Hello Everyone,
We are fortunate to have Matthew Brett coming through York in January and
he will be giving a talk 4pm, 5th January at YNiC. Details to follow.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hi all,
This Friday evening from 9pm we will be upgrading several parts of key
infrastructure at YNiC. During the work no YNiC services will be
available. We expect the maintenance to be completed by the early hours
of Saturday morning.
Thanks, Paul.
--
Paul Elliott, UNIX Systems Administrator
York Neuroimaging Centre (YNiC), University of York
Hello All,
We have a project presentation by David O'connor this week. He will
present his project 'Exploring the impact of environmental factors on
impulsive choice and impulsive action'.
The presentation will be at YNiC.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hi all,
Those of you who use NAF or the python-megdata module may have noticed
that the online documentation has been unavailable for a couple of weeks.
For technical reasons, we've had to move the location of the
documentation. This can now be found at:
https://www.ynic.york.ac.uk/code-docs/
Please update any bookmarks or other references to the old URL
(https://vcs.ynic.york.ac.uk/docs)
Sorry for the inconvenience,
Mark
--
Mark Hymers, Lecturer in Neuroimaging Methods
York NeuroImaging Centre and Department of Psychology
University of York, UK
Please note that my email address is: mark.hymers(a)ynic.york.ac.uk
Responses to messages sent to other addresses may be delayed
Dear All,
We are not aware of anyone needing Presentation software and we are
therefore planning to discontinue with providing it from August 2017
onwards.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello Everyone,
This one is important. In recent weeks we have found that safety screening
forms and consent forms are not being returned appropriately to ynic in all
cases. That is, the personal information on these documents is not being
kept confidential.
Please ensure that after scanning has finished, participant's forms are
returned to YNiC reception. You MUST either hand the forms personally to a
member of YNiC staff or place the forms in the secure gray post-box behind
the reception desk.
During the period of time you are responsible for the forms do not leave
them in open site anywhere in the building and do note take them away from
the building.
Thank you
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello All,
We've had reports of intermittent loss of access to some files and folders.
We are investigating. We may have to reboot some servers controlling our
storage arrays in the near future without notice. More to follow.
Bw
Tony
Dear all,
We have made a small change to the YNiC cluster configuration.
Until now, each cluster job could use as much memory as they wanted.
This has been known to cause problems for users when they submit jobs
which require a large amount of RAM. If multiple jobs which require
large amounts of RAM are put onto the same machine, the jobs may run out
of memory. More problematically, it was sometimes the case that jobs
which did not require much RAM were the ones which failed.
To prevent this, we have added a default RAM limitation to the cluster.
Each "slot" is allocated 8G by default. If the job uses more than this,
it will be killed.
Jobs which require more RAM can still be run on the cluster. To do
this, you will simply need to tell the cluster how much memory to
reserve for your job - this will prevent your job from running out of
RAM by reserving enough for you. This can be done using the -l
h_vmem=xxG argument to the qsub command. We have documented this on the
wiki at:
https://www.ynic.york.ac.uk/docs/ITPages/IT/ClusterScripts
under the "Resource Limitations" section.
We estimate that this will not affect many users. For anybody who is
affected and are using qsub directly, the instructions above provide
information on how to request more RAM to be made available. If you are
find that you are getting memory allocation errors when using any of the
YNiC provided cluster commands (clusterFeat, clusterR, clusterMatlab,
clusterReconAll), or when using NAF, please contact
it-support(a)ynic.york.ac.uk and we will make sure that we adapt the
scripts to use the correct arguments with the qsub command.
If you have any questions, please contact it-support(a)ynic.york.ac.uk
Thanks,
Mark
--
Mark Hymers, Lecturer in Neuroimaging Methods
York NeuroImaging Centre and Department of Psychology
University of York, UK
Please note that my email address is: mark.hymers(a)ynic.york.ac.uk
Responses to messages sent to other addresses may be delayed
Hello All,
A gentle reminder that we mechanisms in place to allow you to provide MRI
images to those participants that request them. Please use this process
rather than printing out 'pictures' of brains.
Many thanks
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Many of you will be aware that we have recently experienced a few
hardware failures on the YNiC computing cluster. We have now escalated
these issues and the manufacturer has committed to attend on site to
attempt to resolve the existing issues. Without being too technical,
this process is essentially an overhaul of the current cluster and
requires two engineers.
Obviously, we are doing out utmost to get your cluster up and running
again but, considering the scale of the job, please be patient. We will
keep you updated.
Thanks,
--
André
************************************************************************
André Gouws
York Neuroimaging Centre
University of York
The Biocentre
York Science Park
Heslington
YO10 5NY
Tel: +44 (0) 1904 435327
Fax: +44 (0) 1904 435356
Dear All,
We have a system for providing CDs at YNiC. However, such is the number of
requests we have to deal with, we now need to rethink how to provide the
anatomical scan data to participants. What’s even more frustrating, is
that although we have a system that alerts participants that their CD is
ready, 58 remain uncollected. We are therefore being asked to allocate
considerable resource to generating CDs that the participants subsequently
have little or no interest in.
Rethink: Moving forward, we will allow researchers to create data CDs for
their participants. The researcher will need to provide their own CD and
execute a script. The script, 'Create subject CD', can be run from the
'Applications' menu under 'YNiC Utilities'. Please follow the instructions
given by the script and note that you (1) have to have the permission of
the participant (2) make sure that the participant receives the CD [you may
want to record their signature] and (3) you record who you have sent CDs to.
Andre is also putting a webpage together to give guidance.
https://www.ynic.york.ac.uk/information/mri/MakeASubjectCD
Requests to YNiC for data CDs will no longer be met after 1/11/2016.
Thank you
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear Users,
Today we will be graced with the presence of Dr Helen Nutall from the
Psychology Department at Lancaster University. She will be giving a talk
entitled:
"Sensorimotor processing in perception of degraded speech"
The talk will be held in room B020 in the Psycholgy Department, at 4pm.
All are welcome and refreshments will be served afterwards.
Best,
Junior
--
Junior Whiteley
York Neuroimaging Centre
junior.whiteley(a)ynic.york.ac.uk
Hello All,
It has been noted that investigators are sometimes asking potential
participants screening questions in reception and other areas where
confidential answers may be overheard. Please make appropriate
arrangements to ensure the confidentiality of your participants responses.
Many thanks
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello everyone,
To avoid confusion for those recently joining the ynic user community,
Thursday seminars are announced, usually early in the week. This week there
is no seminar.
Best wishes
Tony
Hi all,
At the following times during this term, YNiC open plan will be closed
for teaching.
Please note that if any YNiC open plan computers have been left logged
on at the start of the teaching sessions, they will be automatically
logged out.
Week 2:
* Tuesday 4th October 1200-1600
* Thursday 6th October 0900-1300
Week 3:
* Monday 10th October 1200-1600
Week 4:
* Monday 17th October: 1200-1600
Week 7:
* Monday 7th November: 1200-1600
Week 9:
* Monday 21st November: 1200-1600
Timings for the Spring term will be sent around in December.
Thanks,
Mark
--
Mark Hymers, Lecturer in Neuroimaging Methods
York NeuroImaging Centre and Department of Psychology
University of York, UK
Please note that my email address is: mark.hymers(a)ynic.york.ac.uk
Responses to messages sent to other addresses may be delayed
Dear All,
Many of the routine updates to our IT provision have been successfully
completed. We will complete the remaining jobs next week. These involve
the stimulus PCs.
The cluster is currently down. This is an issue that is unrelated to the
routine updates and is being dealt with by HP engineers.
Thanks, Paul, for installing these important updates.
As I wrote previously, please report any issues that arise in your use of
the IT system here (other than the cluster issue, which we know about).
This will help us resolve them speedily.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear All,
A few things to update you on that will be occurring at YNiC over the next
couple of weeks.
During the weeks commencing 5th September and 12th September we will be
performing essential IT maintenance. This is the normal annual procedure
to install updates (as specified below). It will impact on access to the
centre and its IT provision as follows.
1) We will be closing the centre from 5pm, Monday 6th September through to
9am, Wednesday 7th September. There will be no access to computing during
this period.
2) For the week commencing 12th September we will have a ‘soft’ closure.
You may come to the centre, but your work may be disrupted by maintenance
of hardware and software. It may also be a period during which we have to
close the centre at short notice.
We should be able to honour scanner bookings during the fortnight, but
again there may be instances when we have to cancel them at short notice.
OVERVIEW OF UPDATES:
We will be updating our desktop and stimulus PC images. This will mean
that software versions will change. We make every effort to check that
these have minimal impact on researchers’ ability to run their analysis and
stimulus code. However, once our updates are made please check your use of
software to ensure it still works.
Thank you for your patience
Tony
--
Antony Morland, PhD
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear Colleagues
I have just, 7.30pm on the 31st, packed my last box of papers and am
about to vacate my office.
Tomorrow, Professor Tony Morland will become the new Director of the
York Neuroimaging Centre and Professor Alex Wade will be the Deputy Director
I am sure you will join me in welcoming them to their new roles and in
wishing them a very successful future.
I have had a fantastic time as Director for the last 13 years and 9
months. I am moving into new roles to work on newly funded research into
molecular imaging in humans and the associated hardware to accomplish it.
I could not have done this job with out the staff at YNiC and I would
like to publicly acknowledge my sincere thanks for them being such
wonderful colleagues.
We also could not have done this without you - the Users. You have made
it tremendously exciting. A lot of science has been carried out. Over
300 projects with over 700 Users, have scanned over 4000 people.
Thank you
I am not going far - CHyM and the new clinical imaging facilities in
York and Leeds, so I hope to meet you all from time to time.
best wishes
Gary
--
---------------
Gary Green
York Neuroimaging Centre &
Centre for Hyperpolarisation in Magnetic Resonance
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5NY
tel +44 (0) 1904 435349
fax +44 (0) 1904 435356
mobile +44 (0) 788 191 3004
http://www.ynic.york.ac.ukhttp://www.york.ac.uk/chym/https://www.ynic.york.ac.uk/about-us/people/ggrg
If you're wondering why the cluster is currently unavailable, please see
Paul's message below.
-------- Forwarded Message --------
Subject: [Staff] Compute blade maintenance
Date: Tue, 30 Aug 2016 14:12:09 +0100
From: Paul Elliott <Paul.Elliott(a)ynic.york.ac.uk>
To: undisclosed
Hi all,
I'll shortly be disabling the queues for the cluster so that I can work
with HP to resolve the issues with our compute blades after a further
blade failure overnight. If anybody has any urgent jobs for the cluster
then please let me know and I'll try and work around your jobs.
Thanks, Paul.
--
Paul Elliott, UNIX Systems Administrator
York Neuroimaging Centre (YNiC), University of York
_______________________________________________
Staff mailing list
Staff(a)ynic.york.ac.uk
https://www.ynic.york.ac.uk/mailman/listinfo/staff
Hello All,
You may have already been alerted to this, but I wanted to let you know
that the overhead lighting at YNiC is being replaced today. It is not too
disruptive - I am finding it straightforward to work in open plan.
However, there may be occasions when you will be asked to move so the two
fitters can gain access to a specific ceiling panel.
Best wishes
Tony
--
Antony Morland, PhD
Head of the Centre for Neuroscience, Hull-York Medical School.
Deputy Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear colleagues
I am having a clear out before I migrate to another place.
The table in my room has piles of books that are now probably not going
to be read by me again. Feel free to help yourselves.
The ones on my shelf I might read again, or need, so please leave these
for now.
Gary
--
---------------
Gary Green
York Neuroimaging Centre &
Centre for Hyperpolarisation in Magnetic Resonance
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5NY
tel +44 (0) 1904 435349
fax +44 (0) 1904 435356
mobile +44 (0) 788 191 3004
http://www.ynic.york.ac.ukhttp://www.york.ac.uk/chym/https://www.ynic.york.ac.uk/about-us/people/ggrg
Hello All,
David Pitcher will be giving a presentation on two proposed projects; one
TMS and one fMRI.
Best wishes
Tony
--
Antony Morland, PhD
Head of the Centre for Neuroscience, Hull-York Medical School.
Deputy Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear all,
Following the cluster failures on Friday we have attempted to replicate
the issue over the weekend by loading up all the compute nodes within
the cluster to the highest level possible. So far we have not seen any
further failures. As such we will shortly return the cluster to service
but as the root cause of the original failures are still unknown we may
see further sudden and unexpected losses of service. If you submit jobs
to the cluster please keep careful track of which jobs you have
submitted and ensure that you validate your jobs have run successfully
before using any of the output.
HP Enterprise (who manufacture and support our hardware) are currently
investigating the cause of the failures and we hope to have a full
resolution as quickly as possible.
Best wishes,
Paul.
--
Paul Elliott, UNIX Systems Administrator
York Neuroimaging Centre (YNiC), University of York
Hello All,
We are having intermittent faults on some of the blades that make up our
cluster. Given that jobs submitted can fail and we also want to ensure no
damage is done to the cluster, we are taking it off line for the time
being. I am very sorry for inconveniences that may arise.
Best wishes
Tony
--
Antony Morland, PhD
Head of the Centre for Neuroscience, Hull-York Medical School.
Deputy Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
