Posts by valterc
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21) Message boards : Science : H1N1 expansion (Message 2055)
Posted 4 Nov 2020 by Profile valterc
Good news. How can we recognize theese WUs?

Some of the needed genes/isoforms were already expanded in the past. The new ones, related to this project, have the workunit name starting from 175673_Hs to 175921_Hs.
22) Message boards : Number crunching : Server Status - No Work Available (Message 2052)
Posted 29 Oct 2020 by Profile valterc
Gene_generator is down...

restarted just now
23) Message boards : Number crunching : Compiling for AVX-512 (Message 2044)
Posted 26 Oct 2020 by Profile valterc
What's a User?

It's a unique CPID (so, yes, aggregators are counted as a single user)

About AVX-512, I do not have AVX-512 capable computers so it would very difficult for me to build and test a new application. Also please keep in mind that the benefits are unknown, see: AVX-512 slower than AVX. For instance FMA against AVX only provided a very small speed gain, that's one of the reasons I do not distribute FMA for Windows, also at the very beginning FMA was broken for Ryzen.

Anyway, if someone would like to build up a AVX-512 application I can provide some assistance.
24) Message boards : Science : Miscellaneous gene-related news (Message 2036)
Posted 23 Oct 2020 by Profile valterc
I just checked, we have 7 isoforms of the FURIN gene inside our FANTOM db, I just put them on our queue at high priority, you should see them soon floating around.
25) Message boards : News : Paper published on IEEE Transactions on Emerging Topics in Computing (Message 2008)
Posted 16 Oct 2020 by Profile valterc
The following article, "A Computing System for Discovering Causal Relationships among Human Genes to Improve Drug Repositioning," is available under the "Early Access" area on IEEE Xplore. This article has been accepted for publication in a future issue of this journal, but has not been edited and content may change prior to final publication. This paper appears in: IEEE Transactions on Emerging Topics in Computing, Digital Object Identifier: 10.1109/TETC.2020.3031024. You may find it here: https://ieeexplore.ieee.org/document/9224179
Thank you all for your invaluable support!
26) Message boards : Number crunching : Waiting for Validation (Message 2004)
Posted 13 Oct 2020 by Profile valterc
Looking at the server status page shows that there are zero WUs waiting for validation


The number shown is the number of already received couples of WUs waiting to be validated (bitwise comparison) by the server, this process is very fast so this number is usually around zero.
27) Message boards : Number crunching : Lost credits? (Message 1993)
Posted 10 Oct 2020 by Profile valterc
This is very strange, we did not suffer any db crash or similar nasty things (you are also the first, if I remember correctly, that has this problem). Did you start crunching within the gridcoin group? Anyway, if you can tell me (with some proof) the number of missing credits I can add them to you manually.
28) Message boards : Science : AMD COVID-19 HPC Fund (Message 1992)
Posted 10 Oct 2020 by Profile valterc
There is no GPU app available at TN-Grid.


So what is running on the Radeons AMD lent you?


Nothing at the moment, AMD will grant us access in about a month.

Anyway, we will use them to try to develop a slightly modified version of our algorithm, suitable for gpu-style parallelization. Also we will use their specific deep learning power to help us better understand the whole thing (gene expansion, covid, causality etc).
29) Message boards : Number crunching : Server Status - No Work Available (Message 1975)
Posted 30 Sep 2020 by Profile valterc
I just restarted the work generator (there is a mysterious memory leak inside its python code that will slow down the program after some days) and also restarted some services. This should help the systems to increase its speed.
30) Message boards : Science : AMD COVID-19 HPC Fund (Message 1950)
Posted 17 Sep 2020 by Profile valterc
If your new computational resources are sufficient, don't feel the need to "make work" to keep crunchers happy, I have several "silent" projects on my machines, every now and then, one of them pushes a couple of weeks work, then goes silent again. Remember, the crunchers are trying to help you, they should never be a burden.

The AMD grant is an important temporary boost to our computational resources that will hopefully help us to explore new scientific frontiers. The gene@home project doesn't have a deadline. Our algorithms are very "generic", they can easily be applied to other organisms, other datasets (differently built) of the same organism, not only in the biological field, they can be useful whenever you have a lot of variables, each one with different experimental values and you need to find causal relationships among them. The algorithm itself could also be improved, others may be added.
We will continue to move on, with your help.
31) Message boards : News : AMD COVID-19 HPC Fund Adds New Research Institutions (Message 1945)
Posted 16 Sep 2020 by Profile valterc
Our gene@home project (hosted by the University of Trento, Italy) has been chosen by AMD as a recipient for their COVID-19 HPC fund, see the official announcement https://www.amd.com/en/corporate/hpc-fund

We are really grateful to receive this donation, it will give us access to high performance computing nodes, boosting our research. More info and comments here: https://gene.disi.unitn.it/test/forum_thread.php?id=291
32) Message boards : Science : AMD COVID-19 HPC Fund (Message 1944)
Posted 16 Sep 2020 by Profile valterc
I'm in vacation right now, actually... anyway, here are some details about the AMD grant (I will also put a note in the news page of the project).
Our gene@home project was chosen by AMD together with a dozen of prestigious institutions and we are very proud of this. We are a small group and our computational power relies basically on the volunteers contribution, without you we weren't able to do the work we did, thank you all.
The grant will give us access, for one year, to two AMD computational nodes, each one equipped with a AMD Epyc "Rome" and 8 AMD Radeon Instinctâ„¢ MI50 Accelerators.
This will not solve our well known server problem (it would be too complicated to transfer the server to the new machine and come back to the orginal one after one year) but it will give us a tremendous boost to our in-house computational power, also giving us the opportunity to explore Deep Learning algorithms.

A very brief update on what is going on right now:
A paper describing the results we got some time ago working on genes related to the colon cancer has been accepted by a IEEE journal (more details when it will be officially published, very soon)
We are also preparing another two papers, the first one (it will be submitted to Nature Scientific Data) about the COVID-19 related genes we analyzed a couple of months ago and another one (at a very early stage) about the OneGenE experiment we did on Vitis vinifera

We are continuing to analyze (expand) COVID-19 related genes, at the second level, ie expanding the genes that we found at the first ranking positions in the expansion list of the first batch of genes.
33) Message boards : News : Server unreachable (2020-09-09, from 05:30 to 08:00 CEST) (Message 1935)
Posted 8 Sep 2020 by Profile valterc
Wednesday 09/09, from 05:30 to 08:00 CEST, the IT services of UniTrento will not be available because of a planned IT maintenance. The TN-Grid server (hosted by UniTrento) will probably be not reachable during this period.
34) Message boards : Number crunching : Lost Credit ? (Message 1900)
Posted 22 Jul 2020 by Profile valterc
Hi Candido, sorry for the late reply. The project has not changed in time (well, we changed the application name and removed the 'test' from the project name), nor we had any db crash or similar. No-one (AFAIK) suffered loss of credits since the very beginning. I also checked the users' db for any name or e-mail address that may be similar to your one and found nothing...
I was wondering what had happend and I suddendly remembered that WUprop records the hours crunched for each project and since I am also a member of that project I went looking and found out that I have in fact crunched 5,942.45 hours for the project "TN-Grid Test Platform", specificaly for the Gene Network Application.
As I suspected, I have in fact crunched for a TN-Grid project, but there seems to be a difference in the project name. Was that a different project? Is it the same? Should I have credit here? Or might the credit be there in some other TN "Test" Project?

PS: I do not share the link for my WUProp page as I think other users cannot see the relevant data. Anyway, my user name there is "candido" also.
Thanks
Candido
35) Message boards : Wish List : HTTPS Secure Site (Message 1893)
Posted 13 Jul 2020 by Profile valterc
Even Firefox claims that the site is not *fully* secure, the reason is that in many https pages there are references to http only things (such as images, like your signature ;). I don't think this is a serious issue, anyway...
36) Message boards : Number crunching : Android applications on ARM (Message 1869)
Posted 27 Jun 2020 by Profile valterc
Yep, I will start to distribute the Android applications as soon as possible. I'm very busy right now (work issues, papers, projects,...) I will do this after July 10th (please remind me the issue again if it happens that I forgot about... ;)
37) Message boards : Science : SARS-CoV-2 virus (Message 1850)
Posted 25 May 2020 by Profile valterc
The first batch of genes related to COVID-19 has been completed. We sent the results, for further analysis, to the Univ. of Modena & Reggio Emilia School of Medicine, Italy. Starting from today we added another batch of genes, per request of the aforementioned institution. Most of them are antibodies, so the focus right now is the immune system.

Here is the list of the genes: PTPRC CD28 CCR7 PDCD1 SNCA SPATA2 CD27 B3GAT1 IL7 IL2RA ISG20 FAS PTPN13 CD38 CD74 CD24 CR2
38) Message boards : Web site : Change avatar error (Message 1842)
Posted 18 May 2020 by Profile valterc
I think I have fixed it, please retry
39) Message boards : Number crunching : Android applications on ARM (Message 1841)
Posted 18 May 2020 by Profile valterc
Doing some tests we noticed that the recently built applications for OpenWrt/Linux should also run on ARM based Android systems. If you have BOINC running on one of the following platforms

arm-android-linux-gnu Android running on ARM armeabi-v7a (32-bit) aarch64-android-linux-gnu Android running on ARM 64-bit arm64-v8a

you could try to configure your BOINC client to use the alt_platform method inside yours cc_config.xml and request to download the proper application

<alt_platform>arm-openwrt-linux-muslgnueabi</alt_platform> (32-bit) <alt_platform>aarch64-openwrt-linux-musl</alt_platform> (64-bit)

After some testing (I need only a few days if there will be enough statistic) I will start to distribute the Androd/ARM applications "the official way"

[edit] we already have vfpv3/vfpv4 applications for ARM 32-bit
40) Message boards : Science : Scientific results (Comments) (Message 1837)
Posted 17 May 2020 by Profile valterc
Just send me a PM with your email and I will send it to you, tomorrow.


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