Hi all
Here's my list of things that I think still need doing
- update start dir of jupyter server, at least in azure, but best in VM as well to be uniform.
- tagging of CIL, as I find it dangerous to let update_VM.sh get the very latest. But this is a risk for CIL, not for SIRF, so I'll let CCpi make the call. In any case, we cannot wait anymore.
- I see minor changes in SIRF, SIRF-SuperBuild and STIR since the last tags. I don't think these changes are required for now, so we can create the Azure machine without it.
- Optional: adjust Azure scripts to not download data, but attach a different disk where this has been done. Somehow link ~/data to a dir on the attached disk. (Ben and I talked about copying SIRF/data to that disk and linking that, to avoid running out of disk space, but I suggest to leave that.) As it seems that data sizes are smaller than anticipated, I think we can leave this, but just attach an empty (ideally already formatted) disk.
- VM tests (still needed?) and updating of https://www.ccppetmr.ac.uk/node/200
- Azure build
SIRF-exercises: to be done this week
- more synergistic notebooks (Richard)
- probably extra data (Richard)
The SIRF-exercises update seems to mean that we'll need to update all Azure machines afterwards. So be it. (caveat for the CIL master branches).
Did I forget anything? Can we please keep everyone informed of any progress/stumbling blocks?
Kris
> -----Original Message-----
> From: Thielemans, Kris
> Sent: 29 October 2019 10:44
> To: Edoardo Pasca - UKRI STFC <[log in to unmask]>; 'CCP-PETMR-
> [log in to unmask] <[log in to unmask]>; 'Mailing list
> for software developers of the CCP in Tomographic Imaging' <CCPI-
> [log in to unmask]>
> Subject: RE: remaining items for the training school
>
> Thanks
>
> Pretty much everyone in CCP PETMR able to test this VM is at the conference
> now. You'll just have to make the call if this VM is suitable to distribute
> (allowing for further updates). I suggest you accept it.
>
> > Start jupyter for SIRF-Exercises
> > jupyter notebook
> >
> > Start jupyter for CIL-Demos
> > jupyter notebook --notebook-dir=~/devel/CIL-Demos
> >
>
> This won't work on Azure. It implies people will have to log in. Best to start the
> jupyter server in ~/devel then. No idea where that sits (probably in different
> places for the VM and Azure and indeed docker).
>
> Kris
>
>
> > -----Original Message-----
> > From: Edoardo Pasca - UKRI STFC <[log in to unmask]>
> > Sent: 29 October 2019 10:25
> > To: Thielemans, Kris <[log in to unmask]>; 'CCP-PETMR-
> > [log in to unmask] <[log in to unmask]>; 'Mailing
> list
> > for software developers of the CCP in Tomographic Imaging' <CCPI-
> > [log in to unmask]>
> > Subject: RE: remaining items for the training school
> >
> > Hi,
> >
> > The mechanism to download CIL data is analogous to that for SIRF data.
> > As a matter of facts it's the same script.
> >
> > To download you just issue
> > cd ~/devel/CIL-Demos
> > bash scripts/download_data.sh
> >
> > The size is about 120 Mb.
> > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
> > c
> >
> cppetmr.ac.uk%2Fnode%2F200&data=02%7C01%7C%7C02d4865824d04
> > dbca53d08d75c5a45d6%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0
> >
> %7C637079415092445482&sdata=dv%2F3NnmEscl%2FppJervYtWIxfau2
> > Z1lFP%2BrHs81E%2Fn4M%3D&reserved=0
> >
> > In the CCPPETMR_VM symposium2019 branch I added to UPDATE.sh the lines
> > to clone or update the CIL-Demos repo.
> >
> >
> https://github.com/CCPPETMR/CCPPETMR_VM/blob/symposium2019/scripts
> > /UPDATE.sh#L258L265
> >
> > I built a new VM. What I did is run the vagrant script (which runs
> > UPDATE.sh) and then run update_VM.sh which for some reason builds
> something more.
> >
> > I uploaded the newest VM at this link.
> >
> > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fedosi
> > l.n
> >
> et%2Fstfc%2Fsirf%2FSIRF_CIL_Symposium_rc2_20191028.ova&data=02
> >
> %7C01%7C%7C02d4865824d04dbca53d08d75c5a45d6%7C1faf88fea9984c5b
> >
> 93c9210a11d9a5c2%7C0%7C0%7C637079415092445482&sdata=YOE%2
> >
> FWUpQf65XJ%2BcQwfE0Tca%2FIeCGwo4myNNITKhHOMo%3D&reserve
> > d=0
> >
> > Run ctest and currently testing the notebooks (together with Evgueni).
> > Any comments welcome
> >
> > Login password: virtual
> > Jupyter password: virtual%1
> >
> > Start jupyter for SIRF-Exercises
> > jupyter notebook
> >
> > Start jupyter for CIL-Demos
> > jupyter notebook --notebook-dir=~/devel/CIL-Demos
> >
> > Edo
> >
> >
> > -----Original Message-----
> > From: Thielemans, Kris <[log in to unmask]>
> > Sent: 29 October 2019 07:49
> > To: Pasca, Edoardo (STFC,RAL,SC) <[log in to unmask]>;
> > 'CCP-PETMR- [log in to unmask] <CCP-PETMR-
> [log in to unmask]>;
> > 'Mailing list for software developers of the CCP in Tomographic
> > Imaging' <CCPI- [log in to unmask]>
> > Subject: RE: remaining items for the training school
> >
> > Hi all
> >
> > Ben needs to download the data onto the Azure clients.
> > - Edo, can you give him instructions on how to get the CIL data? How big is it?
> > - Richard, the SIRF download_*.sh hasn't been updated. I guess we need
> > Johannes data (but "fixed" for geometry). Where is that? Any other data?
> > - Johannes, the MR data currently already downloaded sits on dropbox.
> > Ben told me this throttles downloads which can give him trouble. Is
> > this data suitable for upload on zenodo? If so, can you still do this
> > today? (sorry, he'd asked me last week but I forgot).
> >
> >
> > Unfortunately, I guess we've missed the boat on making the VM
> > available for most of the participants before Chester but we have to
> > get it ready ASAP anyway. Also, it'll therefore be very important to
> > put it on USB sticks. We should have the data on there as well. That needs a
> bit more thought I guess.
> > Edo/Evgueni, will you be able to take care of this? (should be done
> > with the final version of course). I have a bag of ~20 USB sticks that
> > we can use to duplicate.
> >
> > Any more software tagging?
> >
> > Kris
> >
> >
> > > -----Original Message-----
> > > From: Thielemans, Kris
> > > Sent: 28 October 2019 14:24
> > > To: Edoardo Pasca - UKRI STFC <[log in to unmask]>; CCP-PETMR-
> > > [log in to unmask]; Mailing list for software developers of the
> > > CCP in Tomographic Imaging <[log in to unmask]>
> > > Subject: RE: remaining items for the training school
> > >
> > > Ben needs to start building tomorrow lunch time. All tagging and
> > > testing needs to be done by then. I'll allow changes to the
> > > exercises only after that :-)
> > >
> > > Kris
> > >
> > > PS: anyone testing the VM?
> > > > -----Original Message-----
> > > > From: Edoardo Pasca - UKRI STFC <[log in to unmask]>
> > > > Sent: 28 October 2019 13:28
> > > > To: [log in to unmask]; Thielemans, Kris
> > > > <[log in to unmask]>; Mailing list for software developers of
> > > > the CCP in Tomographic Imaging <[log in to unmask]>
> > > > Subject: Re: remaining items for the training school
> > > >
> > > > I need to tag all the CCPi repos.
> > > >
> > > >
> > > > You're saying we need to do it by tomorrow?
> > > >
> > > >
> > > > I think I'll have the PDHG + regularisation (possibly with MR
> > > > prior) from CIL and Johannes dataset. Or at least that was what I
> > > > was doing some
> > > time ago.
> > > >
> > > >
> > > > The GD + MR + regularisation still exists.
> > > > https://github.com/CCPPETMR/SIRF-
> > > > Exercises/blob/cil/notebooks/MR/Grappa%20and%20CIL.ipynb
> > > >
> > > >
> > > > Edo
> > > >
> > > > ________________________________
> > > > From: CCP-PETMR Developers list <[log in to unmask]>
> > > on
> > > > behalf of Thielemans, Kris <[log in to unmask]>
> > > > Sent: Monday, October 28, 2019 12:41:23 PM
> > > > To: [log in to unmask]
> > > > Subject: remaining items for the training school
> > > >
> > > > Hi all
> > > >
> > > > Ben needs to build the Azure machine. There are some complications
> > > > regarding the number of machines that we require, so this is going
> > > > to take longer than anticipated. I don't know quite how long he
> > > > needs yet, but most likely will have to build Tuesday afternoon at
> > > > the very
> > latest.
> > > >
> > > > We also need the VM. Edo has just made a test VM available for testing.
> > > > Please do this ASAP as we need to give this to participants ASAP.
> > > >
> > > > So....we are running out-of-time.
> > > >
> > > > The update mechanism is available for some small fixes, but major
> > > > changes are dangerous now of course. Note that the update
> > > > mechanism pulls latest release of the SuperBuild but the latest
> > > > master of the notebooks. Also, running the update mechanism on 50
> > > > azure nodes won't be a lot of fun (unless Ben knows a trick). We
> > > > can ask the participants to update before they start, but that should be
> small.
> > > >
> > > > Can you please let both lists know what you still hope to include?
> > > > I will spend most of my time tomorrow to look at the PET demos and
> > > > hope to get some synergistic things going.
> > > >
> > > > Is the CG and smooth prior for MR still on the cards? It'd have to
> > > > be real
> > > soon.
> > > > If not, don't worry.
> > > >
> > > > Kris
> > > >
> > > >
> > > > ________________________________
> > > >
> > > > To unsubscribe from the CCP-PETMR-DEVEL list, click the following link:
> > > >
> > >
> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
> > > > ji
> > > > scmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP-PETMR-
> > > >
> > >
> >
> DEVEL%26A%3D1&data=02%7C01%7C%7C1f73c78b4ee24a3fb6f108d75
> > > >
> > >
> >
> baa9c51%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637078660
> > > >
> > >
> >
> 632824665&sdata=IsDdwaQwZIUvgQbNhH2rowBjDWisLPVPWL0g8F4qr
> > > > 6k%3D&reserved=0
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