Posts by valterc
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1) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2155)
Posted 17 days ago 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...
2) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2152)
Posted 18 days ago 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....)
3) Message boards : Number crunching : FMA application for windows_x86_64 (Message 2143)
Posted 22 days ago 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 problem 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.
4) 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.
5) 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.
6) Message boards : Number crunching : Android applications on ARM (Message 2109)
Posted 26 Nov 2020 by Profile valterc
Hi, any update on this? I confirm that my old phone is still crunching h24 without any error. I think it's safe to add official support to Android in order to allow also users with unrooted phone to participate too.

OK, I completely forgot about this... I will hang a post-it in the proper place...
7) Message boards : Development : Doublevector always uses SSE path instead of AVX (Message 2108)
Posted 26 Nov 2020 by Profile valterc
The Windows source code is exactly the same of the Linux one, it was compiled using gcc/MinGW so I guess the behavior is the same.

Also keep in mind that the second-last command line parameter of the application is the number of columns in the input dataset. Right now, with the current experiment (FANTOM, hgnc_data_mat.csv), this number is 1829 (and this is the largest dataset that we ever used).

I suggest, if you want to benchmark the application in a real case, to download the small validation suite I provided: https://gene.disi.unitn.it/test/files/gene_validation.zip
8) Message boards : Number crunching : Compiling for AVX-512 (Message 2103)
Posted 25 Nov 2020 by Profile valterc
The build script you were using tries first to compile the needed BOINC libraries (which is not so easy). You can skip this part by using the ones I compiled some time ago (although not the latest ones), get them from here https://gene.disi.unitn.it/test/files/boinc_libs-x32-x64.7z. After that you may move inside the pc-boinc/src directory and issue a "make" from here. I don't expect that you will be successful at the first try (the executable, if built, will land in pc-boinc/bin)

Ok, I edited makefile by adding:
# AVX512, 64-bit ARCH += -march=skylake-avx512 -mtune=skylake-avx512 -mavx512f -mpopcnt -maes -mpclmul -m64 -ftree-vectorize
Then in a terminal I ran:
/home/aurum/BOINC_dev/boinc/samples/pc-boinc/src/linux64_build.sh
Lots of lines scrolled by, terminal closed and I can't find an executable. It added a link to libstdc++.a that when I try to open it says archive type not supported (I have Linux Mint 20 Ubuntu 20.04 Focal).

What's next???
9) Message boards : Number crunching : Compiling for AVX-512 (Message 2102)
Posted 25 Nov 2020 by Profile valterc
Regarding your previous message: You may look at this small validation suite for the gene pc-im application (a small and normal input file, with the outputs as reference). Hope it helps.
10) Message boards : Number crunching : Compiling for AVX-512 (Message 2099)
Posted 25 Nov 2020 by Profile valterc
About the 3 lines in client_state.xml: that's because your computer supports all three versions of the applications (sse2, avx, fma). BOINC tries all of them and eventually should choose the faster one.

I guess that at the moment you shouldn't specify avx512 in the app_info (using app_info you override the server logic for distributing applications). The name of the executable doesn't matter. A name like gene_pcim_v1.10_linux64__avx is simply useful because from that you can inherit its characteristics.

Also it seems to me that avx512 is actually a set of AVX512-whatever instructions, I don't know which one would be better to target, probably avx512f. There is some discussion about it here: https://github.com/BOINC/boinc/issues/3180. Is your BOINC client able to detect avx512?
11) Message boards : Number crunching : Compiling for AVX-512 (Message 2097)
Posted 25 Nov 2020 by Profile valterc
it seems to me (but I may be wrong) that you don't need to define the plan_class, instead you should define the platform (like <platform>x86_64-pc-linux-gnu</platform>)

When switching from regular use to anonymous platform I suggest to: wait until there are no workunits in the cache (or abort them all), exit boinc, copy the app_info.xml and the executable in the proper place (check its x bit, chmod a+x), start boinc.

Hope it works, I'm curios about it.

EDIT: which compiler switch did you use? -march=skylake-avx512 ?
12) Message boards : Number crunching : Compiling for AVX-512 (Message 2093)
Posted 19 Nov 2020 by Profile valterc
I applied for a Covid-19 research license to get the Intel compiler. Waiting to hear back.

I suggest to use the latest free gcc on Linux (if you want to play with it), I cannot help you with the Intel compiler but others probably would. You may find the source code of the application here: https://bitbucket.org/francesco-asnicar/pc-boinc/
13) Message boards : Number crunching : Compiling for AVX-512 (Message 2089)
Posted 19 Nov 2020 by Profile valterc
Some time ago, when starting to deploy applications for different architectures we made sure (and this wasn't easy) that the output file matched our "gold" one, which we defined to be the one got using plain Linux x64. Therefore, a Xeon FMA Linux output exactly matches any other one output (like ARM vfpv3 or MacOs). This way both the distribution and the validation of workunits are much easier to handle.
When adding new applications to the system BOINC requires to give them unique name and description.

BTW, as I explained before, I cannot build and test a AVX512 application (I don't have any AVX512 capable computer here). Anyway, it is not difficult to compile the source code (gcc on Linux x64), the tricky thing is to compile the needed BOINC libraries but, if requested, I can provide them.
14) Message boards : Number crunching : Server Status - No Work Available (Message 2069)
Posted 11 Nov 2020 by Profile valterc
Do you remember when I said is not good the "no work available" situacion?

Now, plenty of computers asked for work to some other projects and we moved from 60 genes / day to 44 genes / day.

I have seen than in my own machine.

Well, the server limits are obviously a big issue. However, the recent drop of performance here is mainly due to one single user (with an impressive number of hosts) that decided to stop/pause crunching (I don't see him active in other projects...)
15) Message boards : Science : SARS-CoV-2 virus (Message 2068)
Posted 11 Nov 2020 by Profile valterc
"Ms Frederiksen cited a government report which said the mutated virus had been found to weaken the body's ability to form antibodies, potentially making the current vaccines under development for Covid-19 ineffective."

https://www.bbc.com/news/world-europe-54818615

I've seen an article saying that a new gene in the virus, overlapping with a known gene, is responsible for that. Not easily seen without a paid subscription, though.

There is a reddit about this (minks mutation) https://www.reddit.com/r/COVID19/comments/jrl0f1/working_paper_on_sarscov2_spike_mutations_arising/
16) 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.
17) 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
18) 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.
19) 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.
20) 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!


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