Posts by valterc
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21) Message boards : Science : proterna_vae64lat dataset (Message 2303)
Posted 10 May 2021 by Profile valterc
There is a new data set floating around: proterna_vae64lat

It has been made by "crossing", using machine learning techniques, two different datasets collected from human tissues: protein and RNA expression levels. More (scientific) information will follow.

There will be just a small set of workunits available, at least at the beginning. You may recognize them from the workunit's name containing the string "Hs_PRT-genename". This kind of workunit should be very fast to compute (around half an hour on a decent computer).

Please let me know if you notice something strange with them.
22) Message boards : Development : Maybe avoid file I/O? Just read all input into memory? (Message 2298)
Posted 6 May 2021 by Profile valterc
Hi Steffen
The application reads two input files: the one with the list of tiles (600 tiles for the FANTOM dataset) and the expression dataset. Both of them should already be read at the very beginning, converted to a suitable format and kept in memory until the end (or a restart from the checkpoint). I didn't write, nor check, the logic inside the application, I don't know if there is something wrong with it.

There is the need to look at the source code and do some I/O tracing (unfortunately I'm very busy right now...)
23) Message boards : Number crunching : Bad hosts topic (Message 2289)
Posted 19 Apr 2021 by Profile valterc
This probably belongs to someone that even don't know what it happens here... Anyway, I just blacklisted it
24) Message boards : News : Upgrading the server (Message 2275)
Posted 26 Mar 2021 by Profile valterc
Over 27,000 WUs queued and ready for BOINCers to DL. Looks like you upgraded the server and you're more than ready for the next Race Day.

Well, the WU ready to send are just around 16000...The server is still the old little one. We found some money and ordered a new server, no ETA right now. When ready to do the upgrade we will for sure post a news here.
25) Message boards : Number crunching : World Gene Expansion Challenge 2021 (Message 2264)
Posted 10 Mar 2021 by Profile valterc
I heard that some at SETI did that. They made a custom BOINC client or something like that. Claimed it helped them make it through workless Tuesdays.

It is very easy, just use the following cc_config.xml option
<ncpus>N</ncpus> Act as if there were N CPUs; e.g. to simulate 2 CPUs on a machine that has only 1. Zero means use the actual number of CPUs. Don't use this to limit CPU usage; use computing preferences instead.
26) Message boards : Number crunching : World Gene Expansion Challenge 2021 (Message 2251)
Posted 8 Mar 2021 by Profile valterc
That's why I'm confidant that switching the server to supply only 2 WUs per CPU thread would work great and mean that one could only bunker about 8 hours of work instead of several days worth.

Theoretically. If you really want to maximize your cache of workunits you could also lie about the number of cores (say that you just have 8 but you can easily tell the server that you have 128) or (although not so easy to implement) you may also start a lot of different clients on the same pc. So, at the end, if you really want, you may bypass any server side limitations.
On the other hand, forcing a small user's cache will create problems to users with intermittent network activity.
27) Message boards : Science : AMD COVID-19 HPC Fund (Message 2249)
Posted 8 Mar 2021 by Profile valterc
(apocalyptic mode on) there will be another one (apocalyptic mode off)
The pandemic will be over by the time you get those resources lol
28) Message boards : Science : AMD COVID-19 HPC Fund (Message 2246)
Posted 8 Mar 2021 by Profile valterc
I don't really know the details, anyway, we are still waiting. The actual hardware should be provided by Penguin Computing (as explained here: https://www.amd.com/en/corporate/hpc-fund) and the infrastructure should be brand new.
29) Message boards : Number crunching : Badges (all of them) (Message 2227)
Posted 5 Mar 2021 by Profile valterc
OK, I decided to add some more "expansive" diamonds to the badge list, got some information around and found that it would be pink, purple, blue and red. Already added the pink one, more will follow when I'll find some time... (hope you like them)
30) Message boards : Number crunching : Badges (all of them) (Message 2223)
Posted 4 Mar 2021 by Profile valterc
You should add Platinum at 250,000,000 and Rhodium at 500,000,000.

I thought of adding more badges, I like your suggestion, need to figure out the color... also Diamond is the top right now, should find something more valuable
31) Message boards : News : World Gene Expansion Challenge 2021 (Message 2219)
Posted 2 Mar 2021 by Profile valterc
The volunteers belonging to the BOINC.Italy group have organized the usual (end of winter) challenge on this project: Start: 8th March 2021 12:00 UTC, End : 15th March 2021 12:00 UTC.

Please follow this thread for further info https://gene.disi.unitn.it/test/forum_thread.php?id=307
32) Message boards : Science : SARS-CoV-2 virus (Message 2195)
Posted 5 Feb 2021 by Profile valterc
We already expanded all the genes cited in the second article, published some time ago (we are actually writing a paper about this). I forwarded the most recent to our biologists, it seems very interesting.
Thank you.
33) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2192)
Posted 3 Feb 2021 by Profile valterc
The server software is supposed to try different apps to see which one is faster and more reliable. It needs at least N (don't know exactly this number, could be 10 or 20) successfully validated results for each app before it can get an APR (Average Processing Rate), this was the DCF some time ago. You can see the APR numbers for each app when you look at your computer details under your account. Its supposed to pick the fastest app and occasionally send one of the others to see how they go. (documentation about this feature is not so easy to find...)
34) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2186)
Posted 1 Feb 2021 by Profile valterc
In Linux, my 3900X, 3950X and Epyc 7402P settled on FMA exclusively as fastest app. Takes about two weeks trying out AVX, SSE2 and FMA before declaring a winner.

How come my two fast machines (see links in last post) are almost identical? I can't see how that would change in two weeks, the timings are indistinguishable. Unless it's an OS thing, I only use Windows 10.

It happens that the performances of the various versions are almost the same. If there is not a clear winner the server simply don't care about what to send. Other important factors while comparing computers, for our application, are the RAM speed and CPU cache size.
35) Message boards : Science : AMD COVID-19 HPC Fund (Message 2183)
Posted 1 Feb 2021 by Profile valterc
Another delay, probably next week, we'll see...
36) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2155)
Posted 29 Dec 2020 by Profile valterc
Is there a debug parameter option for the application to produce better failure output?

Unfortunately not. This kind of problem is very low level, related to the specific computational architecture. Running the application from the command line might show some more info about.
The only real solution would be throwing the core dump to a debugger like gdb, on the failing machine (this on Linux, I don't know about how to do this on Windows).

I was concerned about the error number itself, it sounds very strange to me. I had expected to see some "Illegal instructions" (SIGILL, 0x04) in case some computers claimed to be able to execute FMA instructions but were not correctly configured to do this properly, but this seems not the case...
37) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2152)
Posted 28 Dec 2020 by Profile valterc
Got only one host, so far, that have problems with this application (no problems with SSE2 and AVX), this one: https://gene.disi.unitn.it/test/show_host_detail.php?hostid=64398.
Error code 1 (I don't really know the meaning of it....)
38) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2143)
Posted 24 Dec 2020 by Profile valterc
I just deployed the FMA optimized version of the application for Windows x64. It had problems, some time ago, with the early releases of the AMD Ryzen cpus (although, if I remember correctly, the problems were solved with BIOS upgrades).
The application is marked as "beta", if you you want to try it out you need to enable "Run test applications" in your profile.
39) Message boards : Science : Miscellaneous gene-related news (Message 2136)
Posted 14 Dec 2020 by Profile valterc
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?

We have the results about OAS1. I just put the others at the top of the queue.
40) Message boards : Science : AMD COVID-19 HPC Fund (Message 2132)
Posted 12 Dec 2020 by Profile valterc
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

The granting of the aforementioned resources has been delayed, don't know the reasons, I guess that they were actually building up a new computing center from scratch and had some problems. Anyway, they told us to wait until the beginning of January.


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