Improving DCM4CHE performance

[Brandon Driscoll]

Hi,

I'm pretty new to DCM4CHE but have managed to get it installed and finally running error free with study based permissions controlling access to specific studies based on the calling AET based on updating permissions on series stored.

However, sending data to DCM4CHE seems abnormally slow.  On the same PC running the DCM4CHE instance  I have a ClearCanvas workstation hosting a separate AE title on a separate port.  

As a test from my PC in another part of the building I sent the same Image set (~ 2154 images ~90 Mb) via DICOM to both the DCM4CHE instance and the ClearCanvas one.

The set sent to ClearCanvas finished in under 1 minute, the set sent to DCM4CHE took 4 minutes.  Both systems have to copy and index the data and both are on the same PC so the same hardware is being used.  When retrieving data the ClearCanvas instance finished in almost exactly a minute.  From DCM4CHE it took only 45 seconds.

So it seems like the performance is really only bad sending to DCM4CHE.  As a test I also turned off update study permissions on series stored but it still took the same 4 minutes.

Are there places I can speed up the DCM4CHE performance?  I've turned all logging to "warn" and the output is only to FILE and not to CONSOLE.

Any suggestions would be appreciated.

Thanks,

Brandon

[Alvaro G. [andor]]

Hi Brandon,

What OS are you using?
Which database?
What storage system?
What client are you using for sending the images?

Thanks!

El 21/02/13 15:51, Brandon Driscoll escribi�:

>
> Are there places I can speed up the DCM4CHE performance? I've
> turned all logging to "warn" and the output is only to FILE and not
> to CONSOLE.

--
Alvaro "Andor" Gonzalez
an...@pierdelacabeza.com
GnuPG KeyID 0xa1e486f0

[Brandon Driscoll]

Workstation 

Win 7 x64

Using ClearCanvas workstation to send and recieve

Server 

Win 2008 Server x 64

Running both ClearCanvas workstation and DCM4CHE

Database is MySQL

I'm not sure what you mean by storage system..

On Thursday, February 21, 2013 1:17:00 PM UTC-5, andor wrote:

Hi Brandon,

What OS are you using?
Which database?
What storage system?
What client are you using for sending the images?

Thanks!

El 21/02/13 15:51, Brandon Driscoll escribi�:

[Brandon Driscoll]

I should note I see the same results if I just run straight storescu commands from the command line as well.

[Alvaro G. [andor]]

First of all, I may suppose Clearcanvas workstation is sending to both
targets in the same way, and there's no difference on multiframe,
compression, etc. In a 2195 images study you are wasting a lot of time
on DICOM transmission, blocks, headers... even if it only is 90Mb big.

Then, I have truly no idea on performance under Windows, but:

Check system monitor, see which process is using the most CPU while
receiving the DICOM studies.
Check disk activity, look if there is much more read or write activity
from the disk than expected for that 90Mb study.
Check also network activity to see if you find any discrepancies on
transmitted size.
Try to tune your MySQL a bit with one of the InnoDB oriented demo
config files, or even change it to a MySQL 5.6 or Percona 5.5. (Which
MySQL version are you using?).
Raise, in your MySQL, the size of your maximum package allowed, that
could help when your DCM4CHEE makes lots of operations at the same time...

On the storage, I was asking if you are storing your images the same
way on both systems, and what kind of disks you have and how are
configured.

Thanks :D

El 21/02/13 19:24, Brandon Driscoll escribi�:
> _Workstation _ Win 7 x64 Using ClearCanvas workstation to send and
> recieve
>
> _Server_ Win 2008 Server x 64 Running both ClearCanvas workstation

> and DCM4CHE Database is MySQL
>
> I'm not sure what you mean by storage system..
>
> On Thursday, February 21, 2013 1:17:00 PM UTC-5, andor wrote:
>
> Hi Brandon,
>
> What OS are you using? Which database? What storage system? What
> client are you using for sending the images?
>
> Thanks!
>

> El 21/02/13 15:51, Brandon Driscoll escribi�:

>>
>> Are there places I can speed up the DCM4CHE performance? I've
>> turned all logging to "warn" and the output is only to FILE and
>> not to CONSOLE.
>
>

> -- Alvaro "Andor" Gonzalez an...@pierdelacabeza.com <javascript:>
> GnuPG KeyID 0xa1e486f0
>
> -- You received this message because you are subscribed to the
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[Brandon Driscoll]

Thanks for the tips.  

I'm running MySQL server 5.5.28

I know that was a rather odd study to send, it was PET data so it's only 128x128 and thus pretty small compared to standard CT sets. I can test it with a CT set as well as I see the same problems there.

Both filestores are on the same PC but the ClearCanvas install is on the route C: drive which is just a standard ATA drive running NTFS as is the MySQL database for DCM4CHE.  The DCM4CHE image filestore is on a different drive (F:) which is actually a set of 4 much newer 2 TB SATA drives running a software RAID 5.  

I did some quick tests to check performance on the drives and though it appears the Raided drive (F) is a little slower to write to but it's not 4 times slower.

-----------------------------------------------------------------------

CrystalDiskMark 3.0.2 x64 (C) 2007-2013 hiyohiyo

                           Crystal Dew World : http://crystalmark.info/

-----------------------------------------------------------------------

* MB/s = 1,000,000 byte/s [SATA/300 = 300,000,000 byte/s]

           Sequential Read :    73.189 MB/s

          Sequential Write :    71.249 MB/s

         Random Read 512KB :    28.868 MB/s

        Random Write 512KB :    28.237 MB/s

    Random Read 4KB (QD=1) :     0.386 MB/s [    94.2 IOPS]

   Random Write 4KB (QD=1) :     0.765 MB/s [   186.7 IOPS]

   Random Read 4KB (QD=32) :     0.613 MB/s [   149.7 IOPS]

  Random Write 4KB (QD=32) :     0.771 MB/s [   188.3 IOPS]

  Test : 1000 MB [C: 77.4% (180.3/232.8 GB)] (x5)

  Date : 2013/02/22 9:32:56

    OS : Windows Server 2008 R2 Server Standard Edition (full installation) SP1 [6.1 Build 7601] (x64)

  

-----------------------------------------------------------------------

CrystalDiskMark 3.0.2 x64 (C) 2007-2013 hiyohiyo

                           Crystal Dew World : http://crystalmark.info/

-----------------------------------------------------------------------

* MB/s = 1,000,000 byte/s [SATA/300 = 300,000,000 byte/s]

           Sequential Read :   461.996 MB/s

          Sequential Write :    51.761 MB/s

         Random Read 512KB :    54.872 MB/s

        Random Write 512KB :    20.309 MB/s

    Random Read 4KB (QD=1) :     0.757 MB/s [   184.9 IOPS]

   Random Write 4KB (QD=1) :     0.422 MB/s [   102.9 IOPS]

   Random Read 4KB (QD=32) :     2.885 MB/s [   704.3 IOPS]

  Random Write 4KB (QD=32) :     0.746 MB/s [   182.2 IOPS]

  Test : 1000 MB [F: 1.9% (104.3/5589.0 GB)] (x5)

  Date : 2013/02/22 9:14:49

    OS : Windows Server 2008 R2 Server Standard Edition (full installation) SP1 [6.1 Build 7601] (x64)

On Thursday, February 21, 2013 1:44:47 PM UTC-5, andor wrote:

First of all, I may suppose Clearcanvas workstation is sending to both
targets in the same way, and there's no difference on multiframe,
compression, etc. In a 2195 images study you are wasting a lot of time
on DICOM transmission, blocks, headers... even if it only is 90Mb big.

Then, I have truly no idea on performance under Windows, but:

Check system monitor, see which process is using the most CPU while
receiving the DICOM studies.
Check disk activity, look if there is much more read or write activity
from the disk than expected for that 90Mb study.
Check also network activity to see if you find any discrepancies on
transmitted size.
Try to tune your MySQL a bit with one of the InnoDB oriented demo
config files, or even change it to a MySQL 5.6 or Percona 5.5. (Which
MySQL version are you using?).
Raise, in your MySQL, the size of your maximum package allowed, that
could help when your DCM4CHEE makes lots of operations at the same time...

On the storage, I was asking if you are storing your images the same
way on both systems, and what kind of disks you have and how are
configured.

Thanks :D

El 21/02/13 19:24, Brandon Driscoll escribi�:

> _Workstation _ Win 7 x64 Using ClearCanvas workstation to send and
> recieve
>
> _Server_ Win 2008 Server x 64 Running both ClearCanvas workstation
> and DCM4CHE Database is MySQL
>
> I'm not sure what you mean by storage system..
>
> On Thursday, February 21, 2013 1:17:00 PM UTC-5, andor wrote:
>
> Hi Brandon,
>
> What OS are you using? Which database? What storage system? What
> client are you using for sending the images?
>
> Thanks!
>

> El 21/02/13 15:51, Brandon Driscoll escribi�:

[Tiago Vieira]

Hello,

Can you give me some help on setting the study based permissions and controlling access like you did?

Thanks

Tiago

[bjpl]

The reason is MaximumOperationsInvoked in 

service:

QueryRetrieveScp

.

Try to increase value - 20 works for me very well :-)

[Lucy Zhang]

Hi Brandon

I am also trying to install dcm4che on windows server 2008 R2 but failed. Can you please let me know your software versions for dcm4che, mysql, jdk, jboss, java runtime? I would greatly appreciate your help!

Lucy