CentOS - Jul 2019 - Performance issues/difference of two servers running same task (one is quicker)

Hi

I need some advice what to do next, even if someone tells me to
check out (an)other mailing list(s), tuning site or point me in a better
direction how to solve my annoying problem: one server is much faster
for certain tasks although on "shitty" hardware.

I have tried many things to solve my issue
 - changed buffer/pool/cache/etc mysqld
 - changed server settings apache/php
 - changed various OS settings (sysctl) e.g. turned off IPV6
but havent figured it out.

I have a development server (local) and life servers (data center)
Used mainly for many different websites and one online training site.

the development and life server in question run the same software setup:
  - CentOS Linux release 7.6.1810
  - bind 32:9.9.4-74.el7_6.1
  - Apache/2.4.6 (CentOS)
  - PHP 7.1.29
  - mysqld  Ver 5.7.26
  - wordpress, woocommerce, wishlistmember, Sensei etc
  - software are all in the same stages of updates.
  - even many of the linux conf files are the same (/etc/host, bind, etc)
  - the databases are copies/identical

Life server is a Poweredge M710,48GB,2xXeon L5630,LSI Raid1 SSD
Dev  server is a DIY, GIGABYTE MX31-BS0, 32GB, 1xXeon E3-1245,MDADM RAID0 1TB
Seagate Spinners

Clearly the development server is hardware wise way below the specs of the Dell
but
software wise they are identical (they get upgraded at the same time).

During normal operations (i.e. display websites, online training courses etc)
the DELL
displays the websites faster although it sits 1000KM up north in a datacenter on
a different network than the local server on the same network as my machine.

Yet the DEV server outshines the DELL when creating a few large custom tables,
ie
the local server takes 5s while the DELL takes 15s (small tables), more for
bigger tables.

The task is based on:
 - level, member, course, group are all ID's
 - members can belong to a group, a level and can access many courses
 - the ID restricts what they can access and what they belong to.
 - a course for each member can have various stages of completion
 - using an API (wishlist member) that performs LOCAL calls when accessed
locally
   I can get who belongs to what and make up my info I need, then use PHP
   to make up the table.
 - DB calls ARE LOCAL!

Now when I try to create a table of members belonging to the same group level
doing the same course with different stages of completion the DELL takes on
average
3 times longer to complete the table (normally about 20 to 30 rows).

I have put microtime() calls before and after certain calls, and it's
visibly different:
  DEV
    Jul 04 04:57:26 UTC _members took 0.0005459785461425 ms
    Jul 04 04:57:26 UTC _members took 0.0005321502685546 ms
  LIFE
    Jul 04 05:00:36 UTC _members took 0.0014369487762451 ms
    Jul 04 05:00:36 UTC _members took 0.0013291835784912 ms
If I do this 300+ times, the outcome is very different.


So my questions:

 - How can it be that the DELL takes so much longer alltough on the far better
hardware?
 - How can it be allthough everything (software/os/plugins) is the same?
 - This even happens if the DELL is on low load (i.e. middle of the night) and
   only serves a few requests.

Same software, same config, same database, same amount of data in the database
yet on better hardware it's slower?

Any ideas anyone?



-- 
Jobst Schmalenbach

> Hi
>
> I need some advice what to do next, even if someone tells me to
> check out (an)other mailing list(s), tuning site or point me in a better
> direction how to solve my annoying problem: one server is much faster
> for certain tasks although on "shitty" hardware.
>
> I have tried many things to solve my issue
>  - changed buffer/pool/cache/etc mysqld
>  - changed server settings apache/php
>  - changed various OS settings (sysctl) e.g. turned off IPV6
> but havent figured it out.
>
> I have a development server (local) and life servers (data center)
> Used mainly for many different websites and one online training site.
>
> the development and life server in question run the same software setup:
>   - CentOS Linux release 7.6.1810
>   - bind 32:9.9.4-74.el7_6.1
>   - Apache/2.4.6 (CentOS)
>   - PHP 7.1.29
>   - mysqld  Ver 5.7.26
>   - wordpress, woocommerce, wishlistmember, Sensei etc
>   - software are all in the same stages of updates.
>   - even many of the linux conf files are the same (/etc/host, bind, etc)
>   - the databases are copies/identical
>
> Life server is a Poweredge M710,48GB,2xXeon L5630,LSI Raid1 SSD
> Dev  server is a DIY, GIGABYTE MX31-BS0, 32GB, 1xXeon E3-1245,MDADM RAID0
> 1TB Seagate Spinners
>
> Clearly the development server is hardware wise way below the specs of the
> Dell but
> software wise they are identical (they get upgraded at the same time).
>
> During normal operations (i.e. display websites, online training courses
> etc) the DELL
> displays the websites faster although it sits 1000KM up north in a
> datacenter on
> a different network than the local server on the same network as my
> machine.
>
> Yet the DEV server outshines the DELL when creating a few large custom
> tables, ie
> the local server takes 5s while the DELL takes 15s (small tables), more
> for bigger tables.
>
> The task is based on:
>  - level, member, course, group are all ID's
>  - members can belong to a group, a level and can access many courses
>  - the ID restricts what they can access and what they belong to.
>  - a course for each member can have various stages of completion
>  - using an API (wishlist member) that performs LOCAL calls when accessed
> locally
>    I can get who belongs to what and make up my info I need, then use PHP
>    to make up the table.
>  - DB calls ARE LOCAL!
>
> Now when I try to create a table of members belonging to the same group
> level
> doing the same course with different stages of completion the DELL takes
> on average
> 3 times longer to complete the table (normally about 20 to 30 rows).
>
> I have put microtime() calls before and after certain calls, and it's
> visibly different:
>   DEV
>     Jul 04 04:57:26 UTC _members took 0.0005459785461425 ms
>     Jul 04 04:57:26 UTC _members took 0.0005321502685546 ms
>   LIFE
>     Jul 04 05:00:36 UTC _members took 0.0014369487762451 ms
>     Jul 04 05:00:36 UTC _members took 0.0013291835784912 ms
> If I do this 300+ times, the outcome is very different.
>
>
> So my questions:
>
>  - How can it be that the DELL takes so much longer alltough on the far
> better hardware?
>  - How can it be allthough everything (software/os/plugins) is the same?
>  - This even happens if the DELL is on low load (i.e. middle of the night)
> and
>    only serves a few requests.
>
> Same software, same config, same database, same amount of data in the
> database
> yet on better hardware it's slower?
Two ideas:

a) the DELL maybe faster over all but if I'm right single core speed is
slower than on DEV machine.

b) how do the LSI/SSD perform compared to the MDADM/RAID0 on the DEV
server? I'm not sure the DELL is a clear winner here.

Regards,
Simon

On 7/4/19 8:43 AM, Jobst Schmalenbach wrote:
> Clearly the development server is hardware wise way below the specs of the
Dell but
> software wise they are identical (they get upgraded at the same time).
As a first step, you have to test subsystems one by one.

Try this to see how fast the CPU and kernel are (including meltdown/spectre
slowdowns):

time dd 2>/dev/null if=/dev/zero of=/dev/null bs=1 count=1000000

Then try this to see how fast your disks are for DB operations:

cd /a/directory/on/the/filesystem/you/want/to/test
time bash -c "for((i=0;i<1000;i++)); do dd 2>/dev/null if=/dev/zero
of=test bs=1 count=1 conv=fsync;done"
rm test

Regards.
-- 
    Roberto Ragusa    mail at robertoragusa.it

On 7/3/19 11:43 PM, Jobst Schmalenbach wrote:
>   - How can it be that the DELL takes so much longer alltough on the far
better hardware?

It looks like the DIY system has a CPU that's nearly twice as fast as 
the Dell's.? The additional CPU in the Dell will run more tasks 
concurrently, but it won't make a single process faster.

You might also think that the SSD RAID would make the Dell faster, but 
that will only be true if the process that you're testing performs a 
significant amount of IO.? If your DB operations are happening mostly in 
memory (that is, if the data is cached), then the faster CPU will be the 
primary determining factor.

The other thing that you left out of your description is the amount of 
data on each server.? If your live server has a lot of data in its DB 
and the dev system has a small dataset suitable for testing, then 
generally you'd expect that the dev system's data is more likely to live
in cache and avoid disk IO, and processing the smaller set will also 
take less CPU time.

https://www.cpubenchmark.net/cpu.php?cpu=Intel+Xeon+E3-1245+%40+3.30GHz&id=1202

https://www.cpubenchmark.net/cpu.php?cpu=Intel+Xeon+L5630+%40+2.13GHz&id=2086

On Thu, Jul 4, 2019 at 2:43 AM Jobst Schmalenbach <jobst at
barrett.com.au>
wrote:
> the development and life server in question run the same software setup:
>   - CentOS Linux release 7.6.1810
>   - bind 32:9.9.4-74.el7_6.1
>   - Apache/2.4.6 (CentOS)
>   - PHP 7.1.29
>   - mysqld  Ver 5.7.26
>   - wordpress, woocommerce, wishlistmember, Sensei etc
>   - software are all in the same stages of updates.
>   - even many of the linux conf files are the same (/etc/host, bind, etc)
>   - the databases are copies/identical
>
> Life server is a Poweredge M710,48GB,2xXeon L5630,LSI Raid1 SSD
> Dev  server is a DIY, GIGABYTE MX31-BS0, 32GB, 1xXeon E3-1245,MDADM RAID0
> 1TB Seagate Spinners
>
> During normal operations (i.e. display websites, online training courses
> etc) the DELL
> displays the websites faster although it sits 1000KM up north in a
> datacenter on
> a different network than the local server on the same network as my
> machine.
>
> Yet the DEV server outshines the DELL when creating a few large custom
> tables, ie
> the local server takes 5s while the DELL takes 15s (small tables), more
> for bigger tables.
>
>
> I have put microtime() calls before and after certain calls, and it's
> visibly different:
>   DEV
>     Jul 04 04:57:26 UTC _members took 0.0005459785461425 ms
>     Jul 04 04:57:26 UTC _members took 0.0005321502685546 ms
>   LIFE
>     Jul 04 05:00:36 UTC _members took 0.0014369487762451 ms
>     Jul 04 05:00:36 UTC _members took 0.0013291835784912 ms
> If I do this 300+ times, the outcome is very different.
>
>
> So my questions:
>
>  - How can it be that the DELL takes so much longer alltough on the far
> better hardware?
>  - How can it be allthough everything (software/os/plugins) is the same?
>  - This even happens if the DELL is on low load (i.e. middle of the night)
> and
>    only serves a few requests.

As others have said the DEV server is a generation newer CPU. For CPU
details I often reference Intels ?ark? pages:

https://ark.intel.com/content/www/us/en/ark/products/47927/intel-xeon-processor-l5630-12m-cache-2-13-ghz-5-86-gt-s-intel-qpi.html
  12M Cache, 2.13 GHz, 5.86 GT/s Intel? QPI


https://ark.intel.com/content/www/us/en/ark/products/52274/intel-xeon-processor-e3-1245-8m-cache-3-30-ghz.html
  8M Cache, 3.30 GHz

The ?generations? I mentioned are:
   Code NameProducts formerly Westmere EP
<https://ark.intel.com/content/www/us/en/ark/products/codename/54534/westmere-ep.html>
   Code NameProducts formerly Sandy Bridge
<https://ark.intel.com/content/www/us/en/ark/products/codename/29900/sandy-bridge.html>

Westmere systems used DDR at 800/1066MHz.
Sandy Bridge systems used DDR at 1066/1333MHz.
Not a huge difference, but likely another contributing factor of
performance.

I would also look at power settings in the BIOS and c-state settings in the
BIOS and OS as disabling c-states (often enabled by default to meet
green/energy star compliance) can make a noticeable performance difference.


Hope that helps.

On 7/4/19 10:18 PM, Steven Tardy wrote:
> I would also look at power settings in the BIOS and c-state settings in the
> BIOS and OS as disabling c-states (often enabled by default to meet
> green/energy star compliance) can make a noticeable performance difference.

I'd be surprised if it did, but now that you mention it, I think that we 
should probably mention more often that CentOS's default performance 
policy is power-saving, which will cut maximum performance in half.? 
Every physical system running CentOS should have run "tuned-adm profile 
throughput-performance".

http://jperrin.org/centos/boosting-centos-server-performance/

On Thu, Jul 04, 2019 at 09:39:18AM +0200, Roberto Ragusa (mail at
robertoragusa.it) wrote:
> On 7/4/19 8:43 AM, Jobst Schmalenbach wrote:
> >Clearly the development server is hardware wise way below the specs of
the Dell but
> >software wise they are identical (they get upgraded at the same time).
> As a first step, you have to test subsystems one by one.
Thank you for the tips.
Here are the results (DELL is faster overall):
> time dd 2>/dev/null if=/dev/zero of=/dev/null bs=1 count=1000000
[DIY ~] #>time dd 2>/dev/null if=/dev/zero of=/dev/null bs=1 count=1000000
real    0m1.931s
user    0m1.022s
sys     0m0.896s
[DELL ~] #>time dd 2>/dev/null if=/dev/zero of=/dev/null bs=1
count=1000000
real    0m1.308s
user    0m0.389s
sys     0m0.919s

Dell faster overall
> cd /a/directory/on/the/filesystem/you/want/to/test
> time bash -c "for((i=0;i<1000;i++)); do dd 2>/dev/null
if=/dev/zero of=test bs=1 count=1 conv=fsync;done"
> rm test
[DIY /mnt] #>time bash -c "for((i=0;i<1000;i++)); do dd
2>/dev/null if=/dev/zero of=test bs=1 count=1 conv=fsync;done"
real    1m12.944s
user    0m1.604s
sys     0m2.595s
[DELL /mnt] #>time bash -c "for((i=0;i<1000;i++)); do dd
2>/dev/null if=/dev/zero of=test bs=1 count=1 conv=fsync;done"
real    0m2.270s
user    0m0.509s
sys     0m1.475s

Expected the DIY to be slower here, it's running MDADM RAID1 on Seagete
Spinners compared to LSI RAID1 SSD

The result shows the DELL overall is faster, back to the drawing board after I
followed all the other hints in this thread.


Jobst

On Thu, Jul 04, 2019 at 09:07:35AM +0200, Simon Matter via CentOS (centos at
centos.org) wrote:
> > Hi
> 
> Two ideas:
> 
> a) the DELL maybe faster over all but if I'm right single core speed is
> slower than on DEV machine.
Yes, but since BOTH have "other" things to do at the same time the
sheer number of CPUs of the DELL should help
> 
> b) how do the LSI/SSD perform compared to the MDADM/RAID0 on the DEV
> server? I'm not sure the DELL is a clear winner here.
See my answer to the disk task test to another email.

On Thu, Jul 04, 2019 at 10:46:19AM -0700, Gordon Messmer (gordon.messmer at
gmail.com) wrote:
> On 7/3/19 11:43 PM, Jobst Schmalenbach wrote:
> >  - How can it be that the DELL takes so much longer alltough on the
far better hardware?
> It looks like the DIY system has a CPU that's nearly twice as fast
> as the Dell's.? The additional CPU in the Dell will run more tasks
> concurrently, but it won't make a single process faster.
> 
> You might also think that the SSD RAID would make the Dell faster,
> but that will only be true if the process that you're testing
> performs a significant amount of IO.? If your DB operations are
> happening mostly in memory (that is, if the data is cached), then
> the faster CPU will be the primary determining factor.
I made the buffer pool size on the DELL double the size of the DIY
when I started trying to figure out why the speed difference.
> 
> The other thing that you left out of your description is the amount
> of data on each server.? If your live server has a lot of data in
> its DB and the dev system has a small dataset suitable for testing,
> then generally you'd expect that the dev system's data is more
> likely to live in cache and avoid disk IO, and processing the
> smaller set will also take less CPU time.
Most of the DB's are small as they contain websites.
The biggest DB is the Online Training DB, which are the same on both machine
as I constantly copy the data from the life server to the DIY.



Very good analysis indeed.
Makes total sense.


-- 
Jobst Schmalenbach
Road to hell is paved with NAND gates.