Linux Is Linux - Not Always :-)

Tushar Pednekar
Oct 8
3 min read

An OS Migration Exposed a Hidden SystemD Trap

“Linux is Linux.”

It’s what we all say when migrating between distros — until one day, it isn’t.

This is the story of a FinTech customer who migrated their SynxDB cluster from CentOS 7.9 to Amazon Linux 2023, expecting a routine OS upgrade.

Instead, they discovered how a single SystemD configuration default can bring down a production-grade analytics system.

🚀 The Migration That Looked Perfect

The customer ran a 40-segment SynxDB deployment powering high-frequency analytics and fraud scoring.

As CentOS 7 reached end-of-life, they rebuilt their EC2 images on Amazon Linux 2023, keeping everything else the same — same SynxDB version, same configuration, same automation.

Then the logs started filling up with errors like:

FATAL: semctl(1638419, 3, SETVAL, 0) failed: Invalid argument

Queries would complete, then crash during cleanup.

The master detected abnormal terminations and triggered short recovery cycles.

No data loss — but intermittent outages across the entire cluster.

🔍 The Investigation

Our engineers joined the customer’s SRE team and noticed a strange pattern:

crashes occurred right after someone logged out of SSH.

That clue led to the real root cause — and it wasn’t in SynxDB at all.

🧩 The Hidden Culprit: SystemD’s

RemoveIPC

PostgreSQL and SynxDB use System V IPC for inter-process communication: semaphores, shared memory, and message queues.

These resources live in kernel space and normally persist as long as the database is running.

Then came SystemD and its RemoveIPC feature.

When enabled, it deletes all IPC objects belonging to a user when their last session ends.

On CentOS 7, this is disabled (RemoveIPC=no).

On Amazon Linux 2023, it’s enabled (RemoveIPC=yes).

That subtle default change meant:

the moment an administrator logged out, SystemD would quietly delete SynxDB’s semaphores — while the database was still using them.

The Result

When SynxDB tried to release a semaphore on query completion, the kernel responded:

semctl(): Invalid argument

Postmaster interpreted this as a potential corruption event, killed all backends, and triggered crash recovery.

The database wasn’t misbehaving — it was reacting to its environment.

⚙️ The Fix (No Code Changes Required)

Once identified, the solution was straightforward.

Immediate zero-downtime workaround

sudo loginctl enable-linger gpadmin

This keeps a lightweight SystemD session for the database user even after logout, preventing automatic IPC cleanup.

Permanent fix

sudo vim /etc/systemd/logind.conf

[Login]
RemoveIPC=no

Apply and verify:

sudo systemctl restart systemd-logind
loginctl show-user gpadmin | grep RemoveIPC
# RemoveIPC=no

Problem solved — no restart, no downtime.

🧮 Tuning IPC for SynxDB

While diagnosing, we also confirmed semaphore limits suitable for large SynxDB clusters:

# For typical clusters (≤4 segments/host)
kernel.sem = 250 512000 100 2048

# For dense clusters (≥8 segments/host)
kernel.sem = 500 4096000 200 8192

These ensure adequate concurrency and stability during peak workloads.

✅ The Outcome

Within hours of applying the fix:

No more semctl() errors
No recovery cycles
99.99% uptime restored

The customer’s automation pipeline was updated to:

Enforce RemoveIPC=no during provisioning
Enable lingering for all SynxDB nodes
Validate semaphore limits during health checks

What began as a failure turned into a platform-wide improvement — and a shared learning moment across teams.

💡 Key Takeaways

Lesson	Insight
Linux defaults vary	“Same Linux” doesn’t mean identical runtime behavior. Verify SystemD configs during OS upgrades.
Service accounts aren’t users	SystemD treats daemon accounts as session users unless you configure otherwise.
Always look below the database	The issue wasn’t in SQL or SynxDB logic — it was in how the OS cleaned up resources.
Cross-layer debugging matters	Understanding both kernel and database behavior is key to true reliability.

🗣️ Why We Share Stories Like This

At Synx Data Labs, we build enterprise-grade data platforms that span BI to AI, from SynxDB and SynxDB Elastic to SynxML and Apache Cloudberry — the best open-source Postgres for analytics under the Apache Software Foundation.

Our mission is not just to build great data engines, but to help customers run them predictably — across every kernel, container, and cloud.

Because yes, Linux is Linux…

until one config file decides otherwise.

🔗 Read the full technical breakdown (commands, logs, and verification steps):

👉 https://github.com/Synx-Data-Labs/synxdb-docs/blob/main/support-synxdb2-ipc-semctl.md