Posts by Aurum

21) Message boards : Number crunching : Curious (Message 2700)
Posted 5 Jun 2022 by Aurum

I haven't had any in a while but occasionally I will receive a task that runs for under 1 hour (Ryzen 9 3900X). I am guessing these are just shorter tasks. Has anybody else noticed the shorter tasks?

The last workunit of every gene expansion batch is shorter than the others, it is the one containing "wu-294" in its name

Bingo! I perused my list of running WUs and the one that's running will finish in under an hour.

22) Message boards : Number crunching : Curious (Message 2697)
Posted 5 Jun 2022 by Aurum

Sure I've seen a number that ran around an hour. Right now I have plenty that are running around 2.5 hours.
I have 31 completed WUs that won't upload. They're all files under 10 kb and Retrying never sends them up. At some point they do seem to have gone up but the list has been growing longer each day for the last week.
My Validation Pending has grown to over 5000 when normally it's well under 2000 which seems odd since they finish faster.
Just curious.

23) Message boards : Number crunching : Curious (Message 2694)
Posted 4 Jun 2022 by Aurum

Recently the "Last 10 Days" value, not sure what the units are, maybe genes/day, has dropped from 88 to 66. Server status indicates there's still a lot computers working here. Time to complete WUs is still around 4 hours. I've long thought it'd be nice to have a long term chart to understand the change in genes/day.
http://gene.disi.unitn.it/test/gene_science.php

24) Message boards : Science : Miscellaneous gene-related news (Message 2693)
Posted 4 Jun 2022 by Aurum

Evidence mounts for alternate origins of Alzheimerâ€™s plaques

https://scienceblog.com/531082/evidence-mounts-for-alternate-origins-of-alzheimers-plaques/

Reminds me of mucopolysaccharidosis. MPS is caused by a defective enzyme that is supposed to break down mucopolysaccharides for disposal so they accumulate in the lysosomes. The low pH in lysosomes is to unfold and open up proteins so they can be digested by enzymes. The article implies they've yet to figure out what reduces the acidity of neuronal lysosomes. This is a topic well worth keeping an eye on.

25) Message boards : Number crunching : Bad hosts topic (Message 2676)
Posted 18 May 2022 by Aurum

Looks like it's fixed. Installed psensor and watched the CPU temps:

sudo apt-get install psensor psensor-server -y

The E5-2699 v3 has a max CPU temp of 76.4 C before it downclocks the CPUs to protect them and CPUs were all high some up to 88 C. https://www.cpu-world.com/CPUs/Xeon/Intel-Xeon%20E5-2699%20v3.html

It had a CoolMaster CPU cooler and they have the lowest quality fans. Replaced the fan. Also checked thermal paste and it was hard so I replaced with my ThermalRight TF-8. http://www.thermalright.com/product/tf8-thermal-paste-2g/
With TF-8 it stays soft and pliable for months whereas others dry out and harden forming voids with low thermal conductivity.

CPU: Topology: 18-Core model: Intel Xeon E5-2699 v3 bits: 64 type: MT MCP
L2 cache: 45.0 MiB
Speed: 2733 MHz min/max: 1200/3600 MHz Core speeds (MHz): 1: 2608 2: 2609 3: 2610
4: 2295 5: 2610 6: 2611 7: 2611 8: 2611 9: 2611 10: 2611 11: 2611 12: 2612 13: 2609
14: 2612 15: 2612 16: 2612 17: 2612 18: 2612 19: 2613 20: 2613 21: 2613 22: 2613
23: 2299 24: 2609 25: 2614 26: 2614 27: 2614 28: 2614 29: 2614 30: 2614 31: 2609
32: 2609 33: 2609 34: 2610 35: 2610 36: 2610

26) Message boards : Number crunching : Bad hosts topic (Message 2675)
Posted 18 May 2022 by Aurum

Think I see what's happening, the CPU clocks are slowed down:
sudo inxi -C
CPU: Topology: 18-Core model: Intel Xeon E5-2699 v3 bits: 64 type: MT MCP
L2 cache: 45.0 MiB
Speed: 241 MHz min/max: 1200/3600 MHz Core speeds (MHz): 1: 250 2: 240 3: 235 4: 237
5: 248 6: 236 7: 236 8: 235 9: 234 10: 240 11: 223 12: 222 13: 255 14: 221 15: 212
16: 219 17: 230 18: 250 19: 307 20: 226 21: 221 22: 246 23: 238 24: 236 25: 228
26: 263 27: 249 28: 219 29: 221 30: 291 31: 236 32: 234 33: 245 34: 231 35: 237
36: 238

I had these two lines in my cc_config:

<process_priority>3</process_priority> <process_priority_special>2</process_priority_special>

I never noticed they caused a problem before so I just left them alone. I changed them to:

<process_priority>0</process_priority> <process_priority_special>0</process_priority_special>

and the clocks sped up:
CPU: Topology: 18-Core model: Intel Xeon E5-2699 v3 bits: 64 type: MT MCP
L2 cache: 45.0 MiB
Speed: 1247 MHz min/max: 1200/3600 MHz Core speeds (MHz): 1: 1205 2: 1295 3: 1199
4: 1343 5: 1277 6: 1210 7: 2525 8: 2310 9: 2051 10: 1199 11: 1226 12: 1325 13: 1282
14: 1300 15: 1387 16: 1199 17: 1247 18: 1199 19: 2298 20: 1199 21: 1199 22: 1199
23: 1291 24: 1254 25: 1199 26: 1199 27: 1877 28: 1980 29: 2001 30: 1199 31: 1199
32: 1287 33: 1199 34: 2179 35: 1209 36: 1850
Well that was with CPU utilization at 12% (4t). When I switched it back to 95% (34t) all the clocks went back to 250ish.
I guess it's better to just let the CPU regulate itself and not force it into a different state. Maybe it's just something about the E5-2699 v3.

27) Message boards : Number crunching : Bad hosts topic (Message 2672)
Posted 17 May 2022 by Aurum

I suspended all but 5 and went away. They're running much faster now. The CPU is 18c/36t so I'm going to work my way up to 18 WUs. Feels like the problem when WUs load too much into the L3 cache and choke the CPU traffic cop.

What feels so strange is that TN-Grid is the only project I'm running and yet this only affected a single computer. I sorted BoincTasks by WU name and other WUs with the same prefix on other computers are running at normal speed.

Does anyone know of a utility that monitors CPU cache utilization?

28) Message boards : Number crunching : Bad hosts topic (Message 2670)
Posted 17 May 2022 by Aurum

I have a slug of WUs that are going to take over 3 days to run, e.g. http://gene.disi.unitn.it/test/workunit.php?wuid=35037615

My wingman completed it in a few hours as normal. It's all the WUs running on the same computer Rig-31 with a Xeon E5-2699 v3 with 4x8 GB RAM. I've rebooted and reduced the CPU utilization but that does not speed them up.

My wingman Technologov is also running Linux with an E5-2680 v4 (14c/28t) with 56 processors so must be a dual CPU server MB and 64 GB RAM.
http://gene.disi.unitn.it/test/show_host_detail.php?hostid=78642

I can't see any reason for this computer to run them so slow. But, I've been running BOINC 24x7 for years and I'm literally wearing out MBs. Some ooze oil from the PWM caps or stop communicating with one or more PCIe slots. This ASRock X99 Extreme4 may be at the end of its life and ready for the scrap heap.

Penny for your thoughts if you have a suggestion as to what might be my problem. TIA

29) Message boards : Science : Miscellaneous gene-related news (Message 2662)
Posted 13 May 2022 by Aurum

The Human Cell Atlas is pinpointing where our bodies break

https://www.popsci.com/science/human-cell-tracking-genetic-tracking/

Is our TN_Grid work contributing to the Human Cell Atlas?

30) Message boards : Science : Miscellaneous gene-related news (Message 2616)
Posted 4 Apr 2022 by Aurum

The end of inflammation? New approach could treat dozens of diseases.
Cancer, aging, and severe COVID-19 have all been linked to damage from inflammation. Now scientists are flipping their focus to find new drugs that may revolutionize treatments.

https://www.nationalgeographic.com/science/article/the-end-of-inflammation-new-approach-could-treat-dozens-of-diseases?rid=A2E8D651A715289A902F5351370E3E0A&cmpid=org=ngp::mc=crm-email::src=ngp::cmp=editorial::add=SpecialEdition_20220304

31) Message boards : Number crunching : Badges (all of them) (Message 2595)
Posted 27 Mar 2022 by Aurum

Time to create the next badge :-)

32) Message boards : Science : Miscellaneous gene-related news (Message 2589)
Posted 16 Mar 2022 by Aurum

Treating tough tumors by exploiting their iron â€˜addictionâ€™

https://scienceblog.com/528655/treating-tough-tumors-by-exploiting-their-iron-addiction/

The Fe+2 activation scheme is very clever!

33) Message boards : Number crunching : Why I get different tasks for SSE2 and for AVX platform ? (Message 2529)
Posted 16 Feb 2022 by Aurum

Why restrict it? Easier to let the system choose the fastest and youâ€™ll get more work done.

Right you are, just my idiosyncrasy.

34) Message boards : Science : Miscellaneous gene-related news (Message 2526)
Posted 15 Feb 2022 by Aurum

Compound might defeat multidrug-resistant bacteria found in hospitals

https://scienceblog.com/527600/compound-might-defeat-multidrug-resistant-bacteria-found-in-hospitals/

Very nice work! I wonder if there isn't a bacteriophage that can kill Acinetobacterâ€¯baumannii.

35) Message boards : Number crunching : Why I get different tasks for SSE2 and for AVX platform ? (Message 2525)
Posted 15 Feb 2022 by Aurum

This is the way I restrict all WUs to FMA:
http://gene.disi.unitn.it/test/forum_thread.php?id=304&postid=2209#2209
You need to save a copy of the FMA executable that you can copy to all your computers:
/var/lib/boinc-client/projects/gene.disi.unitn.it_test/gene_pcim_v1.10_linux64__fma
Beware that when you install this and then click "Read config files" BOINC will wipe out all your WUs in the TN-Grid project folder so you might as well Abort them first.
Also, if you're new to BOINC you may benefit from a couple of tweaks to your cc_config.xml file.
I also recommend using BoincTasks to manage so many computers.

36) Message boards : Number crunching : Compiling for AVX-512 (Message 2444)
Posted 6 Jan 2022 by Aurum

Intel is abandoning avx512

"...so if you are able to make use of AVX-512 support, youâ€™d best not upgrade your BIOS from now on if you can help it."
I wonder if they're going to disable AVX-512 for previous generations.
I only run fma for TN-GRID. Are there BOINC projects that benefit with from AVX-512?

37) Message boards : Wish List : Donations Wishlist (Message 2389)
Posted 16 Oct 2021 by Aurum

Gridcoin wallets have a split-staking feature where I can send my newly earned GRC to other addresses. If TN-Grid had a GRC donation address I'd gladly send you what's in my wallet plus future staking. Then you could get one of these jewels :-)
https://www.dell.com/en-us/work/shop/povw/storage-sc7020#features_section

38) Message boards : News : Storage problem (Message 2388)
Posted 16 Oct 2021 by Aurum

Can we donate our GRC so you can buy your own storage node?

39) Message boards : Science : Miscellaneous gene-related news (Message 2323)
Posted 12 Jun 2021 by Aurum

New discovery could help take down drug-resistant bacteria

https://www.livescience.com/game-changer-antibiotic-resistant-superbugs.html?utm_source=Selligent&utm_medium=email&utm_campaign=LVS_newsletter&utm_content=LVS_newsletter+&utm_term=4875497&m_i=y_jNPvkxXSRdv30TmQjO0JUxiThr4_Ra4gFxzxlmnKfMScW0uWEjsw1ap79_IOaKlAxq2OD1gaqocx2nmoBEs2D8bPcFEOI8RDMumvmyyB&lrh=a8a9a81e018d68ee94223125f7a6c0186af911ef83f29920ccc2b9fbbb46d9bc

40) Message boards : Science : proterna_vae64lat dataset (Message 2309)
Posted 13 May 2021 by Aurum

Thanks toma. That sounds like the combinatorials are endless. I'm not familiar with the field of gene expression but things like various skin diseases and osteoporosis come to mind. Are there examples of how eGTEx might lead to new or better diagnostics or treatments?

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