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Re: [Gnumed-devel] GNUmed (PostgreSQL) on USB thumbdrive benchmark

From: Dave Cramer
Subject: Re: [Gnumed-devel] GNUmed (PostgreSQL) on USB thumbdrive benchmark
Date: Fri, 26 Jun 2009 10:21:26 -0400

Postgresql is really not setup for this.

Remember it uses wal logs to write transaction logs before writing anything.

Berkley DB is designed for flash.


On Fri, Jun 26, 2009 at 10:14 AM, Sebastian Hilbert <address@hidden> wrote:
The idea of running PostgreSQL off a removable drive such as USB thumbdrive or
flash drive is appealing. However performance can sluggish. Who is to blame ?
Is it PostgreSQL that is too slow or poorly configured ? Is it GNUmed that
stresses the database too much ? Or is it the storage media that slows things
down ?

This clearly calls for some sort of benchmark. Google has little to offer on
how to benchmark perfomance. Representative or not we are going to benchmark a
few use cases.

1.) The storage media performance
2.) Real world installation performance
3.) Real world GNUmed client startup performance

- Storage media performance:
I am not aware of any GNU/Linux tool that can test read/write speed of both
harddisk and usb-thumbdrives. Sure there is hdparm but it only works for
harddisks. I reverted to HdTach and hdbench form CT magazine. One more word on
theoretical performance. I use USB 2.0 so performance should be in the area of
60MB/s. I have seen reports that USB-connected removable drives that have S-
ATA II storage media can reach throughput of up to 55MB/s.
have tested USB-thumbdrive perfomance with HD-Tach and the list top read
performance from 7,9 to 51,2 MB/s.

Let's see how the USB thumbdrives I bought for GNUmed compare:

Harddrive Seagate IDE 60GB native: avg. sequential read 22,9MB/s | random
access 15ms |
Thumbdrive Intenso 2GB native: avg. sequential read 23,7 MB/s | random access
0,4 ms | sequential write 6,4 MB/s
Thumbdrive Buffalo 2GB native: avg. sequential read 8,7 MB/s | random access
8,7ms | sequential write 2,4 MB/s
Thumbdrive Samsung 8GB native: avg sequential read 18MB/s | random access
1,7ms | sequential write 5,5 MB/s
Generic Business Card 1GB native: avg sequential read 16MB/s | sequential
write 2,9 MB/s

The bigger the file size the faster the drive.

Same on VMware:
Harddrive (S-ATA native) in VMware : avg. sequential read 317MB/s  | random
access 23ms
Thumbdrive Intenso 2GB on Vmware: avg. sequential read 8MB/s
Thumbdrive Buffalo 2GB on Vmware: avg. sequential read 4,5MB/s
Thumbdrive Samsung 8GB on Vmware: avg sequential read 5,7MB/s | random access

Conclusion: a) Performance in VMWare is let's say not what we need here. Good
to know since I guess a few people might try running it in a virtual machine.
Don't. If you must copy the stuff from the thumbdrive to the virtual harddrive
of the virtual machine. b) Native performance to the 2GB USB drive is nowhere
close to the theoretical maximum for USB 2.0 but comes close to the IDE
harddrive in this fairly old PC (1,6GHz AMD 2600+, 1,5GB RAM) c) The Buffalo
2GB thumbdrives is cheap but unusable performance wise.

- PortableApps Suite installation (355MB as many files)
Harddrive Seagate IDE 60GB native : avg write 1,6 MB/s = 1667KB/s (3 minutes
38 seconds)
Thumbdrive Intenso 2GB native : avg write 0,307 MB/s = 314KB/s (19 minutes 15
Thumbdrive Bufallo 2GB native :avg write 0,091 MB/s = 93KB/s (125 minutes)
Thumbdrive Samsung 8GB native:

Conclusion: a) The slower Buffalo stick has half the read speed compared to
the faster Intenso stick. The write speed for the 355MB written to the faster
drive is devastating at 0,3 MB/s compared to the harddisk installation at
1,6MB/s. The installation to the faster USB thumbdrive is 7x faster then to
the slower one.

- PortablePostgresql installation (171 MB as many files)
This involves unzipping 40,7MB to the USB drive. This is potentially limited
by the unzip operation and host-PC speed but relative speeds still apply.

Harddrive Seagate IDE 60GB native: avg write 2,85 MB/s = 2918KB/s (1minute)
Thumbdrive Intenso 2GB native: avg write 0,63 MB/s = 650 KB/s (4 minutes 25
Thumbdrive Bufallo 2GB native: avg write 0,05 MB/s = 59KB/s (49 minutes 15
Thumbdrive Samsung 8GB native: avg write  0,21 MB/s = 214KB/s (13 minutes 35

Unzipping the Postgresql Server to this the slower USB (Buffalo) drive took
12x longer than to the faster one (Intenso). The slower USB drive is 49x
slower then the harddrive. The 8GB Samsung drive doesn't come close to the
harddrive. This implies that bigger drives don't neccessarly have better

- PortableGNUmed client time to login window (first start uncached, second
start cached)
Harddrive Seagate IDE 60GB native: (4 sec , 3 sec
Thumbdrive Intenso 2GB native: (5 sec, 5 sec )
Thumbdrive Bufallo 2GB native: (8 sec, 6 sec )
Thumbdrive Samsung 8GB native: (2min 29 sec, 1min 30 sec)

- PortableGNUmed client time from login window to first window (first login,
second login)
Note that both client and server are running off the same drive. For the
second login times are shorter since much data is cached.

Harddrive Seagate IDE 60GB native: (17 sec , 10 sec )
Thumbdrive Intenso 2GB native: (54 sec ,  21 sec )
Thumbdrive Bufallo 2GB native: ( 2 min 41 ,  59 sec )
Thumbdrive Samsung 8GB native: (2min 22 sec, 1min 38 sec )

conclusion: The Intenso drive is the clear winner. The Buffalo and Samsung
drives have disappointing performance. The startup performance is interesting
but the real performance of the database can only be measured during heavy sql

- Pushing a 12 MB document into the database
Harddrive Seagate IDE 60GB native: 30 sec
Thumbdrive Intenso 2GB native: 5 minutes 1 sec
Thumbdrive Bufallo 2GB native: 15 minutes 30 sec
Thumbdrive Samsung 8GB native: 32 minutes sec

The results are somewhat helpful to get a feeling for the database speed. Note
that even for the harddrive it takes 7x its drive speed to complete the task.
Be aware that I cannot say if these results are reproducable.

- Retrieving a 12 MB document from the database
Harddrive Seagate IDE 60GB native: 5 sec
Thumbdrive Intenso 2GB native: 12 sec
Thumbdrive Bufallo 2GB native: 12 sec
Thumbdrive Samsung 8GB native: 1 min 11 sec

Conclusions: In theory the user oriented performance should be identical
between the USB thumbdrive and the harddisk. Unfortunately it is not always
the case. If you can make sure you get a decent USB thumbdrive. The 32GB OCZ
Rally2 is fairly usable at 30MB/s sequential read and 22MB/s sequential write
performance. But be aware that the Corsair Flash Voyager while not bad at all
comes in second at 22MB/s read and 10MB/sec write performance. There is a
catch. A huge difference exists between the sequential read/write values and
the random read/write vaues. According to the random read
performance is 6MB/s and the write performance is 3MB/s. Those are the values
you are looking for.

Only the best USB thumbdrives come close to the el-cheapo IDE harddisk I used
for testing. This is really disappointing since the first batch of USB drives
I ordered for GNUmed is really only useful as storage media. I had to order a
second batch. If you intend to use one of these in production for GNUmed you
should really be ready to spend the $79 for an adequate 32GB USB thumbdrive.
If you wanna go cheap make you can go with something like the 2GB Intenso
since it gives you acceptable performance.

The road ahead:
None of the storage media I had available really come close to a real
harrddrive. Options to pursue in the future are flash media, solid state
drives and external harddrives. External legacy harddrives are error prone due
to many moving parts. Flash or SSD might be a way out.

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