SeqAn and ReadTheDocs

 

So you find a typo in the SeqAn read the docs manual and you think "I will be a good citizen and correct it", but before you issue a pull request you want to test that the URLs work. To do this you need to 'compile' the docs, a little like you do with LaTeX. Here we go;

I've done all this on a AWS Ubuntu "14.04.5 LTS, Trusty Tahr" instance for a clean install so you can see only what is required.

Install Dependencies

$ sudo apt-get update

$ sudo apt-get install python-sphinx python-pip git

 Install Sphinx extensions

$ pip install --user sphinx_rtd_theme

$ pip install --user sphinxcontrib-bibtex

$ pip install --user seqansphinx

Go to your development directory, clone SeqAn and 'Compile' the docs

$ mkdir development

$ cd development

$ git clone https://github.com/seqan/seqan.git

$ cd seqan/manual

$ make html

 

There you go, you can now edit the SeqAn manual and view the resulting HTML pages on your local machine (assuming you're not being daft and doing it on an AWS instance to ensure you get only the minimum dependencies like me).

 

Getting Paypal Identity token for Woocommerce

 

Paypal has changed the layout of the website dashboard since most of the 'how to' guides have been written so here is my updated one.

So, for woocommerce you may wish to setup a Paypal Identity token which helps to solve some of the IPN errors you may encounter. Especially those where you have two or more email addresses linked to your paypal account and woocommerce places the order on hold due producing the following error:


IPN Response is for another account: [email protected] Your email is [email protected]

Annoyingly I've not been able to resolve this in a sensible fashion, in this example here, [email protected] is the primary address with paypal, so why does it try to send the IPN response using my login email? Anyway...

You can't see your Paypal Identity token UNTIL you've activated Payment Data Transfer. 

To find the Paypal Identity token, log into paypal.

  • Click Profile (top right)
  • Click Profile and Settings (from the drop down box)
  • Click My Selling preferences (left menu)
  • Click Update on the right of the Website preferences option
  • Turn on both Auto Return and Payment Data Transfer
  • Click Save at the bottom of the page
  • This will return you to the previous menu page
  • Click Update on the right of the Website preferences option again to take you back into the previous option
  • Scroll down and beneath the Payment Data Transfer option you should see your token

Talk about faffy!

 

 

Scaleway - ARMv8

 

Martin Rusev at Anom.cx wrote a great analysis of the Scaleway ARMv7 and Digtial Ocean droplets some time ago (not sure exactly when but around 2015 from the github comment). Yesterday I received an email from Scaleway announcing their ARMv8 machines so I thought I would give one a go. Martin Rusev noted that against a DO droplet there was certainly a drop in performance with the ARMv7. So let's see how the v8 gets on.

I booted up a 2C ARMv8 with 2GB RAM as well as a 4C ARMv8 with 4GB RAM. It took around 10 minutes to get a console on one of these in the Paris DC. I would imagine that since the Amsterdam DC is out of stock of a lot of these they are getting quite a lot of demand.

CPU Test

To begin with I run the single core test, along with 2C and 4C (because 4C was run on Martin Rusev's test too).

Single Core

[email protected]:~# sysbench --test=cpu --cpu-max-prime=20000 run
sysbench 0.4.12: multi-threaded system evaluation benchmark

Running the test with following options:
Number of threads: 1

Doing CPU performance benchmark

Threads started!
Done.

Maximum prime number checked in CPU test: 20000

Test execution summary:
total time: 29.9082s
total number of events: 10000
total time taken by event execution: 29.9016
per-request statistics:
min: 2.94ms
avg: 2.99ms
max: 10.56ms
approx. 95 percentile: 3.02ms

Threads fairness:
events (avg/stddev): 10000.0000/0.00
execution time (avg/stddev): 29.9016/0.00

Dual Core

[email protected]:~# sysbench --test=cpu --cpu-max-prime=20000 run --num-threads=2

sysbench 0.4.12: multi-threaded system evaluation benchmark

Running the test with following options:
Number of threads: 2

Doing CPU performance benchmark

Threads started!
Done.

Maximum prime number checked in CPU test: 20000

Test execution summary:
total time: 14.9265s
total number of events: 10000
total time taken by event execution: 29.8405
per-request statistics:
min: 2.94ms
avg: 2.98ms
max: 3.42ms
approx. 95 percentile: 3.00ms

Threads fairness:
events (avg/stddev): 5000.0000/0.00
execution time (avg/stddev): 14.9203/0.00

Quad Core

[email protected]:~# sysbench --test=cpu --cpu-max-prime=20000 --num-threads=4 run
sysbench 0.4.12: multi-threaded system evaluation benchmark

Running the test with following options:
Number of threads: 4

Doing CPU performance benchmark

Threads started!
Done.

Maximum prime number checked in CPU test: 20000


Test execution summary:
total time: 14.9632s
total number of events: 10000
total time taken by event execution: 59.8098
per-request statistics:
min: 2.94ms
avg: 5.98ms
max: 20.55ms
approx. 95 percentile: 11.01ms

Threads fairness:
events (avg/stddev): 2500.0000/1.22
execution time (avg/stddev): 14.9525/0.01


ARMv8 4Core 4GB RAM

 

Running the test with following options:
Number of threads: 1

Doing CPU performance benchmark

Threads started!
Done.

Maximum prime number checked in CPU test: 20000


Test execution summary:
    total time:                          29.8729s
    total number of events:              10000
    total time taken by event execution: 29.8657
    per-request statistics:
         min:                                  2.96ms
         avg:                                  2.99ms
         max:                                  8.31ms
         approx.  95 percentile:               3.00ms

Threads fairness:
    events (avg/stddev):           10000.0000/0.00
    execution time (avg/stddev):   29.8657/0.00

 

[email protected]:~# sysbench --test=cpu --cpu-max-prime=20000 --num-threads=4 run
sysbench 0.4.12:  multi-threaded system evaluation benchmark

Running the test with following options:
Number of threads: 4

Doing CPU performance benchmark

Threads started!
Done.

Maximum prime number checked in CPU test: 20000


Test execution summary:
    total time:                          7.5198s
    total number of events:              10000
    total time taken by event execution: 30.0429
    per-request statistics:
         min:                                  2.94ms
         avg:                                  3.00ms
         max:                                 15.02ms
         approx.  95 percentile:               3.01ms

Threads fairness:
    events (avg/stddev):           2500.0000/5.79
    execution time (avg/stddev):   7.5107/0.00

 

I/O

[email protected]:~# sysbench --test=fileio --file-total-size=6G prepare
[email protected]:~# sysbench --test=fileio --file-total-size=6G --file-test-mode=rndrw --max-time=300 --max-requests=0 --file-extra-flags=direct run

Operations performed: 336060 Read, 224040 Write, 716822 Other = 1276922 Total
Read 5.1279Gb Written 3.4186Gb Total transferred 8.5464Gb (29.172Mb/sec)
1866.99 Requests/sec executed

Test execution summary:
total time: 300.0018s
total number of events: 560100
total time taken by event execution: 156.6031
per-request statistics:
min: 0.21ms
avg: 0.28ms
max: 10.57ms
approx. 95 percentile: 0.32ms

Threads fairness:
events (avg/stddev): 560100.0000/0.00
execution time (avg/stddev): 156.6031/0.00

ARMv8 4Core 4GB RAM

 Operations performed:  327880 Read, 218587 Write, 699392 Other = 1245859 Total
Read 5.0031Gb  Written 3.3354Gb  Total transferred 8.3384Gb  (28.462Mb/sec)
 1821.55 Requests/sec executed

Test execution summary:
    total time:                          300.0013s
    total number of events:              546467
    total time taken by event execution: 152.3080
    per-request statistics:
         min:                                  0.22ms
         avg:                                  0.28ms
         max:                                 17.58ms
         approx.  95 percentile:               0.34ms

Threads fairness:
    events (avg/stddev):           546467.0000/0.00
    execution time (avg/stddev):   152.3080/0.00


MySQL

mysql Ver 14.14 Distrib 5.7.18, for Linux (aarch64) using EditLine wrapper 

ARMv8 2Core 2GB RAM

[email protected]:~# sysbench --test=oltp --oltp-table-size=1000000 --mysql-db=benchmark --mysql-user=root --mysql-password=password123 prepare

[email protected]:~# sysbench --test=oltp --oltp-table-size=1000000 --mysql-db=benchmark --mysql-user=root --mysql-password=password123 --max-time=60 --oltp-read-only=on --max-requests=0 --num-threads=8 run

sysbench 0.4.12: multi-threaded system evaluation benchmark

No DB drivers specified, using mysql
Running the test with following options:
Number of threads: 8

Doing OLTP test.
Running mixed OLTP test
Doing read-only test
Using Special distribution (12 iterations, 1 pct of values are returned in 75 pct cases)
Using "BEGIN" for starting transactions
Using auto_inc on the id column
Threads started!
Time limit exceeded, exiting...
(last message repeated 7 times)
Done.

OLTP test statistics:
queries performed:
read: 276500
write: 0
other: 39500
total: 316000
transactions: 19750 (329.05 per sec.)
deadlocks: 0 (0.00 per sec.)
read/write requests: 276500 (4606.75 per sec.)
other operations: 39500 (658.11 per sec.)

Test execution summary:
total time: 60.0206s
total number of events: 19750
total time taken by event execution: 479.8237
per-request statistics:
min: 16.70ms
avg: 24.29ms
max: 84.53ms
approx. 95 percentile: 26.47ms

Threads fairness:
events (avg/stddev): 2468.7500/37.75
execution time (avg/stddev): 59.9780/0.01

ARMv8 4Core 4GB RAM

No DB drivers specified, using mysql
Running the test with following options:
Number of threads: 8

Doing OLTP test.
Running mixed OLTP test
Doing read-only test
Using Special distribution (12 iterations,  1 pct of values are returned in 75 pct cases)
Using "BEGIN" for starting transactions
Using auto_inc on the id column
Threads started!
Time limit exceeded, exiting...
(last message repeated 7 times)
Done.

OLTP test statistics:
    queries performed:
        read:                            537012
        write:                           0
        other:                           76716
        total:                           613728
    transactions:                        38358  (639.13 per sec.)
    deadlocks:                           0      (0.00 per sec.)
    read/write requests:                 537012 (8947.79 per sec.)
    other operations:                    76716  (1278.26 per sec.)

Test execution summary:
    total time:                          60.0161s
    total number of events:              38358
    total time taken by event execution: 479.5496
    per-request statistics:
         min:                                  5.95ms
         avg:                                 12.50ms
         max:                                 33.54ms
         approx.  95 percentile:              13.75ms

Threads fairness:
    events (avg/stddev):           4794.7500/46.71
    execution time (avg/stddev):   59.9437/0.00

 

Results ARMv8 against published ARMv7

 

 

CPU Single Core

Total Time (s)

CPU Quad Core

Total Time (s)

Disk I/O

Mb/sec

MySQL Transactions

per sec

MySQL read/write

requests per sec

ARMv7 685.512 171.3962 16.347 467.07 6539.00
ARMv8 2C 2GB RAM 29.9082 14.9632 29.172 329.05 4606.75
ARMv8 4C 4GB RAM 29.8729 7.5198 28.462 639.13 8947.79


So the CPU and Disk I/O show performance increases (the ARMv8 CPU performs the prime calculations faster than the DO droplet Martin Rusev used. However as you can see there is a performance decrease in the MySQL results of the 2 core ARMv8 vs the ARMv7. I would imagine this is because the 4C ARMv7 used has a performance advantage over the faster clockspeed but lower number of CPU cores of the ARMv8 2 core.

Conclusion

Well after spending a week migrating my production webserver from a 1GB Single-Core DO droplet to a 2GB Single-Core Linode VM last month I am now wondering if I it would be beneficial to go for one of Scaleways 4C ARMv8 with 8GB RAM which costs the same price as the Linode VM.

My only real concern for production is the support and stability as I'm new Scaleway and they don't have the best reviews yet. My own experience hasn't been smooth sailing with the brief interactions I have had with them. They locked my account I'd set up a few years ago and faffed around telling me I couldn't use that email account anymore and I'd have to use a new one. After escalating the support thread to a manager it was resolved. I'm sure these customer service type issues will iron themselves out in the future. 

In the meantime I am going to stick with this small ARMv8 and play around with it. Personally I really hope these micro dedicated servers become the norm. No more noisy neighbours and great performance for the price. 

 

 

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