Discussion:
High load and MySQL slow without apparent reason
(too old to reply)
Darek Margas
2018-10-17 02:25:31 UTC
Permalink
Hi Everyone,

I'm trying to refresh my old FreeBSD experience by moving MySQL platform
from Linux onto FreebSD+ZFS.

Before I ask for your help I would like to give you some context.

The machine is Dell server 2x20 cores, Intel IXL NIC, 1TB of RAM and lots
of SAS SSD drives.
The kernel is slightly modified by removing some unused stuff, replacing
ixl driver with latest from Intel website and enabling NUMA.
The whole thing runs number of MySQL daemons packed in jails (bridged
network) with settings optimized for ZFS ARC caching (O_DIRECT, small
buffers, etc).

This is 11.2-RELEASE.

When I tested it first time I found troubles with back pressure on ARC
whilst short in memory leading machine do death. I also found that
disabling ARC compression solved silent death but decided to make some
tunes to keep more memory free for sudden need.

Ran some tests, used it for replication salves, etc.

Here is the thing - how I crashed this machine without understanding what
has happened.

First my tunes. I adjusted v_free_target and v_free_min aiming to 128G and
64G respectively. However, I overlooked fact that this is in pages not in
1k blocks. As result I set:

- 700G max ARC size
- 512G v_free_target
- 256G v_free_min

Obviously this is a nonsense, however, the machine worked calm until ARC
got half of memory. Then shit happened. As I made machine with no swap at
all I have got number of zombies and problems with reclaiming console (say,
open VI which works, then exit and VI stays on console while became zombie).
That was "fixed" by disabling swapping via sysctl. I also noticed 25% of
CPU taken by "system" with nothing popping in top except pagedaemon and zfs
(on arc_reclaim).

I have added 40G of swap, rebooted machine but kept wrong settings.

It was again calm until ARC got half of memory. This is when I found what I
did and fixed v_free stuff to be

- 128G v_free_target
- 64G v_free_min

The machine started managing memory the right way, wiping inactive to
laundry and laundering only when needed. I still observed 25% of
unexplained load from "system" (floating 5-60%) but all seemed OK.

At this point I switched one replica to be master and put production
queries on it.

Summarizing the above - the machine had issues and has not been rebooted
but seemed OK with memory management while having unexplained system load.

Once I switched my SQLs from Linux master to FreeBSD I noticed slow
performance. There is stored proc called every 15 minutes. On old machine
and all others it takes around 30-40s to complete and previous master had
spike in ROW executions to 650kps (one minute sample) while new one got it
up to 350kps and run for nearly 3 minutes.

I started looking deeper and found:
- Made all MySQL settings the same (when possible as some follow platform)
with no improvement
- MySQL reload did not help
- Stopping all replicas running around on the same machine (5 of them) to
release resources made it worse (over 5 minutes to complete call). Starting
replicas made it better again by one minute.

BTW - jail was limited to one NUMA zone and half cores. Not all replicas
had the same NUMA and CPU group.

I copied ZFS content to test machine which is exactly the same and kicked
the same MySQL in same jail and with same settings.
- Test instance ran correctly within similar completion time to old Linux
master
- ARC on test machine was loaded up to 700G so I thought it would be good
enough to compare but machine still had lots of memory

To make it closer I compiled "memory allocator" which simply allocates and
fills memory until killed or system dies.

Run it on test machine first:
- No effect until v_mem_target passed
- Once passed pagedaemon kicked in, memory got wiped and shifted, swap got
full (paging only anyway)
- Load around 20% appeared from system, similar to broken production machine
- Got down to 50G passing v_free_min
- KIlled allocator
- After 1-2s freezing all got back to normal, load from system was gone.
- Swap was in use for some time after but finally got clean (that was only
4G swap on test machine)
- After some time machine is still calm and MySQL fast

Repeated the same on production machine:
- All as above, except:
- after killing allocator machine got frozen for, say, 10-15s
- memory was released but load did not change - neither got much higher
while allocating memory nor lower after.
- Machine remained slow

Finally I rebooted whole machine and now it is fast while building ARC. I
believe it won't have the same issue soon as v_free stuff is set correctly,
however, I need to understand why this MySQL process suffered and whether
it was possible to recover it without reboot. I can imagine it was
something running in a loop or contention on something otherwise unused or
simply another clash in settings triggering something in unusual way but
have no idea where to look to investigate it. Well, it's possible that
there is a bug too.

Before reboot I collected various vmstats, tops, ran ktrace on MySQL and
sysctl to dump settings. Not posting as don't know what would be useful.

Could you please point me in right direction?

Cheers,
Darek
Allan Jude
2018-10-17 03:31:44 UTC
Permalink
Post by Darek Margas
Hi Everyone,
I'm trying to refresh my old FreeBSD experience by moving MySQL platform
from Linux onto FreebSD+ZFS.
Before I ask for your help I would like to give you some context.
The machine is Dell server 2x20 cores, Intel IXL NIC, 1TB of RAM and lots
of SAS SSD drives.
The kernel is slightly modified by removing some unused stuff, replacing
ixl driver with latest from Intel website and enabling NUMA.
The whole thing runs number of MySQL daemons packed in jails (bridged
network) with settings optimized for ZFS ARC caching (O_DIRECT, small
buffers, etc).
This is 11.2-RELEASE.
When I tested it first time I found troubles with back pressure on ARC
whilst short in memory leading machine do death. I also found that
disabling ARC compression solved silent death but decided to make some
tunes to keep more memory free for sudden need.
Ran some tests, used it for replication salves, etc.
Here is the thing - how I crashed this machine without understanding what
has happened.
First my tunes. I adjusted v_free_target and v_free_min aiming to 128G and
64G respectively. However, I overlooked fact that this is in pages not in
- 700G max ARC size
- 512G v_free_target
- 256G v_free_min
You likely want to tune 'vfs.zfs.arc_free_target' to a value very close
to v_free_target or atleast v_free_min to cause ZFS to give back memory
at that level of memory shortage as well.
Post by Darek Margas
Obviously this is a nonsense, however, the machine worked calm until ARC
got half of memory. Then shit happened. As I made machine with no swap at
all I have got number of zombies and problems with reclaiming console (say,
open VI which works, then exit and VI stays on console while became zombie).
That was "fixed" by disabling swapping via sysctl. I also noticed 25% of
CPU taken by "system" with nothing popping in top except pagedaemon and zfs
(on arc_reclaim).
I have added 40G of swap, rebooted machine but kept wrong settings.
It was again calm until ARC got half of memory. This is when I found what I
did and fixed v_free stuff to be
- 128G v_free_target
- 64G v_free_min
The machine started managing memory the right way, wiping inactive to
laundry and laundering only when needed. I still observed 25% of
unexplained load from "system" (floating 5-60%) but all seemed OK.
At this point I switched one replica to be master and put production
queries on it.
Summarizing the above - the machine had issues and has not been rebooted
but seemed OK with memory management while having unexplained system load.
Once I switched my SQLs from Linux master to FreeBSD I noticed slow
performance. There is stored proc called every 15 minutes. On old machine
and all others it takes around 30-40s to complete and previous master had
spike in ROW executions to 650kps (one minute sample) while new one got it
up to 350kps and run for nearly 3 minutes.
- Made all MySQL settings the same (when possible as some follow platform)
with no improvement
- MySQL reload did not help
- Stopping all replicas running around on the same machine (5 of them) to
release resources made it worse (over 5 minutes to complete call). Starting
replicas made it better again by one minute.
BTW - jail was limited to one NUMA zone and half cores. Not all replicas
had the same NUMA and CPU group.
I copied ZFS content to test machine which is exactly the same and kicked
the same MySQL in same jail and with same settings.
- Test instance ran correctly within similar completion time to old Linux
master
- ARC on test machine was loaded up to 700G so I thought it would be good
enough to compare but machine still had lots of memory
To make it closer I compiled "memory allocator" which simply allocates and
fills memory until killed or system dies.
- No effect until v_mem_target passed
- Once passed pagedaemon kicked in, memory got wiped and shifted, swap got
full (paging only anyway)
- Load around 20% appeared from system, similar to broken production machine
- Got down to 50G passing v_free_min
- KIlled allocator
- After 1-2s freezing all got back to normal, load from system was gone.
- Swap was in use for some time after but finally got clean (that was only
4G swap on test machine)
- After some time machine is still calm and MySQL fast
- after killing allocator machine got frozen for, say, 10-15s
- memory was released but load did not change - neither got much higher
while allocating memory nor lower after.
- Machine remained slow
Finally I rebooted whole machine and now it is fast while building ARC. I
believe it won't have the same issue soon as v_free stuff is set correctly,
however, I need to understand why this MySQL process suffered and whether
it was possible to recover it without reboot. I can imagine it was
something running in a loop or contention on something otherwise unused or
simply another clash in settings triggering something in unusual way but
have no idea where to look to investigate it. Well, it's possible that
there is a bug too.
Before reboot I collected various vmstats, tops, ran ktrace on MySQL and
sysctl to dump settings. Not posting as don't know what would be useful.
Could you please point me in right direction?
Cheers,
Darek
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--
Allan Jude
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