Hi Edward. You are probably right.
What you refer to is the latest wiki page I am "playing with". http://wiki.nmr-relax.com/Install_relax_cloud.sagemath.com#Checkout_relax_and_build Here I have a "free" account, and William Stein has for free granted me "Network" access to a test project. This is so I can use the internet to checkout relax with subversion. I can install relax on the cloud.sagemath.com. And the systemtests are now running in the terminal. So, it seems that this is an easy possible way to run relax in the terminal. It simply works. But it seems that you try to hit "the big nail", and I only try to figure out if there is some way to let users do some initial analysis. I still find it interesting to allow for an online possibility, like http://sherekhan.bionmr.org/ With a decent tutorial, a researcher can get relax running an analysis fast. Just to get convinced to do a proper install at home or at a cluster. Best Troels 2015-11-24 10:16 GMT+01:00 Edward d'Auvergne <edw...@nmr-relax.com>: > Hi Troels, > > I'll respond to this message here on the relax-devel mailing list, > before it gets too far. I think that the SageMath servers are far > from ideal for running relax. Such 'cloud' servers, or others you can > 'rent' from internet service providers, are not designed for serious > number crunching. The ideal would be something like WeNMR > (https://www.wenmr.eu/). I.e. to get relax into a funded grant system > to run on real number crunching hardware, with a supercomputer cluster > running relax instances (and maybe other NMR calculation software such > as NMRPipe, Dyana/Cyana, XPLOR-NIH, ARIA, CCPN, etc.). When you are > looking at days or weeks of calculation time for a full model-free > analysis, or 2-6 months for the new frame order analysis - all on the > fastest hardware out there - for this you really have to set up a > dedicated number crunching system. You also have to consider options > that will allow for disconnecting and drop outs to allow the user to > log back in. In any case, funding is required to pay for the server > system, and for that a grant needs to be applied for (or joined onto). > And in the granting systems, it would be easier to get funding to buy > the full supercomputing infrastructure than to buy a yearly > subscription to someone else's cloud servers. This is why I have > always leaned towards web application frameworks, such as Django, Ruby > on Rails, etc., as we'd then have full control to take advantage of > the number crunching abilities of a cluster. Such technology would > also give us a greater ability to implement the user functions, a spin > viewer, and other complex elements. > > Also, I wouldn't recommend you spend too much time on this, at least > for now, as I see the complete implementation of a relax web UI as > requiring a time frame of at least half a year! From experience with > the GUI and implementing the other UIs, I think this would be a tight > minimal timeframe to have a finished and fully functional product by. > The web UI would need to expose the full power of relax, including all > user functions, rather than being a crippled interface only allowing > for certain types of auto-analysis. The prompt UI, script UI, > graphical UI and web UI all need to be on the same level. A better > way to do this would be to include it in the funding proposal, to hire > someone for a year to code a fully functional web UI. Unfortunately > I'm in no position at the moment to apply for such funding, but this > will hopefully change in the future. > > Regards, > > Edward > > > > On 23 November 2015 at 18:31, William Stein <wst...@sagemath.com> wrote: > > On Mon, Nov 23, 2015 at 2:15 AM, Troels Emtekær Linnet > > <tlin...@nmr-relax.com> wrote: > >> Dear Sagemath. > >> > >> Thank you for an *excellent* software solution at: > >> https://cloud.sagemath.com/ > >> > >> I have happily used this in some teaching of python. > >> > >> I am a PhD student at the BIO center of Copenhagen University, at > SBiNLab > >> www.bio.ku.dk/sbinlab > >> > > > > Cool -- I was in Copenhagen for a few weeks for SageMath workshop > > during summer 2104. I skated the beautiful vert ramp across the > > street from one of the universities a few times (in Fallenparken). I > > also know people in the math department there, including Ian Kiming. > > > >> During my time at my PhD, I have helped developing "relax". > >> http://www.nmr-relax.com/ > >> https://gna.org/projects/relax > > > > First question: Is there a reason you don't post a package on > > https://pypi.python.org/pypi? Then I could just do > > > > pip install nmr-relax > > > > and it would take care of dependencies, auto-updates, etc. As it is > > now, I have to write some special purpose code to automate > > installation of relax, which involves possibly scraping your site for > > the most recent tarball, downloading it, etc., -- it's far more error > > prone. Most python packages get installed via pypi these days, I > > think. (OK, so SageMath itself doesn't yet, but it's huge.) > > > >> "The program relax is a software package designed for the study of > molecular > >> dynamics through the analysis of experimental NMR data. Organic > molecules, > >> proteins, RNA, DNA, sugars, and other biomolecules are all supported. > It was > >> originally written for the model-free analysis of protein dynamics, > though > >> its scope has been significantly expanded." > >> > >> Recently we published this paper: http://www.nmr-relax.com/refs.html > >> Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., > >> Tollinger, M., Teilum, K., Gagné, S., Marion, D., Griesinger, C., > >> Blackledge, M., and d'Auvergne, E. J. (2014). > >> relax: the analysis of biomolecular kinetics and thermodynamics using > NMR > >> relaxation dispersion data. > >> Bioinformatics > >> > >> We always seek to help our users as much as possible. > >> We have this wiki: > >> http://wiki.nmr-relax.com/Main_Page > >> > >> The "first barrier" for new users, is always installation. > >> http://wiki.nmr-relax.com/Category:Installation > >> > >> I have been "thinking" that it would be of great benefit, if we could > have > >> relax > >> in "the cloud", and let researchers try relax here, before fiddling with > >> their own installation. > >> > >> I have been looking af: > >> https://cloud.sagemath.com/policies/pricing.html > >> > >> The optimal solution would be, if we could have a place where > researchers > >> could "login", and use for example 5 cores. > >> > >> To try relax out, until they are "convinced" to fiddle with their own > >> installation. > >> > >> It is hard to say how popular this service will be. > >> > >> Would it be possible to establish: > >> > >> * 2 admin accounts and 5 temporary user accounts > >> * Access to 3-5 cores ? > > > > We don't currently provide admin account or dedicated SMC servers. > > However, if you were able to purchase a subscription for $ 49 / month > > (or $499/year), then you can apply the quotas listed here to any > > projects: > > > > - 16 upgrades Member hosting > > - 40 upgrades Network access > > - 8 days Idle timeout > > - 24 GB Memory > > - 40 GB Disk space > > - 4 shares CPU shares > > - 2 cores CPU cores > > > > One way you could use this is that somebody would go to your nmr > > website, then go to SMC, create a project, and just start instantly > > using your library -- one minute in, and they are using it via Jupyter > > notebooks, writing .py files, the terminal, or Sage worksheets (all > > 100% for free). Then they would add you as a collaborator to their > > free project, and you would click a button to upgrade their project to > > "member hosting", add network access, increase the cpu shares, etc -- > > whatever you want. There's a page you'll have which lists, for each > > project, what upgrades you have applied, and you can also see if the > > project is being used. You can remove upgrades at any time (in any > > granularity). > > > > The value of upgrading to "member hosting" is that it is *much* > > faster. The free pool of computers are typically *massively* loaded > > during the week. They work fine, but they can easily be 15% of the > > speed of the members-only machines. I've attached a screenshot I > > took right now showing the load on the free machines (top 4) and the > > members-only machines (bottom 2). With the $49/month subscription, you > > get to move 16 projects to members-only machines. > > > > We also have subscriptions in the bottom row aimed at courses, which > > let you move a large number of projects to members only machines. > > > >> What the researchers should be possible to do: > >> * Sign up for account (could be by email to us, so we create account) > > > > Even if they create it, as long as they add you to a project they > > create, *you* can then contribute any upgrades you want to their > > project. They can also contribute upgrades later if they want, and > > they just add together. > > > >> * Use ssh to send data to the server > > > > Supported right now, even for free projects. See the button "ssh to > > your project" in project settings. There is currently also a default > > 3GB disk quota; you can also use /tmp for more space (for temporary > > data). > > > >> * The uploaded data for the researcher should be private > > > > Even for free projects, data in projects is only visible to > > collaborators on that project and nobody else. SMC is not like github, > > where free = public by default. With SMC everything is private by > > default, even for free users. However, people can also explicitly > > share any file or directory tree, and that makes it publicly available > > (so good way to share data related to a paper or research project). > > > >> * Use relax in the terminal in the server > > > > Fine for free projects. > > > >> * Download the results to preview > > > > Yep. > > > >> I hope for a reasonable prizing. > >> > >> Personally I will probably pay for the first prizing. > >> So I hope this will be "low", until we have figured out if this is a > good > >> idea and if it "works". > >> > >> If the service gets very popular, and demand for CPU is high, you > should of > >> course > >> be compensated for this. > > > > On our free machines, the more the better. However, as mentioned > > above, it will often be quite slow during peak times. > > > >> But then it would be easier to apply for funding in the NMR community, > and > >> argument with the traffic at the page. > > > > It would be fantastic were this to happen. Note that SMC runs on in > > the cloud on Google Compute Engine, so at least technically it is > > trivial to provision arbitrarily large amounts of compute power. > > > >> I would be happy to hear if you have ideas how we could engage in this. > >> > >> Thank you again for a super great service. > >> You are breaking down the barriers of "installation" problems. > > > > Thanks, > > > > William > > > >> > >> Best > >> Troels Emtekær Linnet > >> PhD student > >> Copenhagen University > >> SBiNLab, 3-0-41 > >> Ole Maaloes Vej 5 > >> 2200 Copenhagen N > >> Tlf: +45 353-22083 > >> Lync Tlf: +45 353-30195 > >> > >> > >> > >> > > > > > > > > -- > > > > Best Regards, > > William > > > > Found/CEO of SageMath, Inc. > > > > Professor of Mathematics > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel mailing list > relax-devel@gna.org > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-devel > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
