrusted files.
- Rebuild static artifacts: For statically linked binaries, rebuild with the patched HDF5 or transition to dynamic linkage to simplify future updates.
- Test and validate: After deploying fixes, run regression tests and fuzz jobs against relevant parsing paths to ensure the fix is effective in your runtime environment.
- Monitor telemetry: Watch for after‑patch regressions, persistent crashes, or signs that attackers are probing ingestion endpoints with malformed .h5 files.
Risk analysis — strengths, weaknesses and caveats
Strengths (what defenders can rely on)
- The vulnerability is well documented and tracked by multiple authoritative databases (NVD, Ubuntu, SUSE), making detection and patching actions straightforward to prioritize.
- Upstream commits and PR discussions provide concrete remediation artifacts that packagers and integrators can verify and backport.
- Modern exploit mitigations (ASLR, hardened allocators, PIE/RELRO) increase the work required to convert a heap overflow into reliable remote code execution.
Weaknesses and risk drivers
- The availability of public PoC material lowers attacker development time and increases the likelihood of automated scanning for vulnerable endpoints.
- Scientific and HPC environments often lag in applying updates because of concerns about reproducibility and software compatibility; static linking exacerbates this problem.
- Packaging disparity across distributions means that patched builds may not appear uniformly or quickly in all vendor repositories; administrators must verify the exact commit or package changelog rather than assume that an OS upgrade removed the issue.
Unverifiable or evolving claims (flagged)
- Public advisories and vendor notes point to possible escalation from heap overflow to RCE under certain allocator and environment conditions, but a broadly reproducible RCE chain for CVE‑2025‑6269 has not been independently confirmed in the public record at the time of writing. Label any RCE claims as unverified until supported by multi‑party exploit writeups.
Practical checklist for administrators (actionable priorities)
- Immediate (0–48 hours)
- Inventory all systems and images that include HDF5 1.14.6 or earlier.
- Identify ingestion endpoints and disable unauthenticated uploads of .h5 files where practical.
- Enable process crash monitoring and collect core dumps for analysis.
- Short term (48 hours – 7 days)
- Apply vendor patches where available; confirm package changelogs reference the upstream fix or CVE.
- If no vendor package exists, rebuild HDF5 from source with the upstream patch and redeploy static artifacts.
- Run regression tests and targeted fuzzing against patched builds.
- Medium term (1–3 weeks)
- Rebuild container images and CI artifacts to bake in fixed library versions.
- Harden HDF5 processing services with sandboxing and least privilege.
- Review and update incident response playbooks for file‑ingest services.
- Ongoing
- Track public exploit intelligence and vendor advisories for any escalation to public RCE exploits.
- Maintain an internal changelog mapping CVEs → package versions → deployable artifacts for audit and compliance.
Why this matters beyond a single CVE
HDF5 is foundational to many scientific and engineering workflows. Memory‑safety defects in core format libraries create a high operational burden: they cross language boundaries (bindings for Python, R, MATLAB), platform and deployment models (containers, HPC modules, embedded appliances), and integration patterns (statically linked vendor binaries vs dynamic libraries). A single heap overflow in the cache reconstruction path can produce a wide blast radius because it is reachable across many consumer frameworks. The CVE‑2025‑6269 disclosure is part of a cluster of HDF5 memory‑safety fixes in the 1.14.6 timeframe, underscoring the need for systematic dependency management and reproducible build processes for scientific environments.Conclusion
CVE‑2025‑6269 is a real and present risk for systems that use HDF5 1.14.6 or earlier and process untrusted .h5 files. The vulnerability is a heap‑based overflow in H5C__reconstruct_cache_entry (H5Cimage.c) that can be triggered by malformed inputs, and public proof‑of‑concept material exists. Administrators should treat server‑side ingestion services and statically linked binaries as priority targets for remediation. The correct long‑term fix is to deploy HDF5 builds that explicitly include the upstream remediation or vendor packages that document the fix; in the interim, apply conservative mitigations such as blocking untrusted .h5 uploads, sandboxing processing workloads, rebuilding static artifacts, and monitoring for crashes. Prioritize verification of package changelogs and upstream commit SHAs rather than solely relying on package version numbers — this prevents mistaken assumptions about remediation status and ensures a defensible patch posture.Source: MSRC Security Update Guide - Microsoft Security Response Center
