Posts by bozz4science
log in
1) Message boards : News : Paper published on Biomolecules (Message 2413)
Posted 24 Nov 2021 by Profile bozz4science
That's great! I'll look forward to reading it.
2) Message boards : Science : AMD COVID-19 HPC Fund (Message 2379)
Posted 5 Oct 2021 by Profile bozz4science
Any news?
3) Message boards : Science : AMD COVID-19 HPC Fund (Message 2337)
Posted 23 Jun 2021 by Profile bozz4science
Thanks for providing a timely feedback. Much appreciated!

Any way to keep us in the loop with the running of the experiments until September? Would love to hear about is being experimented with in the meantime. Maybe a short update by mid-July/August and a dedicated thread about the deployment of the AMD node in September.
4) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2330)
Posted 20 Jun 2021 by Profile bozz4science
How would the app_info.xml file look like for a Win10 machine? Tried various ways, but none worked for me. Any pointer highly appreciated. Thx
5) Message boards : Science : AMD COVID-19 HPC Fund (Message 2325)
Posted 15 Jun 2021 by Profile bozz4science
Hey valterc, hope that everything is going smoothly and you could slowly transition to the new compute nodes. Are they already up and running? Will they run on a special unique infrastructure (own work queue etc.) or will they also be visible on the server page due to a rising compute average?

Don't wanna be the annoying person here always pushing this request, but it's been almost another 3 weeks. Would highly appreciate any update!
6) Message boards : Number crunching : Badges (all of them) (Message 2318)
Posted 25 May 2021 by Profile bozz4science
I think they look great, but not gonna be relevant for me for a long time :)
7) Message boards : Science : AMD COVID-19 HPC Fund (Message 2317)
Posted 24 May 2021 by Profile bozz4science
That’s awesome! I am glad AMD finally granted access to the promised hardware. Hopefully that’ll boost the overall computational power, albeit temporarily :)
I would love to read a short follow up once the hardware is fully operational!

Cheers mate!
8) Message boards : Science : AMD COVID-19 HPC Fund (Message 2315)
Posted 24 May 2021 by Profile bozz4science
I don't want to make this an annoying habit to inquire on a monthly basis whether the promised hardware can yet be accessed or not, but I am starting to question AMD's commitment at this stage. Has the project lead already exerted a bit of pressure on this topic?
... Just curious.
9) Message boards : Science : AMD COVID-19 HPC Fund (Message 2232)
Posted 6 Mar 2021 by Profile bozz4science
Personally, this whole thing is
(1) either horribly planned and logistics are executed in the worst way imaginable OR
(2) I just cannot imagine the complexity going into that project but AMD ridiculoulsy oversold their promise to help by offering access to hardware resources temporarily OR
(3) it is starting to feel rightfully so just as some huge PR campaign

I hope it is one of the first two reasons that I mentioned, bc that means that eventually they WILL get access to the hardware. - Just at a later point in time ....

The story continues ....
10) Message boards : Science : AMD COVID-19 HPC Fund (Message 2214)
Posted 26 Feb 2021 by Profile bozz4science
Do you finally have access to the resources?
11) Message boards : Science : Miscellaneous gene-related news (Message 2137)
Posted 14 Dec 2020 by Profile bozz4science
That's awesome. Thanks for making this adjustment. Have a great day!
12) Message boards : Science : AMD COVID-19 HPC Fund (Message 2133)
Posted 12 Dec 2020 by Profile bozz4science
All right! Thanks for getting back to us. That's definitely very unfortunate especially after all the buzz they intentionally created around this project (corporate press releases, own website) and their huge public announcement. If the resources aren't yet available, I guess it will also impact the other universities and institutions that were also promised access to the HPC resources. Hope they'll figure it out rather quickly :)
13) Message boards : Science : AMD COVID-19 HPC Fund (Message 2131)
Posted 12 Dec 2020 by Profile bozz4science
Still interested in how these resources are being used if at all... If you're allowed to publicly disclose this information, I would appreciate sharing them with us. It's been a while... Just saying
14) Message boards : Science : Miscellaneous gene-related news (Message 2130)
Posted 12 Dec 2020 by Profile bozz4science
Hey valterc, I just saw this Reuters article (published 12/11) talking about 5 genes that are currently thought of as potential/partial cause for very severe courses of SARS-CoV-2. The article names the following genes: IFNAR2, TYK2, OAS1, DPP9 and CCR2.

Did we already expand those gene networks or can they skip the queue if not?

Five key genes linked to severe COVID-19 found, suggesting drug targets This research is also published in the journal Nature
Link to the article's abstract
Link to the PDF
15) Message boards : Science : AMD COVID-19 HPC Fund (Message 2072)
Posted 12 Nov 2020 by Profile bozz4science
I would be interested in any news surrounding this topic as well. Could the resources already be deployed and put to use? Or any plan how to best deploy them in the future to accelerate the work here? Thx
16) Message boards : Science : Miscellaneous gene-related news (Message 2064)
Posted 9 Nov 2020 by Profile bozz4science
7 isoforms of the FURIN gene inside our FANTOM db, I just put them on our queue at high priority
It's great that you as project lead always react to new circumstances rather swiftly! Much appreciated!
17) Message boards : News : Paper published on IEEE Transactions on Emerging Topics in Computing (Message 2047)
Posted 28 Oct 2020 by Profile bozz4science
Enjoyed reading it very much! Thanks for sharing.
18) Message boards : Number crunching : Server Status - No Work Available (Message 1976)
Posted 30 Sep 2020 by Profile bozz4science
Thank you valterc! The work generator seems to be doing its job properly now again. The queue is continually rising almost back up to 4k tasks waiting to be sent out. That's great :)
19) Message boards : Science : AMD COVID-19 HPC Fund (Message 1973)
Posted 30 Sep 2020 by Profile bozz4science
Well, those AMD Radeon Instinct accelerators are real compute beasts! Those 8 will be doing more combined than the rest of us :) That should be a incredible speedup in WU turnover.

The dataset we are using right now is very big, a floating point matrix 87554x1829, it's size on the hard disk is ~0.5Gb and contains, for many genes, different isoforms/transcripts. The computational time for an algorithm's iteration, because of its 'complexity', is longer than the previous experiments.

Any single gene expansion is packed up into 294 workunits. Any workunit you receive has a name like this: 142041_Hs_T155402-MAP1B_wu-(1 to 294), a counter, Hs, an internal T code, a mnemonic for the gene/isoform. The T code is just a shortcut for the gene coordinates, for example T155402 is chr5:71403265..71403276,+


Considering the original announcement of the experiment back own 2018, if I am not mistaken the dataset is a floating point matrix. Not knowing exactly what precision is needed for those computations (F16/32/64 precision), with 8 x Radeon Instinct MI 50 accelerator compute units, the peak compute capability at F16 would be 212 TFLOPs, the min at F64 at 52.8 TFLOPs. (Data according to https://www.amd.com/en/products/professional-graphics/instinct-mi50-32gb)

As of today (09/30) on the server page:
16771.51 GFLOPs of all volunteers which translates to ~16.8 TFLOPs.

The ratio by which AMD's sponsored accelerators surpass the crunchers' current computing power is a whopping ~3.1 x (at the lower F64 end).

Hope there is no flaw in my quick calculations.... If this were true anyway, that would be awesome for TN-Grid!!

... and if there is sth to the rumour of a GPU client application to be eventually deployed on TN-Grid, even my ancient GTX 750 Ti could do wonders in terms of compute capability compared to the current CPU-only powered compute force of us crunchers.

By no means I want to reignite the whole GPU/CPU debate that I am well aware of, but rather highlight the awesome performance boost through AMD's sponsored hardware as well as color this bright future of what could become reality soon.... Who knows? :)
20) Message boards : Number crunching : Server Status - No Work Available (Message 1972)
Posted 30 Sep 2020 by Profile bozz4science
My queue is also drying up slowly, even though my turnover is slow and my buffer tends to be very small as well...

Edit: I just received 7 WUs (HOXC4). That's great :)


Next 20

Main page · Your account · Message boards


Copyright © 2022 CNR-TN & UniTN