- /home is mounted on /dev/md125, which is a RAID 5 consisting of three disks, formatted with ext4
I'm not really sure what else I might try, and I'm reaching out to the community to see if anyone has any suggestions for identifying and fixing the problem.
Hi all,
I'm experiencing some unexpected disk I/O latency on a newly built server. Here are some of the details:
- Supermicro motherboard with Intel PCH RAID [1]
- Debian 13.6 installed
- / is mounted on /dev/nvme0n1p2, which is an NVMe SSD, formatted with ext4
- /home is mounted on /dev/md125, which is a RAID 5 consisting of three disks, formatted with ext4
$ sudo mdadm -D /dev/md125
/dev/md125:
Container : /dev/md/imsm1, member 0
Raid Level : raid5
Array Size : 9279152128 (8.64 TiB 9.50 TB)
Used Dev Size : 4639576064 (4.32 TiB 4.75 TB)
Raid Devices : 3
Total Devices : 3
State : active
Active Devices : 3
Working Devices : 3
Failed Devices : 0
Spare Devices : 0
Layout : left-asymmetric
Chunk Size : 64K
Consistency Policy : resync
UUID : 2fbd736b:9b750e2a:e723b80c:df2f2c33
Number Major Minor RaidDevice State
2 8 0 0 active sync /dev/sda
1 8 16 1 active sync /dev/sdb
0 8 32 2 active sync /dev/sdc
I'm getting some weird latency issues with fsync on the RAID disk (/home on /dev/md125):
(Caveat: I'm doing a file transfer that is writing to /home, so I might expect some latency, but nothing like this.)
$ for i in {1..5}; do time sync; done 2>&1 | grep real
real 0m21.647s
real 0m11.770s
real 0m5.234s
real 0m3.023s
real 0m0.462s
Even when I turn off the file transfer, I still get something like this:
$ for i in {1..10}; do time sync; done 2>&1 | grep real
real 0m0.147s
real 0m0.077s
real 0m0.003s
real 0m0.004s
real 0m0.003s
I've tried turning on and off smart monitoring with smartctl to see if that would help, and it didn't seem to help.
I'm not really sure what else I might try, and I'm reaching out to the community to see if anyone has any suggestions for identifying and fixing the problem.
Thanks,
Casey
[1] https://www.supermicro.com/manuals/other/Intel_PCH_RAID_Config.pdf
On Jul 29, 2026, at 6:51?PM, David Christensen<dpchrist@holgerdanske.com> wrote:
What is the model number/ part number of your motherboard?
Have you disabled Intel PCH RAID in Setup -- e.g. so that themotherboard disk interface ports appear as non-RAID ports (SATA/SAS)?
How are the disk drives connected to the motherboard? What is thespeed rating of the cables? Do the cables have locking connectors? If
Have you run SMART long tests on each of the three disk drives in theRAID5? If not, please do so now. Please post the extended reports from
How are you transferring files? Please post your console session.
On Jul 29, 2026, at 6:51?PM, David Christensen <dpchrist@holgerdanske.com> wrote:
What is the model number/ part number of your motherboard?
MBD-X12DPI-N6-O
Have you disabled Intel PCH RAID in Setup -- e.g. so that the motherboard disk interface ports appear as non-RAID ports (SATA/SAS)?
No, I haven't tried that.
How are the disk drives connected to the motherboard? What is the speed rating of the cables? Do the cables have locking connectors? If you are using backplanes/ racks, what is their speed rating?
Thanks. These are all good questions. I don't have the cable specs or speed ratings on hand (and won't be able to check them for a few days, unfortunately), but they are the cables that came with the motherboard.
In the mean time, I'll try some of the other tests that you (and others) have kindly suggested.
As a point of reference, however, I built another machine with the same drives and cables (different motherboard), and I haven't experienced these issues.
Have you run SMART long tests on each of the three disk drives in the RAID5? If not, please do so now. Please post the extended reports from the top through and including the end of the section "SMART Attributes Data Structure revision number: ...".
I've started the SMART long tests on the three drives in the RAID5. It will take a few hours to run, so I'll report back.
How are you transferring files? Please post your console session.
From a different machine:
$ sudo rsync -av /home/someuser root@newmachine:/home/
Thank you!
Casey
On Jul 29, 2026, at 5:28?PM, Andy Smith <andy@strugglers.net>wrote:
On Wed, Jul 29, 2026 at 04:38:55PM -0600, Casey Deccio wrote:three disks, formatted with ext4
- /home is mounted on /dev/md125, which is a RAID 5 consisting of
I did not see anywhere in your email the details of what hardwarethese
disks are.
the community to see if anyone has any suggestions for identifying andI'm not really sure what else I might try, and I'm reaching out to
I would start by a process of simplification. For example, does thesync
still take a long time when /home is not actually mounted? If so then
the issue is with your NVMe.
If it does occur when /home is mounted, then it is the disks in theRAID
setup or the RAID setup itself. Does each individual disk perform anomalously?only
"fio" is a good tool,to carry out performance testing of storage
devices. Have a look what the random 4k read and write I/O is like in
terms of IOPS, and the sequential disk transfer rate in MB/s for reads
or writes. You can try that on the array and then break the array and
try it on each individual disk. Obviously this is destructive to the
data.
If the performance is as expected on a per-disk basis but terrible
with RAID, it may be time to post to the linux-raid mailing list asthis
is unlikely to be a Debian-specific issue. I would then also bechecking
if it happens in other RAID configurations like RAID-1.a
150 IOPS of random reads (not coming from RAM) is reasonable for a
single 7.2kRPM SATA disk. You could expect 2-3x this from a RAID-5 of
three identical disks.
Write IOPS is a bit more difficult to guess and will depend on whether
you have disabled the write cache in the drives themselves. Due to the
RAID-5 write penalty (read-modify-write) you may expect only 50-70% of
single disk's IOPS for random writes.
Of course, if your sd[abc] are SSDs then there should be plenty ofIOPS
available and those sync times are very weird.
"iostat -x 5" can give some more hints about what is going on.
If there is other I/O happening that you aren't expecting then "iotop"
can help identify it.
On Jul 29, 2026, at 10:23?PM, David Christensen<dpchrist@holgerdanske.com> wrote:
That looks like a nice motherboard:
https://www.supermicro.com/en/products/motherboard/X12DPi-N6
motherboard disk interface ports appear as non-RAID ports (SATA/SAS)?Have you disabled Intel PCH RAID in Setup -- e.g. so that the
No, I haven't tried that.
I expect Intel PCH RAID is turned off, or you would not see all threedisks. But, it would be good to double check.
speed rating of the cables? Do the cables have locking connectors? IfHow are the disk drives connected to the motherboard? What is the
or speed ratings on hand (and won't be able to check them for a fewThanks. These are all good questions. I don't have the cable specs
The motherboard has "14 SATA3 (6 Gbps)" ports and I expect theincluded cables will match. I just wanted to make sure that you were
For single SATA cables, I do prefer locking cables -- to preventaccidental disconnects when I am working inside the case. These cables
others) have kindly suggested.In the mean time, I'll try some of the other tests that you (and
same drives and cables (different motherboard), and I haven'tAs a point of reference, however, I built another machine with the
If that motherboard is more recent than Debian Stable, the includedLinux kernel might not support the C621A chipset and/or other chips on
Does dmesg(1) report any error messages during transfers?
the RAID5? If not, please do so now. Please post the extended reportsHave you run SMART long tests on each of the three disk drives in
It will take a few hours to run, so I'll report back.I've started the SMART long tests on the three drives in the RAID5.
Okay.
How are you transferring files? Please post your console session.From a different machine:
$ sudo rsync -av /home/someuser root@newmachine:/home/
Rather than timing sync(1) commands on the destination machine, addthe --progress option to rsync(1) on the source machine. Alternatively,
Seagate BarraCuda 5TB Internal Hard Drive HDD ? 2.5 Inch SATA 6Gb/s 5400 RPM 128MB
If that motherboard is more recent than Debian Stable, the included Linux kernel might not support the C621A chipset and/or other chips on the board. Please check if the Linux kernel in Debian 13.6 has support for the Intel C621A chipset. Also check if there are bug reports for that combination. If support is lacking, or if there are issues, you might need a newer kernel from backports or you might need to run Testing.Since it's a software RAID, I wonder if this might be the issue. I'll check the driver support to see what is in the kernel and also if there are proprietary drivers that Intel provides.
Does dmesg(1) report any error messages during transfers?Not that I can see.
I'm getting some weird latency issues with fsync on the RAID disk
(/home on /dev/md125): (Caveat: I'm doing a file transfer that is
writing to /home, so I might expect some latency, but nothing
like this.)
$ for i in {1..5}; do time sync; done 2>&1 | grep real
real 0m21.647s
real 0m11.770s
real 0m5.234s
real 0m3.023s
real 0m0.462s
I might add insult to the injury, but are you sure you need RAID-5 if it consists of just 3 drives?On Jul 29, 2026, at 5:28\u202fPM, Andy Smith<andy@strugglers.net> wrote:Thanks for that very helpful information. I've run fio on the still-assembled array, and here's what I get for read/write:
...
If it does occur when /home is mounted, then it is the disks in the RAID
setup or the RAID setup itself. Does each individual disk perform
anomalously?
"fio" is a good tool,to carry out performance testing of storage
devices. Have a look what the random 4k read and write I/O is like in
terms of IOPS, and the sequential disk transfer rate in MB/s for reads
or writes. You can try that on the array and then break the array and
try it on each individual disk. Obviously this is destructive to the
data.
If the performance is as expected on a per-disk basis but terrible only
with RAID, it may be time to post to the linux-raid mailing list as this
is unlikely to be a Debian-specific issue. I would then also be checking
if it happens in other RAID configurations like RAID-1.
150 IOPS of random reads (not coming from RAM) is reasonable for a
single 7.2kRPM SATA disk. You could expect 2-3x this from a RAID-5 of
three identical disks.
Write IOPS is a bit more difficult to guess and will depend on whether
you have disabled the write cache in the drives themselves. Due to the
RAID-5 write penalty (read-modify-write) you may expect only 50-70% of a
single disk's IOPS for random writes.
read: IOPS=237
write: IOPS=79
I'm not sure exactly what to make of that...
I might add insult to the injury, but are you sure you need RAID-5 if it consists of just 3 drives?
Usually around 30% per drive's capacity will be sacrificed to hold error correction data for the array,
so maybe it will be much better to use 2 drives in RAID-1 (Mirror) configuration, if you need decent write performance.
Third drive could be used as spare device for the array, or a separate storage without redundancy.
On Jul 30, 2026, at 9:32?AM, Andy Smith <andy@strugglers.net>wrote:
On Thu, Jul 30, 2026 at 07:17:01AM -0600, Casey Deccio wrote:6Gb/s 5400 RPM 128MB
Seagate BarraCuda 5TB Internal Hard Drive HDD ? 2.5 Inch SATA
Almost all high capacity 2.5" SATA drives are SMR (shingled magnetic recording) and are really intended for use in laptops, not for seriousserver
server purposes. I haven't checked this model but I would be very
surprised if it's not SMR, and the 5.4kRPM also suggests not for
use.the
SMR drives have a write cache and after this write cache is filled,
write performance is absolutely terrible. A lot of people find them unsuitable for use in RAID arrays (or zfs pools) because even thecost
periodic scrub can't complete in a reasonable time period.
This could easily explain the very low performance under write load
here. Have you used these models of drive before with a better
performance outcome?
Consumer-level SATA SSDs will definitely perform better though the
will be eye-watering (in comparison) for 3x ~4TB or 3x ~8TB. This isan
issue I have struggled with myself - very very hard to find decently performing 2.5" SATA drives.
On Jul 30, 2026, at 10:36?AM, Franco Martelli<martellif67@gmail.com> wrote:
On 30/07/26 at 15:40, Casey Deccio wrote:Linux kernel might not support the C621A chipset and/or other chips on
If that motherboard is more recent than Debian Stable, the included
I'll check the driver support to see what is in the kernel and also ifSince it's a software RAID, I wonder if this might be the issue.
Have you enabled "non-free-firmware" in /e/a/sources.list to installthe required Intel firmware packages?
Does dmesg(1) report any error messages during transfers?Not that I can see.
To be absolutely sure please run:
~$ sudo journalctl -k -p 4 -b 0
On Jul 30, 2026, at 1:04?PM, Alexander V. Makartsev <avbetev@gmail.com> wrote:Great ideas. I originally did RAID5 because I wasn't sure how many drives I wanted in the array, and I wondered if I might grow the array at some point. But I'll consider RAID 1 if I settle on three drives.
On 7/30/26 18:17, Casey Deccio wrote:
I might add insult to the injury, but are you sure you need RAID-5 if it consists of just 3 drives?On Jul 29, 2026, at 5:28?PM, Andy Smith <andy@strugglers.net> <mailto:andy@strugglers.net> wrote:Thanks for that very helpful information. I've run fio on the still-assembled array, and here's what I get for read/write:
...
If it does occur when /home is mounted, then it is the disks in the RAID >>> setup or the RAID setup itself. Does each individual disk perform
anomalously?
"fio" is a good tool,to carry out performance testing of storage
devices. Have a look what the random 4k read and write I/O is like in
terms of IOPS, and the sequential disk transfer rate in MB/s for reads
or writes. You can try that on the array and then break the array and
try it on each individual disk. Obviously this is destructive to the
data.
If the performance is as expected on a per-disk basis but terrible only
with RAID, it may be time to post to the linux-raid mailing list as this >>> is unlikely to be a Debian-specific issue. I would then also be checking >>> if it happens in other RAID configurations like RAID-1.
150 IOPS of random reads (not coming from RAM) is reasonable for a
single 7.2kRPM SATA disk. You could expect 2-3x this from a RAID-5 of
three identical disks.
Write IOPS is a bit more difficult to guess and will depend on whether
you have disabled the write cache in the drives themselves. Due to the
RAID-5 write penalty (read-modify-write) you may expect only 50-70% of a >>> single disk's IOPS for random writes.
read: IOPS=237
write: IOPS=79
I'm not sure exactly what to make of that...
Usually around 30% per drive's capacity will be sacrificed to hold error correction data for the array,
so maybe it will be much better to use 2 drives in RAID-1 (Mirror) configuration, if you need decent write performance.
Third drive could be used as spare device for the array, or a separate storage without redundancy.
On Jul 30, 2026, at 1:04?PM, Stefan Monnier<monnier@iro.umontreal.ca> wrote:
queue,I'm getting some weird latency issues with fsync on the RAID disk
(/home on /dev/md125): (Caveat: I'm doing a file transfer that is
writing to /home, so I might expect some latency, but nothing
like this.)
$ for i in {1..5}; do time sync; done 2>&1 | grep real
real 0m21.647s
real 0m11.770s
real 0m5.234s
real 0m3.023s
real 0m0.462s
Why do you expect "nothing like this"?
I have no idea if your numbers are normal or not, but 21s on a 3-disk
RAID writing at max speed (i.e. 6Gb/s) is 6Gbx21 =~ 16GB.
So if the file transfer has accumulated 16GB of data in the write
it's perfectly normal for `sync` to take 20s.transferred
And if the file transfer goes at about 400MB/s, you'll have
about 8GB during those 20s, so it stands to reason that the next sync
will still have 8GB to write to disk which will take another 10s,
and then 5s for the next, ...
[The disk drives] are all:
Seagate BarraCuda 5TB Internal Hard Drive HDD ? 2.5 Inch SATA 6Gb/s 5400 RPM 128MB
Almost all high capacity 2.5" SATA drives are SMR (shingled magnetic recording)
and are really intended for use in laptops, not for serious
server purposes. I haven't checked this model but I would be very
surprised if it's not SMR, and the 5.4kRPM also suggests not for
server use.
Thanks for the info. For this system I did optimize for cost,understanding that there would be some tradeoffs with regard to
The problem originally manifested itself when I was running commandsthat called the fsync() system call, inducing long I/O delays. For
On Jul 30, 2026, at 1:04?PM, Alexander V. Makartsev <avbetev@gmail.com> wrote:
On 7/30/26 18:17, Casey Deccio wrote:
I might add insult to the injury, but are you sure you need RAID-5 if it consists of just 3 drives?On Jul 29, 2026, at 5:28?PM, Andy Smith<andy@strugglers.net> wrote:Thanks for that very helpful information. I've run fio on the still-assembled array, and here's what I get for read/write:
...
If it does occur when /home is mounted, then it is the disks in the RAID >>>> setup or the RAID setup itself. Does each individual disk perform
anomalously?
"fio" is a good tool,to carry out performance testing of storage
devices. Have a look what the random 4k read and write I/O is like in
terms of IOPS, and the sequential disk transfer rate in MB/s for reads >>>> or writes. You can try that on the array and then break the array and
try it on each individual disk. Obviously this is destructive to the
data.
If the performance is as expected on a per-disk basis but terrible only >>>> with RAID, it may be time to post to the linux-raid mailing list as this >>>> is unlikely to be a Debian-specific issue. I would then also be checking >>>> if it happens in other RAID configurations like RAID-1.
150 IOPS of random reads (not coming from RAM) is reasonable for a
single 7.2kRPM SATA disk. You could expect 2-3x this from a RAID-5 of
three identical disks.
Write IOPS is a bit more difficult to guess and will depend on whether >>>> you have disabled the write cache in the drives themselves. Due to the >>>> RAID-5 write penalty (read-modify-write) you may expect only 50-70% of a >>>> single disk's IOPS for random writes.
read: IOPS=237
write: IOPS=79
I'm not sure exactly what to make of that...
Usually around 30% per drive's capacity will be sacrificed to hold error correction data for the array,
so maybe it will be much better to use 2 drives in RAID-1 (Mirror) configuration, if you need decent write performance.
Third drive could be used as spare device for the array, or a separate storage without redundancy.
Great ideas. ˙I originally did RAID5 because I wasn't sure how many drives I wanted in the array, and I wondered if I might grow the array at some point. ˙But I'll consider RAID 1 if I settle on three drives.
Thanks,
Casey
Hi,That is an interesting idea.
On Fri, Jul 31, 2026 at 12:04:30AM +0500, Alexander V. Makartsev wrote:
I might add insult to the injury, but are you sure you need RAID-5 if itOn Linux mdadm you can also do a RAID-10 across three drives which still allows for the loss of any single drive and provides both better read
consists of just 3 drives?
Usually around 30% per drive's capacity will be sacrificed to hold error
correction data for the array,
so maybe it will be much better to use 2 drives in RAID-1 (Mirror)
configuration, if you need decent write performance.
Third drive could be used as spare device for the array, or a separate
storage without redundancy.
and write performance compared to RAID-5 of the same devices. The
capacity would be 1.5 drives as opposed to 2.
On Jul 31, 2026, at 12:40?AM, Tom Dial <tddial@comcast.net> wrote:
On 7/30/26 14:49, Casey Deccio wrote:Thanks for the assessment. And also thanks to all the other respondents for their contributions.
On Jul 30, 2026, at 1:04?PM, Alexander V. Makartsev <avbetev@gmail.com> wrote:Great ideas. I originally did RAID5 because I wasn't sure how many drives I wanted in the array, and I wondered if I might grow the array at some point. But I'll consider RAID 1 if I settle on three drives.
On 7/30/26 18:17, Casey Deccio wrote:
I might add insult to the injury, but are you sure you need RAID-5 if it consists of just 3 drives?On Jul 29, 2026, at 5:28?PM, Andy Smith<andy@strugglers.net> wrote:Thanks for that very helpful information. I've run fio on the still-assembled array, and here's what I get for read/write:
...
If it does occur when /home is mounted, then it is the disks in the RAID >>>>> setup or the RAID setup itself. Does each individual disk perform
anomalously?
"fio" is a good tool,to carry out performance testing of storage
devices. Have a look what the random 4k read and write I/O is like in >>>>> terms of IOPS, and the sequential disk transfer rate in MB/s for reads >>>>> or writes. You can try that on the array and then break the array and >>>>> try it on each individual disk. Obviously this is destructive to the >>>>> data.
If the performance is as expected on a per-disk basis but terrible only >>>>> with RAID, it may be time to post to the linux-raid mailing list as this >>>>> is unlikely to be a Debian-specific issue. I would then also be checking >>>>> if it happens in other RAID configurations like RAID-1.
150 IOPS of random reads (not coming from RAM) is reasonable for a
single 7.2kRPM SATA disk. You could expect 2-3x this from a RAID-5 of >>>>> three identical disks.
Write IOPS is a bit more difficult to guess and will depend on whether >>>>> you have disabled the write cache in the drives themselves. Due to the >>>>> RAID-5 write penalty (read-modify-write) you may expect only 50-70% of a >>>>> single disk's IOPS for random writes.
read: IOPS=237
write: IOPS=79
I'm not sure exactly what to make of that...
Usually around 30% per drive's capacity will be sacrificed to hold error correction data for the array,
so maybe it will be much better to use 2 drives in RAID-1 (Mirror) configuration, if you need decent write performance.
Third drive could be used as spare device for the array, or a separate storage without redundancy.
A bit of analysis suggests this is a low performance server, mainly if not entirely because of the disks. The server board surely is not the bottleneck. As an earlier post suggested, the sync times noted are quite as should be expected.
The bottleneck almost certainly is the 6GBit/Sec consumer disks. The 6GBits/Sec transfer speed is only attainable on the cables from the system board to the individual disks. It implies a maximum transfer rate around 600 MBytes/Sec. but in sustained transfers, the disks cannot write that fast. AI query suggests 100-180 MB/Sec (depending on what part of the disk is being accessed) for CMR disks and 10-30 MB/Sec(!) for SMR disks. Raid 5 with 3 disks will reduce those to around 50% -75%, around 8-24 MB/sec so the expected average sustained write speed is unlikely to be more than 100MB/Sec. even with CMR disks. That is about, or slightly above, what is available from a Gigabit Ethernet transfer; for SMR disks, expect no more than around 25 MB/Sec. Large writes will take a while.
The pattern of sync times reported is consistent with that, suggesting that rsync makes the data available for writing somewhat faster than it can be written to the disk surfaces. Note that this doesn't apply to reading; the RAID will read and deliver data roughly twice as fast as a single disk and continue to do so on sustained reads as long as the data read is consumed at least as fast. Once the bulk data is transferred, performance may be satisfactory even with the low-spec drives.
The system with the Megaraid card would appear to perform better due to its internal cache: it will report write completion as soon as the data is in its cache (thus unblocking sync) and handle transfer to the disks internally. AI suggestion for the new server: set Write-Back rather than Write-Through for PCH Cache settings if that is not already done; that will allow the Intel driver to treat main memory as cache. It will not, however, make the data transfer any more quickly to the disks in the array.
AI was used here, but not extensively.
Perhaps the MegaRAID card caches writes to battery-backed RAM, reports >synchronous write completion to the OS, and then writes the cache to
the disk drives later (?). This would allow OS and application
synchronous writes to complete quickly.
On 7/30/26 14:49, Casey Deccio wrote:
Great ideas. ˙I originally did RAID5 because I wasn't sure how many
drives I wanted in the array, and I wondered if I might grow the array
at some point. ˙But I'll consider RAID 1 if I settle on three drives.
On 7/31/26 01:09, Andy Smith wrote:
On Linux mdadm you can also do a RAID-10 across three drives which still allows for the loss of any single drive and provides both better readThat is an interesting idea.
and write performance compared to RAID-5 of the same devices. The
capacity would be 1.5 drives as opposed to 2.
The RAID-10 configuration you proposing should then consist of 3 RAID-1 (mirror) groups, so 3 drives must be partitioned in halves and to finish RAID-10 array, there should be a RAID-0 (stripe) array created across all 3 groups.
Will the RAID-0 (stripping) layer of RAID-10 configuration significantly improve the write performance of the array in comparison to a basic RAID-1 array?
If your disks are SMR type then you might want to avoid ZFS. I think eventually, newer SMR disks will play nicer with ZFS than the first generations did. Maybe they're already there, I haven't followed SMR news recently.
... thanks to all the other respondents for their contributions.
I can't really change the hardware I have, but this is helpful for figuring out how to move forward, both with my current system and for future system design.
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