CVE-2025-2912: Heap Overflow in HDF5 H5O_msg_flush Fixed in 1.14.6

A heap-based buffer overflow has been disclosed in the HDF5 library that can be triggered while flushing object messages: the flaw exists in the function H5O_msg_flush in src/H5Omessage.c (tracked as CVE‑2025‑2912) and affects HDF5 releases up to and including 1.14.6. The issue can be provoked by crafted or malformed HDF5 content and has a publicly available proof‑of‑concept in the upstream issue tracker; distributors and OS vendors have cataloged the CVE and treat it as a medium‑risk memory‑corruption defect that requires remediation.

Background / Overview​

HDF5 (Hierarchical Data Format 5) is a widely used binary container and C library for storing large numerical arrays, chunked datasets, and rich hierarchical metadata. It is embedded in command‑line tools, scientific language bindings (for example, h5py for Python), containerized pipelines, and vendor appliances. Because HDF5 is frequently linked directly into processes that open or parse untrusted files, memory‑safety defects in the library can translate quickly into operational vulnerabilities for a broad set of consumers.
CVE‑2025‑2912 was publicly recorded in late March 2025 and appears in multiple vulnerability trackers (NVD, Ubuntu, Debian and others). The canonical description identifies H5O_msg_flush in src/H5Omessage.c as the faulty routine and summarizes the root cause as improper buffer boundary handling that can lead to a heap‑based overflow when certain message header calculations are performed. Several downstream distributors have opened tracking entries and assigned a medium priority in their triage systems.

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What the bug is — technical anatomy​

Where it occurs​

The defect is located in the object‑message flushing code path. The vulnerable function, H5O_msg_flush, computes a pointer into a message chunk image and then uses that pointer for header encoding and related write operations. In particular the code computes:

• p = mesg->raw - H5O_SIZEOF_MSGHDR_OH(oh);

If the computed subtraction makes p point before the start of the allocated buffer for mesg->raw, subsequent writes can step one byte (or a small number of bytes) past the allocation boundary — a classical heap‑buffer‑overflow. The upstream issue reproducer demonstrates this exact pointer arithmetic and the resulting one‑byte invalid write under AddressSanitizer.

Why the pointer arithmetic matters​

The value returned by H5O_SIZEOF_MSGHDR_OH(oh) depends on fields in the object header structure (oh) — notably the version and size fields. If a malformed header or adversary‑controlled value makes that macro evaluate to an unexpectedly large size (for example, when oh->version has a particular value that increases the header size), subtracting it from mesg->raw produces a pointer that points out of the intended buffer range. Because the code then uses p as a target for writes, even a one‑byte out‑of‑bounds write can corrupt adjacent heap metadata or nearby heap objects depending on allocation layout and allocator behavior. The GitHub issue contains an ASan trace and a tiny h5 file reproducer demonstrating a single‑byte write that triggers a heap overflow.

Attack model and reachability​

Formally the CVE is classified with a local attack vector: an attacker must cause a process that links the vulnerable HDF5 library to parse or process a crafted .h5 file. In practice, however, many server‑side ingestion pipelines, previewing services, container images and automated conversion processes accept HDF5 uploads or input without manual review. In those configurations an unauthenticated remote actor can upload a malicious .h5 file and cause a server process to exercise H5O_msg_flush, converting a local‑only classification into a realistic remote Denial‑of‑Service (DoS) scenario and, potentially, a more severe memory‑corruption exploit chain in specific environments. This attack surface amplification is a recurring theme for HDF5 CVEs in the same release family.

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Evidence, exploitation maturity, and vendor tracking​

• A detailed upstream bug report with proof‑of‑concept reproduction steps is available in the HDFGroup GitHub repository; the report documents the vulnerable source line, an ASan trace showing a one‑byte invalid write, and a minimal fuzzer harness to reproduce the crash. This materially increases the exploitability of the defect in the short term because PoC artifacts lower the effort required for attackers or penetration testers to validate the problem against local builds.
• National and distribution trackers (NVD, Ubuntu, Debian, SUSE) have created entries for CVE‑2025‑2912. Scoring varies across feeds; Ubuntu lists a CVSS v3 base around 3.3 (Low) while some CNAs and aggregators map a CVSSv4 base around 4.8 (Medium). The consensus treatment in most vendor trackers is that the immediate impact is availability (DoS), with integrity/confidentiality impacts and remote code execution (RCE) considered theoretically possible but environment dependent.
• Debian’s tracker explicitly references the upstream GitHub issue and records that the problem is fixed in the upstream tree by a commit (commit SHA provided in the tracker) and that the fix is associated with the 2.0.0 development milestone. This is important: upstream commits and release tags are the authoritative artifacts packagers and security teams must map to their own rebuilds.
• Multiple independent vulnerability databases and security vendors mirror the same technical facts and classify the exploit maturity as PoC. That increases urgency for administrators who process untrusted HDF5 inputs.

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Affected footprint and likely impact​

HDF5 is rarely a stand‑alone, user‑visible app; its risk surface comes from the many projects and packages that embed or link the library:

• Desktop and command‑line tools (h5dump, h5ls, h5repack) used by researchers and administrators.
• Language bindings and wheels (for example, h5py binary wheels that embed a specific HDF5 runtime).
• Server‑side ingestion services and previewers that accept user uploads and parse .h5 files.
• Container images, CI runners and vendor appliances that bundle the library as a dependency or statically link it into proprietary binaries.

Because many Python wheels and conda packages include a bundled HDF5 runtime, Windows and Linux users who install scientific packages from prebuilt wheels or conda channels should assume they may carry the vulnerable library until their chosen package providers publish patched builds. Static linking makes remediation more complex: statically linked applications require a rebuild with the patched HDF5. Trackers and distribution advisories emphasize inventorying all binaries and images to find exposures.
The most immediate, realistic impact is Denial‑of‑Service: repeatable crashes can be driven by a crafted file in many environments. Escalation to remote code execution is plausible in theory but depends on several environmental conditions (allocator behavior, presence of information leaks, exploit mitigations such as ASLR/DEP, hardened allocators). Public writeups at the time of disclosure do not document a trivial RCE chain that works reliably across common platforms; treat RCE claims as unverified until demonstrated reproducibly by independent researchers.

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Mitigation and remediation (practical playbook)​

The single correct remediation is to run versions that include the upstream fix or to apply vendor patches/backports. Where immediate patching is not possible, the following staged mitigations reduce attack surface and blast radius.

• Inventory and prioritize (immediate)
• Locate every binary, container image, package, and wheel that links HDF5 1.14.6 or earlier.
• Use package manifests, SBOMs, pip/conda freeze outputs, container image inspections and supply‑chain metadata to enumerate affected artifacts.
• Patch and rebuild (high priority)
• Prefer vendor packages or an upstream HDF5 release that explicitly lists the fix commit(s). Confirm patch inclusion by checking package changelogs or commit SHAs.
• For statically linked binaries, rebuild the application with a patched HDF5 library and rotate the artifact. Debian’s tracker includes the commit that fixed the issue in upstream; vendors should map that SHA to their packages.
• Reduce exposure and block untrusted inputs (compensating control)
• For services that accept user uploads, quarantine HDF5 files and block direct automatic processing. Replace immediate processing with a sandboxed pipeline that validates files offline.
• Enforce authentication and strict ACLs on upload endpoints. Throttle and validate file sizes and types at the edge.
• Containment and hardening
• Run HDF5‑processing tasks in isolated containers with least privilege (seccomp, AppArmor, SELinux, restricted cgroups and ulimits).
• Use separate microservices for previewing and metadata extraction so crashes are localized and worker churn is visible and recoverable.
• Detection and monitoring
• Alert on repeated or unexplained HDF5‑related process terminations (core dumps, segmentation faults, sanitizer logs).
• Record and retain suspicious uploads for forensics; capture input files that trigger crashes and preserve relevant container images and logs for reproduction.
• Communication and supply‑chain controls
• Coordinate with package maintainers and upstream library owners to understand patch timelines and verify backports.
• Maintain SBOMs that record library versions and static linkages to speed triage.

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Detection signatures and forensic hints​

• AddressSanitizer and UBSAN builds will show a one‑byte heap buffer overflow originating from H5Omessage.c at the line where p is computed. If you can reproduce the crash in a sanitizer build, the ASan output will include the exact write location and stack trace shown in the upstream PoC.
• In production, look for abrupt termination of worker processes that read .h5 files without prior logging, especially during flush/close operations; common crash indicators include SIGSEGV, abnormal exit codes, or repeated restarts during batch jobs.
• If an ingestion service crashed after receiving a previously unseen .h5 upload, preserve the original file and the process memory or core dump for reproduction. These artifacts matter for mapping whether an observed crash corresponds to this CVE or to a different HDF5 defect in the same release window.

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Vendor response and status​

• Upstream — The HDFGroup issue tracker contains the original report and associated reproduction artifacts; the issue was triaged and closed after commits that address the boundary checks. Administrators should look for a downstream vendor release that explicitly includes the upstream fix commit(s) or a published point release that documents CVE fixes.
• Distributors — Ubuntu, Debian, SUSE and other OS/distribution trackers have entries for CVE‑2025‑2912 and have mapped affected packages in their trees. Debian’s tracker records the upstream commit SHA that fixes the issue and marks the problem as fixed in the upstream commit history; however, the availability of patched distro packages varies by release and may require manual rebuilds or backporting for older stable distributions. Operators must confirm their distribution’s package includes the fix before declaring hosts remediated.
• Microsoft’s MSRC tracking page also lists HDF5 memory‑safety CVEs in this release family — keep an eye on vendor advisories and CVE pages for updated scoring and remediation notes. (Microsoft’s tracker historically aggregates public CVE details; consult it for mapping to Microsoft products that may include HDF5 runtimes.

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Practical guidance for Windows users and scientific environments​

• If you use Python packages such as h5py installed from pip or conda, check the wheel’s bundled HDF5 version. Many prebuilt wheels include an embedded HDF5 runtime; a patched h5py wheel is the normal remediation path for Windows Python users. If your environment uses conda/conda‑forge packages, prefer updated conda packages that list the patched HDF5 runtime.
• For Windows servers that run automated ingestion or preview services, isolate file‑handling services and disable automatic opening of user‑provided .h5 files in monolithic processes. Use dedicated, disposable worker containers or sandboxed processes to limit the impact of a crash.
• For packaged vendor appliances or proprietary binaries that embed HDF5 statically, contact the vendor for an update and request the exact commit SHA or release that addresses CVE‑2025‑2912. If the vendor cannot provide a timely update, apply compensating controls such as blocking .h5 uploads at the gateway or routing them to an offline validation system.

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Strengths of the public disclosure and the known technical evidence​

• The vulnerability is well‑documented: the upstream GitHub issue includes a reproducible PoC, a sanitizer trace and precise code excerpts that identify the faulty pointer calculation. This high level of technical detail means defenders can reproduce and validate patches quickly.
• Multiple independent vulnerability databases and distros have indexed the CVE and mapped it to affected packages. That redundancy helps operators find the status of fixes across packaging ecosystems and reduces ambiguity about whether an environment is vulnerable.
• The concrete upstream commit that fixes the defect is traceable in distribution trackers (for example, Debian lists a fixing commit SHA), which enables maintainers to verify a backport or patched package precisely. This improves confidence in remediation.

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Risks, caveats and unresolved questions​

• Although the PoC demonstrates a reproducible heap overflow and reliable crashes under sanitizers, claims of trivial remote code execution remain unproven in public writeups at the time of disclosure. Turning a one‑byte write into stable RCE generally requires additional primitives (information leak, predictable allocations) and is environment dependent. Treat RCE statements with caution until multiple independent exploit writeups demonstrate a reproducible chain.
• The CVE’s formal classification as local masks the practical reality: many server environments effectively render this a remotely triggerable DoS via file upload. Security teams must interpret the formal vector in the context of their deployment topology.
• Patch availability varies by distribution and packaging channel. Upstream commits may be merged on the project’s development branch and not immediately appear in vendor packages; distributors that perform conservative backports can lag. Operators must validate the presence of the fix commit in packaged binaries — do not assume a package labeled with a higher version number is fixed without verifying the commit SHA. Debian’s tracker provides the exact upstream commit for verification.
• Some CVE aggregations show varying CVSS numbers and severity assessments; that inconsistency stems from differing threat models and whether assessors weigh the presence of a public PoC more heavily. Use the published evidence (PoC + ASan trace + vendor tracking) to drive remediation urgency rather than relying solely on a single numerical score.

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Recommended timeline and prioritization​

• Immediate (0–72 hours)
• Inventory HDF5 usage across the estate and quarantine public upload endpoints that accept .h5 files without validation. Apply access controls to reduce immediate exposure.
• Short term (72 hours–2 weeks)
• Apply vendor patches as they become available. For environments that consume prebuilt wheels or conda packages, upgrade to patched wheels and verify the embedded HDF5 version. Rebuild statically linked artifacts where practical.
• Medium term (2–8 weeks)
• Harden ingestion pipelines: add file scanning, sandboxed processing, rate limiting and monitoring of anomalous crashes. Ensure SBOMs are maintained to make future triage faster.
• Longer term
• Revisit development practices that depend on untrusted file parsing in privileged contexts and consider introducing stricter sandboxing and policy enforced boundaries between file parsers and sensitive application logic.

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Conclusion​

CVE‑2025‑2912 is a concrete, reproducible heap‑based buffer overflow in H5O_msg_flush (src/H5Omessage.c) of HDF5 ≤ 1.14.6 that results from insufficient bounds checks around message‑header pointer arithmetic. The vulnerability is accompanied by a public proof‑of‑concept and has been cataloged by major trackers and distributors; upstream fixes are available in the HDF5 repository and downstream packaging teams are in various stages of backporting or rebuilding. The immediate operational risk is Denial‑of‑Service for systems that process untrusted HDF5 files; escalation to remote code execution is theoretically possible in favorable exploit conditions but remains unproven in general. Operators should treat ingestion endpoints as highest priority, inventory HDF5 usage, and deploy patched builds or vendor updates as soon as they can be validated. Acknowledging the availability of a reproducible PoC, defenders must move quickly: apply verified vendor or upstream patches, sandbox HDF5 processing, and monitor for crashes and suspicious uploads until all affected artifacts have been remediated.

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Source: MSRC Security Update Guide - Microsoft Security Response Center