Liquid Cooling Commissioning: How to Flush, Fill and Purge a Cold Plate Loop Before Go-Live

The AI racks have landed. The piping is in, the CDUs are set in place, and the project manager wants load on the servers by Friday. On a lot of sites, liquid cooling commissioning gets treated as a formality: flush some water through, fill the loop, check for drips, done.

The trouble is that a cold plate loop has almost no tolerance for dirt or air. Flow channels in a typical single-phase cold plate are around 100 µm wide, and microchannel designs go narrower still. A bit of weld slag, a flake of pipe debris or a single trapped air pocket can make one GPU run 10°C hotter than its neighbors on the same loop, and then throttle. Finding that after the servers go live costs far more than getting commissioning right the first time. In fact, avoiding a single rack rework often pays for the entire pre-commissioning effort.

This guide walks through liquid cooling commissioning in the order it actually happens on site, from pressure test to handover. For each step, you'll see what to do, what counts as a pass, and what to write down.

What Is Liquid Cooling Commissioning?

Liquid cooling commissioning is the on-site work that takes a liquid cooling loop from "installed" to "ready to run reliably for years" before the servers go live. For a direct-to-chip cold plate loop, the standard sequence is:

1. Pressure test the loop for leaks
2. Clean and flush out construction debris
3. Fill with coolant
4. Purge air from the loop
5. Start the CDU and connect the racks
6. Balance flow and verify under load
7. Record a baseline and hand over to operations

Steps 1 through 3 are often called pre-commissioning, and field crews sometimes shorten them to "flush and fill." They happen before the racks are connected, and they decide how clean the loop will be for the rest of its life.

Key Takeaways

• Order matters. Keep CDUs off the loop until the piping has been pressure tested, cleaned and flushed, and connect racks only after the CDUs have run clean on final coolant.
• Flush to a number, not a feeling. Outlet conductivity within 10 to 20 µS/cm of the procedure water and turbidity under 5 NTU are common pass criteria.
• Don't let water sit. Untreated water shouldn't stand in the loop for more than 24 hours, and a loop that will wait more than a week should be laid up dry.
• Purge air at every connection. Each new batch of racks brings air in through its quick disconnects.
• Check flow branch by branch. A healthy total flow can hide racks that are running short.
• Keep the baseline. Commissioning data is the reference every later diagnosis depends on.

What Does Commissioning Cover, and Who Is Responsible?

This guide focuses on the technology cooling system (TCS), the secondary loop made up of the row manifolds, rack manifolds, CDU secondary side and, eventually, the cold plates. The facility water system (FWS) on the primary side needs commissioning too, but it behaves much like a conventional HVAC water system, so we only touch on it where it meets the CDU.

Most commissioning problems don't come from any one technical step. They come from handoffs. The mechanical contractor installed the piping, the water treatment vendor supplies the coolant, the CDU comes from an equipment maker, and the cold plates and servers come from yet another supplier. That's why industry guidance treats commissioning as one stage in a chain that runs from component manufacturing through transport and installation, not as a standalone task. Spell out who owns what before work starts:

Data center commissioning is usually split into Levels 1 through 5: L1 is factory testing, L2 is delivery inspection, L3 is installation and startup, L4 is functional performance testing of each system, and L5 is integrated systems testing. The seven steps in this guide fall mostly in L3 through L5.

Before You Start: Commissioning Prerequisites

Before anyone opens a valve, have these in place:

• A P&ID drawn for flushing. Mark where the temporary flushing equipment connects, where the loop backs go, which valves are open or closed, and every vent and drain point. Flow paths during flushing differ from normal operation, and without this drawing it's easy to miss a branch.
• Clean procedure water. Use reverse osmosis (RO) or deionized (DI) water that meets roughly these limits: conductivity no higher than 50 µS/cm, pH no lower than 6, and total aerobic bacteria no higher than 1,000 CFU/ml. Flushing with water that misses these numbers plants the seeds of scale and biofilm.
• Flushing equipment. A flushing skid typically includes a pump, a full-flow filter, pressure gauges, a flow meter, a pot feeder and a sample port. Flush a rental skid before you use it. Clean on the outside doesn't mean clean on the inside.
• A wastewater discharge plan. Cleaning and flushing generate a lot of chemical-laden water. Get the disposal plan approved by the local authority early, because this is often what holds up the schedule.
• No CDUs or racks on the loop. During flushing, the CDUs stay disconnected from the row piping, rack manifold drops are tied together with loop backs, and no servers or cold plates are in the circuit.

For the vents, drains and fill points that need to be designed in from the start, see our data center liquid cooling design guide.

Step 1: Pressure Test the Loop

Start with a gas pressure test to catch obvious leaks, then run a hydrostatic test. Hydrostatic test pressure is typically 1.3 to 1.5 times working pressure. Use the value in your design documents.

A few points that often get missed:

• Fill from the bottom, vent from the top. Even for test water, fill slowly at the lowest point and vent at the highest point. Trapped air skews pressure readings.
• Don't break tested joints. If a section has to come apart for any reason afterward, retest it.
• Start circulating right away. Stagnant water breeds bacteria. Without chemical treatment, don't let water sit in the loop without circulation for more than 24 hours. The safest approach is to move straight from the hydrotest into recirculation and log the pressure, flow and duration of every step.

The site pressure test checks the piping and joints installed on site. Cold plates, manifolds and other components should have their tightness verified at the factory with a more sensitive method. Our helium leak testing guide covers how. For what's at stake if a loop does leak, see what happens if liquid cooling leaks.

Step 2: Clean and Flush

Clean and flush the TCS until the water leaving the loop is within 10 to 20 µS/cm of the procedure water and below 5 NTU turbidity. This step decides whether the loop stays clean for its whole service life. It has two stages: cleaning, which lifts debris and residue off the pipe walls, and flushing, which carries the cleaning chemicals back out.

Cleaning:

1. Initial recirculation. Circulate procedure water through a coarse 50 to 100 µm filter to catch the big particles first. Keep the valves to the rack drops closed so large debris can't get into the smaller pipes.
2. Chemical cleaning. Add the cleaner your water treatment vendor recommends (with a copper corrosion inhibitor if there's any copper in the system). Circulate for at least 4 hours, until filter differential pressure stops rising.
3. Drain. Drain the loop completely from its lowest points. Low-pressure nitrogen can help push out the last of the water.

Flushing: Refill with procedure water, circulate, drain, and repeat until the water leaving the loop meets spec.

Step the filtration down in stages. Final ratings in industry practice range from 1 to 25 µm, and 5 µm is a commonly recommended target. Change the filter element when differential pressure reaches about 10 psi. And watch for the opposite: a filter showing zero differential pressure may have ruptured.

Flushing velocity matters most. Too slow, and particles just shift around inside the pipe instead of reaching the filter. Minimum flushing velocities for row piping typically fall around 3 to 5 ft/s (roughly 1 to 1.3 m/s), with larger pipes needing higher velocity. Because AI racks already run coolant faster in normal operation, some commissioning engineers push for TCS flushing velocities of 10 to 20 ft/s, so debris comes loose during the flush rather than after the servers are connected.

Isolate branches one at a time so every section sees full flushing velocity. When the main flush is done, give every capped connection and dead leg a terminal flush. Those spots never see flow in normal operation, which makes them prime hiding places for debris. Retrofits are especially prone to this, because existing halls often hide dead legs and lack enough drain points.

Cleaning and flushing pass criteria:

Finish by sending a water sample to a lab for conductivity, turbidity, pH and bacteria. That report is your written proof the loop was clean.

Step 3: Fill with Coolant

Fill immediately after flushing. Don't leave a gap.

• Use the permanent fill points. Inject through the fill connections built into the loop, using a stainless steel, variable-speed pump, and slow down as the loop approaches full.
• Fill low, vent high. Keep an eye on every high-point vent throughout the fill.
• Start circulating at about 90% full. This mixes the coolant and helps work air out. Use the flushing skid, or the CDU pumps if the CDUs have already been flushed and verified clean.
• Sample for uniformity. Once full, circulate at least 3 system volumes, then pull samples from 3 locations and check pH, turbidity, inhibitor level and glycol concentration (for PG25). If results differ by more than 5% between locations, keep circulating until they match.
• Check every tote. Review the quality documentation on each coolant delivery and spot-test a sample. If any equipment arrives pre-filled, confirm its fluid matches the loop's coolant by brand, concentration and formulation.

Water left over from flushing dilutes PG25, and glycol concentration can drop noticeably once the coolant mixes with water held up in the CDU and other equipment. For first-week sampling frequency and long-term water quality limits, see our direct-to-chip coolant guide.

Glycol-based coolant such as PG25 is biostatic at the right concentration, so it can sit for a while once filled. A water-based coolant can't: it needs continuous recirculation so the biocide reaches every part of the loop.

If the coolant hasn't arrived yet, or commissioning is more than a week out, don't leave the loop sitting full of water. Lay it up dry instead: circulate a biocide, drain, dry the piping, cap every opening and blanket the loop with dry nitrogen.

Step 4: Purge Air from the Loop

To purge air from a liquid cooling loop, fill from the lowest point, circulate at low pump speed, and bleed air from vents at every high point until flow and pressure hold steady. Do it once after the first fill, then again in Step 5, every time racks are connected and their cold plates join the loop.

Air is one of the sneakiest problems in a liquid cooling loop. It collects in cold plate channels and at high points, shrinking the effective heat transfer area. Once the pump pulls it in, flow turns unstable, and in bad cases the pump starts to cavitate.

Where air hides:

• Inside cold plate channels and cavities
• At the high points and local humps of piping and manifolds
• In the small slug of air that comes in with every quick disconnect mating
• In bubbles whipped in by filling too fast

How to get it out:

• Circulate slowly first. Run the pump at low speed after filling so bubbles can gather at the high points, then bleed them off through the vents. At high pump speed, bubbles break into tiny ones that stay suspended and are much harder to remove.
• Put a vent at every high point. Automatic air vents work well for long-term operation. During commissioning, pair them with manual venting for a more thorough job.
• Cycle the pump. When the pump stops, bubbles float up and collect. When it restarts, they're carried to the vents. A few cycles will clear out air lodged in the flow channels.
• Hold static pressure. Precharge the expansion tank high enough that the highest point in the loop always stays above atmospheric pressure. If pump inlet pressure drops below atmospheric, the loop will pull air in through its fittings.

How to tell the air is out:

• Flow and pressure readings are steady, with no periodic swings
• The pump runs smoothly and quietly, and the gauge needles don't flutter
• Parallel branches on the same loop show about the same temperature rise (ΔT)

Purging isn't a one-time job. Purge again every time you connect a new batch of racks, swap a cold plate or finish service work. How much air a quick disconnect lets in varies by product, so check it when you specify couplings. Our liquid cooling quick disconnect guide explains what to ask for. If you see sawtooth swings in temperature and flow after go-live, our cold plate cooling troubleshooting guide covers how to track down trapped air.

Step 5: Start the CDU and Connect the Racks

CDUs, liquid-cooled load banks and any other equipment that arrives from a vendor need flushing before they connect to the loop. Don't assume anything shows up clean.

CDU commissioning comes next. Once the CDU is connected and running, a safe practice is to circulate the final coolant through the CDU's own pumps in a closed loop for about a week before connecting any racks, using the operational filter rating or one size finer. Watch the CDU's filter differential pressure that week. If it keeps climbing, there's still debris in the loop, and once the racks are on, your operations team will be stuck changing filters constantly.

When differential pressure holds steady, connect the racks in batches:

• After each batch, check every quick disconnect, hose fitting and manifold connection at operating pressure, including the drip trays under the racks and the routing of leak detection cable
• After each batch, purge air again
• Test the CDU's leak detection and, if equipped, automatic isolation: confirm the alarm triggers and the isolation valves close as they should

For how a CDU works and what's inside one, see what is a CDU. For how in-rack and in-row CDUs differ in commissioning, such as coolant volume and the number of filter points, see in-rack vs. in-row CDU.

Step 6: Balance Flow and Verify Under Load

To balance a liquid cooling loop, measure the actual flow in every rack and branch, compare it with design flow, and adjust balancing valves until each one is on target, then prove it under heat load. A clean loop with no air is only the start. Whether the cold plates can carry heat away from the chips depends on every branch actually getting its design flow.

Set CDU operating parameters. Keep secondary supply temperature above the room dew point so cold plates and piping don't sweat. Confirm the setpoints for supply pressure, differential pressure and flow, along with every alarm threshold.

Check flow branch by branch. Total CDU flow isn't enough. The total can look fine while the racks nearest the CDU take more than their share and the racks at the far end run short. Check actual against design flow for every rack and every branch, and adjust the balancing valves where needed. Any valve touched during commissioning has to end up back in its correct position. For how manifolds split flow across a rack, see what is a liquid cooling manifold.

Use load banks first, then real load. Before expensive GPU servers go live, you can use liquid-cooled load banks to emulate GPU heat load and flow resistance, verifying CDU control, flow uniformity across branches and valve operation. On one large direct-to-chip project in Sydney, for example, the operator used liquid-cooled load banks for Level 3 to Level 5 commissioning of both the primary and secondary sides of the CDUs.

Once the load banks pass, connect the real servers and run them at high load for a sustained period, often 24 hours or more. Log supply and return temperatures, ΔT per rack, flow and pressure, and check every fitting for weeping. This is the stage where uneven flow and leftover air are most likely to show up.

Step 7: Record the Baseline and Hand Over

The data you capture at the end of commissioning is your best reference for telling later whether the system has drifted. At minimum, the handover package should include:

• Pressure test records (test pressure, hold time, result)
• Cleaning and flushing records (flow at each stage, filter differential pressure, filter changes, water test reports)
• Fill records (fill volume, coolant batch, results from each sampling point)
• CDU setpoints and alarm thresholds
• Measured flow for every rack and branch
• Load test data (supply and return temperatures, ΔT, pressure)
• Baseline CDU filter differential pressure from commissioning
• As-built P&ID
• Ongoing sampling plan

Ideally, define monitoring points, install sample ports and capture baseline data during the very first fill. For water quality management and sampling after go-live, see our coolant guide.

Liquid Cooling Commissioning Checklist

7 Common Liquid Cooling Commissioning Mistakes

1. Flushing with the CDU already connected. Construction debris goes straight into the CDU's heat exchanger and filters.
2. Letting the loop sit after the hydrotest. More than 24 hours of untreated, stagnant water gives bacteria a head start.
3. Flushing too slowly. Particles never reach the filter. They just settle somewhere else.
4. Skipping dead legs and capped connections. These see no flow day to day, and their debris gets washed into the loop the day you expand.
5. Leaving the loop empty too long after flushing. All the flushing work gets undone by recontamination while you wait.
6. Not purging after connecting racks. Air introduced by quick disconnects settles in cold plate channels.
7. Watching total flow instead of branch flow. Total flow looks fine while the racks at the far end run starved.

How APALTEK Hardware Makes Commissioning Easier

A lot of commissioning headaches trace back to the condition parts are in when they leave the factory. As a manufacturer of cold plates, manifolds and CDUs, APALTEK works to stop those problems at the factory:

• Every liquid cooling component is helium leak tested. It's a mandatory check before anything leaves our factory, and it finds leak paths too small for pressure decay testing to catch. See our testing and validation capabilities.
• Quick disconnects pre-installed, whole assembly leak tested. Cold plates and manifolds can ship with quick disconnects already installed and the complete assembly leak tested, so there are fewer joints to make on site and fewer places for leaks to start.
• CDUs designed and built in-house. APALTEK's in-rack and in-row CDUs are both in production, with redundant pumps (typically N+1), leak detection and automatic isolation. See our AIDC thermal management products.
• Thermal tests on your coolant. Cold plate thermal tests run on PG25 by default, and we can switch to water or DI water at your request so factory data matches your site conditions.
• Thermal simulation before prototyping. We typically run thermal simulation free of charge before prototyping, so the cold plate design is checked against your heat load and planned flow before any hardware is built. Agree on a design flow for each cold plate up front, and you have a clear target to balance against during commissioning.

If you need custom cold plates, start with our cold plate products.

FAQ

What is the difference between pre-commissioning and commissioning?

Pre-commissioning prepares the piping: pressure testing, cleaning, flushing and filling, usually before any CDU or rack is connected. Commissioning then brings the system online and proves it works, from CDU startup and rack connection to flow balancing, load testing and handover.

How long does liquid cooling commissioning take?

It depends on the size of the loop and site conditions. Filling, purging and checking a single rack loop can often be done in a few days. For a large data center, cleaning and flushing the row piping, a week of CDU circulation on final coolant and load testing often add up to several weeks. Flushing is the last place to cut schedule.

Can you flush through the cold plates and CDU?

It's not recommended. While the row piping is cleaned and flushed, the CDUs stay disconnected, rack manifold drops are tied together with loop backs, and no cold plates or servers are on the loop. Connect the CDUs once the piping meets cleanliness criteria, and connect the racks in batches once the CDUs are running stable.

What water should you use for flushing?

RO or DI water, typically with conductivity no higher than 50 µS/cm, pH no lower than 6 and total aerobic bacteria no higher than 1,000 CFU/ml. Don't use tap water. Its chlorides, hardness and microbes lead to pitting, scale and biofilm.

How do you know all the air is out of the loop?

Look for three signs: flow and pressure readings are steady with no periodic swings, the pump runs smoothly and quietly, and parallel branches on the same loop show about the same temperature rise. Purge again every time you connect new racks or finish service work.

Can a loop sit empty after flushing before you fill it?

Ideally, no. Fill with coolant right after flushing. If you have to wait more than a week, lay the loop up dry: circulate a biocide, drain and dry the piping, cap every opening and blanket it with dry nitrogen to keep out bacteria and debris.

What flushing velocity do you need?

Minimum flushing velocities for row piping typically fall around 3 to 5 ft/s (roughly 1 to 1.3 m/s), with larger pipes needing more. Because AI rack loops run at higher velocities in normal operation, some engineers recommend higher flushing velocities for the TCS. Calculate the actual value for each pipe size in your flushing plan.

Commissioning Quality Is Decided Before You Place the Order

How easy a loop is to commission is largely settled during design and procurement: whether vents and drains were designed in, how clean the cold plates are when they ship, how rigorous the leak testing was, how many joints have to be made on site, and whether the CDU has proper leak detection and isolation. By the time the commissioning team arrives, they can only work with what they've been given.

If you're planning a cold plate liquid cooling project, send APALTEK your loop schematic and rack list. Our engineering team will review the design with flushing, filling and purging in mind, match it with cold plates, manifolds and CDUs, and run thermal simulation before prototyping, free of charge in most cases. We typically reply to quote requests within one business day.

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