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firewall and Leginon and other problems
Added by Anonymous almost 20 years ago
We've run into a couple of problems with setting up
Leginon in Leeds. I've confirmed that the security
arrangements for the Tecnai PC will complicate the
choice of configuration. The Tecnai PC is currently
behind its own firewall (a Linux PC). (Leeds
University campus itself has a firewall - although
this shouldn't be a problem unless we want to be able
to control the microscope off campus or access the
Leginon web site.) It might be possible to have the
Leginon/ Linux PC behind the firewall together with
the microscope PC which could be simpler; but it may
be limiting in terms of location of the Leginon PC.
So it looks like the Leginon PC will have to talk to
the microscope PC through the microscope PC firewall.
Do you know what ports we have to allow through the
firewall? (I'm not sure if we are going to allow
network traffic through for particular ports or IP
addresses or have both types of restriction in place.
The problem with IP addresses is that we will probably
have initially a Leginon laptop PC which will go back
to using DHCP and so have a dynamic IP address.) The
other problem is that I've been told by Neil Ranson
that FEI require us to obtain express permission to
install software on the microscope PC to avoid
invalidating the warranty. I'm waiting for the
contact person to reply to my request for permission
to install Leginon on the microscope PC.
At the moment, I'm also trying to set up the Tecnai
simulator together with Leginon on another Windows PC
for testing purposes. There seem to be some
installation problems with this - probably due to the
Tecnai software. The pyscope installer complains
about a missing CAMC4 library and the notes mention
that CAMC4.EXE needs to be installed for the Tietz
camera.
The Tecnai Software CDs include a CAMC.EXE (not a
CAMC4.EXE) which does not install (and I'm going to
contact FEI about various problems with the Tecnai
CDs). This is a bit unfortunate as we actually have a
Gatan camera, not a Tietz camera, although I suppose
all of the libraries have to be there anyway,
William
Replies (4)
- Added by Anonymous almost 20 years ago
Since you have a Gatan camera, you can ignore the error about CAMC4.
-Christian
- Added by Anonymous over 19 years ago
Okay, thanks. Unfortunately, we still haven't got
through the bureaucracy at FEI so we haven't obtained
permission to install Leginon on the microscope PC.
I've got a bit further with setting up a simulator PC.
(I discovered that I was missing some important CDs,
including Gatan's CDs with Digital Micrograph.) At
the moment I have Leginon running on the laptop sort
of talking to the Leginon client running on the
simulator PC (which is started up after FEI's
temserver for the microscope simulator, the Tecnai
user interface and DM). I went into the "Manual"
application and attempted to acquire an image.
Everything just hangs though - I'm not sure if
something is missing or if the problem is that the
simulator PC is too slow and does not have enough
memory. On one attempt, the Leginon client crashed,
due to running out of memory, and Leginon on the
laptop gave errors on the attempts to acquire images;
but usually what happens is that Leginon/ Manual just
sits there waiting for the image to come in. (In the
attempt that crashed with memory problems, I had tried
to increase the logging level in the Leginon client
from Settings->Logging.) DM on the simulator PC
appears to hang (and does not refresh properly). I'm
not sure if I have installed the correct software from
FEI and Gatan to run a simulator (or if I have
configured it correctly). I installed the Tecnai
simulator from FEI,additional Tecnai software (from
the CDs for the real microscope, a Tecnai F20) and
Gatan Microscopy Suite. GMS was installed as the
"on-line" version (rather than the offline version) on
the simulator PC - with options for the Ultrascan
4000SP camera and acquisition device Windows/
firewire, I think, which may not be correct. Also,
the Leginon documentation and/or instrument database
refer to a Gatan simulator rather than a Tecnai
simulator, so I'm not sure I have the correct
simulator software,
William
- Added by Jim Pulokas over 19 years ago
William,
While Leginon is running, several ports are used
when they are needed.
Any port between 49152 and 65535 could be used by
Leginon. This range
is defined as "dynamic/private" by the organization
that decides on port
assignments
(see http://www.iana.org/assignments/port-numbers )
We allow Leginon to use any available port in that
range. Those ports
are used for communication between Leginon nodes.
It is also important
to open ports for MySQL so that all nodes can access
the server. The
numbers used by MySQL can probably be found in the
mysql config files or
also in the web page I mentioned.
It may also be necessary to open ports for NFS if
leginon will be
storing files on a remote system.
Let me know if you need more info on this.
Jim
- Added by Anonymous over 19 years ago
Thanks. By the way, is anybody using off-campus
access to Leginon? I think the Scripps campus has a
firewall. The reason I am asking is that John Trinick
is interested in allowing people to use Leginon
off-campus to control the microscope (for working
from home and also for a demonstration at a meeting in
Sheffield, in June, I think). A problem with this is
that this means going through two firewalls - the
Leeds University campus firewall and the local
firewall (which entails getting permission from two
sets of people - one set is basically in our group,
fortunately). The options for the campus firewall
appear to be to allow network traffic through for the
specified ports or basically allow everything for the
microscope PC (or possibly another PC that
communicates with it) - what Leeds University ISS
calls JIPS access - or possibly have VPN access to the
microscope PC (or another on-campus PC that talks to
it). There will be a certain amount of bureaucracy
and paperwork for any of these options. My guess is
that JIPS access is the least secure option but it
will probably be less of a technical headache to deal
with subsequently,
William