Orthanc installation

[SBI]

Hello,

I just installed the Orthanc Linux version to CentOS6 but getting segmentation fault when uploading Dicom files to the URL. Also is there any Linux installation that I can use for reference. Greatly appreciate for any assistance.

[Sébastien Jodogne]

Hello,

There is currently no official package of Orthanc for CentOS.

I guess you have tried to copy and use some Orthanc binary coming from another Linux distribution (such as Fedora, Debian or Ubuntu) on CentOS. This approach is doomed to failure: In most cases, a Linux software will only run on the distribution it was compiled for.

You will have either to build Orthanc from source on CentOS, or use Docker. The instructions are available in the Orthanc Book:

https://orthanc.chu.ulg.ac.be/book/users/cookbook.html#obtaining-binaries

As a last remark, at the University Hospital of Liège, Orthanc is daily used on CentOS5. So, be sure you will get Orthanc working on your setup.

HTH,

Sébastien-

[John Roberts]

I have Orthanc running in Docker on a CentOS 7 system.  Once I had Docker working properly, it wasn't too difficult to get the Docker version working.

Getting Docker working on CentOS itself was the challenge.  There are two issues to address with Docker on CentOS/Fedora distributions:

1. There may be issues with Redhat's default configuration of storage for their native Docker distributions.  Perhaps the problem has been solved, but when I set up our system, the two solutions appeared to be
• Rebuild the host CentOS/Fedora machine and set up a dedicated disk partition for Docker use.
• Accept Redhat's default Docker storage configuration and possible problems under heavy load.  This was the approach we took, mainly because ours is a research use and we don't anticipate the sorts of system load that cause problems for Docker on Redhat in the default configuration.
2. Docker likes working with iptables and does not play well with firewalld.  I tried working with a hybrid system, keeping firewalld and fixing things when Docker would break it, but I eventually turned off firewalld and reverted to using iptables.

Once I had Docker playing nice with CentOS 7, it was very easy to get Orthanc up and running with Sebastien's Orthanc Docker images.

John.

[Gustavo Fernandez Guirland]

Hi John
Do you have any comments about performance and maintenance of Orthanc with Docker in Centos?
I have not deployed it using Docker, if I did it in Centos 7 virtualized. My question is about using it with Docker-Centos in production.
Do you think that for usual sysadmin tasks there are difficulties or critical points to consider comparing it with a virtualized classic installation?

Best regards

[Thibault Nélis]

On Thu, 2016-11-03 at 13:00 -0700, John Roberts wrote:
> Getting Docker working on CentOS itself was the challenge. There are
> two issues to address with Docker on CentOS/Fedora distributions:
> There may be issues with Redhat's default configuration of storage
> for their native Docker distributions. Perhaps the problem has been
> solved, but when I set up our system, the two solutions appeared to
> be

The devicemapper driver used to be the default, and they provide a
special oneshot service (run by default) to set up a logical volume for
it automatically. If you still want to use it (it may or may not still
be the fastest approach), all you need to do is leave enough space on a
volume group and everything works out-of-the-box.

Today however you don't need to do anything: the latest version of the
'docker' package uses overlayfs2 by default. This is backed by the
filesystem, not a block device, so no configuration necessary. I reckon
the 'docker-latest' package defaults to it as well.

> Accept Redhat's default Docker storage configuration and possible
> problems under heavy load. This was the approach we took, mainly
> because ours is a research use and we don't anticipate the sorts of
> system load that cause problems for Docker on Redhat in the default
> configuration.

This wasn't much of a default as it was a fallback so you could at
least test Docker even if you didn't leave it enough space for it to
store its image layers on the VG. It simply created loopback block
devices backed by files on the filesystem. The levels of indirection
are numerous (fs->loop->fs->vol as opposed to fs->vol) and it really
isn't recommended.

> Docker likes working with iptables and does not play well with
> firewalld. I tried working with a hybrid system, keeping firewalld
> and fixing things when Docker would break it, but I eventually turned
> off firewalld and reverted to using iptables.

It used to be that you had to make sure you started Docker after
firewalld, and although it was set up that way by default and I never
experienced any issues in the past, even that doesn't seem to be true
anymore (and indeed they stopped documenting it). I've just tested
restarting firewalld in a sandbox and everything seems to work fine
(container published ports are still accessible).

tl;dr I recommend using the latest point release. Everything has been
working seamlessly for us (at multiple production sites) so far. YMMV.

Best regards,
--
Thibault Nélis <t...@osimis.io>
Osimis

[Thibault Nélis]

On Tue, 2017-11-14 at 11:48 -0800, Gustavo Fernandez Guirland wrote:
> Hi John
>
> Do you have any comments about performance and maintenance of Orthanc

> with Docker about Centos?

With the default overlayfs2 driver performance will be impacted by the
backing filesystem. By default CentOS uses xfs whereas other
distributions might use ext4 or other filesystems, so you might want to
compare these.

Aside from that, performance out-of-the-box should be the same as
everything else (and of course you can still switch to another
filesystem).

When it comes to maintenance most major distributions are in healthy
competition nowadays. For everything one does better than the other,
the other does something else better than the first. You usually can't
go very wrong with either of them. I'd focus on support and other
factors.

> I have not deployed it using Docker, if Centos 7 Virtualized. My

> question is about using it with Docker-Centos in production.

We usually work in VMs, nothing special to report. Docker doesn't
exactly virtualize anything on top, it merely namespaces (isolates)
processes, so it's a very negligible overhead.

Regarding use in production, we've been using CentOS/RHEL in many
organisations for a long time. Along with Debian and Ubuntu, CentOS and
RHEL are the big ones. We never had a problem recommending them when
given the choice.

> Do you think that for the usual tasks of sysadmin there are
> difficulties or points to take into account comparing it with a
> virtualized classic installation?

For CentOS specifically, we've never observed any more or less
difficulties than any other OS.

There used to be some real issues (which we've never actually
encountered in practice, even in the past) but at least those discussed
in this thread are or appear to be fixed.

https://groups.google.com/forum/#!msg/orthanc-users/w-uPAknnRQc/naOlLAQ
uCgAJ

Hope this helps,

[John Roberts]

Thanks, Thibault, for all the useful information.  Docker for us was a means to an end and we more or less adapted to its initial constraints and didn't look back.  As I've gained more experience, I periodically return to streamline our usage and take advantage of the newer features that have been added to Docker since we started.

To answer Gustavo's questions, we don't really use Orthanc in a heavy production environment.  Our group is a small imaging research group that had a need for a good adaptable DICOM anonymizer and Orthanc fits the requirement very nicely.  In the US, we have regulatory requirements related to the storage of patient information that can be difficult and expensive to come into compliance with.  So the preferred route has been to anonymize research data.

Once other groups in our department with similar DICOM anonymization requirements heard about our success with Orthanc, we received requests to set up a number of different instances.  Docker has made it easy to spin up new instances, with adaptations as necessary to meet each particular group's requirements.  We currently have around a dozen Orthancs running under Docker on a single server.

To date, our busiest Orthanc might store at a maximum around 1500 different studies at rest, with a study or two added each week.  As you can see, we don't operate in a heavy load environment.

Orthanc has been great for our purposes, fitting seamlessly into our PACS network and giving the researchers a way to pretty quickly anonymize their data sets so that they can proceed with their research without worrying about a lot of the requirements that come with storing patient information. 

John.

[Gustavo Fernandez Guirland]

Thank you very much Thibault Nélis and John Roberts.

Your contributions have been very useful.
I commented that I am testing the 2 platforms, ie Virtualized on Centos7 with filesystem ext4 and I am starting to test Docker.
In my case, the objective is to cover 30 Public Hospitals throughout the country and therefore I am in the testing phase of the best alternative. There are about 1,300,000 patients and around 700,000 annual studies
I will tell you about my progress in this exchange that I found very productive

Best regards