Posts by JoshuaScholar

1) Message boards : Cafe Rosetta : Moderators Contact Point (Explanations, Assistance etc) Post here! (Message 94036)
Posted 10 Apr 2020 by JoshuaScholar
I heard Zelenko's interview, he sounded knowledgeable but he was certainly claiming success too early.
He'd only been treating patients for 9 days at the point that article was written, only a small fraction of those people he treated were vulnerable enough that he gave them the medicine - and the average time to death from first symptoms was calculated in China as 15 days.

I checked back a few days later and the New York Times was saying his people had seen 900 patients, actually given his protocol to 300 something of them, 6 were in the hospital and 2 were on ventilators.

Now that may not be a bad outcome for such a vulnerable subgroup, but he's certainly gonna get some deaths. The probability of surviving COVID-19 if you're on ventilator is only 1 in 3.

I think his main insight is that ALL studies show that the virus' outcome is mostly improved when virus suppressing medications are given BEFORE serious symptoms appear.

Also there are OTHER (and safer) ionophores that have been shown to let zinc into cells, if zinc turns out to work (note that the South Koreans use zinc and chloroquin). There's a doctor in Canada who is using quercetin as an ionophore along with zinc to treat COVID-19. That's a bioflavinoid that you can get over the counter. His protocol is 50 to 100 mg per one Kg of a person's weight. Don't know how much zinc.

You know, if a medication helps but not very much, then I think the math is that may take a huge sample to be sure that it's helping and you're not just seeing random variation. I get that impression from calculating ELO scores, it sure takes a lot of games to nail down an ELO score difference.
2) Message boards : News : Help in the fight against COVID-19! (Message 93991)
Posted 9 Apr 2020 by JoshuaScholar
I mentioned this before. but on my Xeon E5s I find there's a bug with Numa (turn it off unless you want all instances to run on one socket) and there's a problem with hyperthreading (turn it off unless you're not going to run more than half threads).
3) Questions and Answers : Macintosh : Rosetta 4.12 problem on older iMac? (Message 93538)
Posted 5 Apr 2020 by JoshuaScholar
Since I'm getting no work units from Rosetta, and Folding@Home work units aren't coming (they haven't caught up with new volunteers either, though they've had weeks - though maybe it's because I have them set as GPU only), I added WorldCommunityGrid to BOINC. They're also doing medical research. Currently running tasks for cancer and microbiom.
4) Message boards : Number crunching : Partial use of many CPUs vs. Complete use of one CPU? (Message 93467)
Posted 5 Apr 2020 by JoshuaScholar
I'm not happy what happens when you set the CPU to anything but 100% because the program shuts all of the threads down together and brings them back up together, which makes the temperature of the whole CPU package continually bounce which also confuses my fan control program.

It has to be a worst case for the longevity of your motherboard and cpu to have the machine continually cycle from 0 to 100% just slow enough for the cpu package temp to bounce for months on end.
5) Message boards : News : Help in the fight against COVID-19! (Message 93295)
Posted 3 Apr 2020 by JoshuaScholar
You can program non-temporal accesses to memory (bypassing the cache) in assembly language but that never seems to improve anything.
6) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93208)
Posted 3 Apr 2020 by JoshuaScholar
Even though I have 64 bit windows, it was using the 32 bit version of 4.12. when the virus program went nuts on it.
*Since I had to reset everything, I can see that it's stuck while trying to load the 64 bit version.
Progress is stuck at 99.63% 85.77/86.09 MB I think that happened last time too.
Never mind, it finished downloading and the task list on the website shows that the files it started after that point are running in 64 bits.
Why I was having problems with a 32 bit version before, I don't know.

*correction, after retry it started working.
7) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93200)
Posted 3 Apr 2020 by JoshuaScholar
Sadly exceptions for ransomware are by program, not by folder. It seems my choices are:
1) turn off ransomware protection altogether
2) except Rosetta_4.12_windows_intelx86.exe and know that I'm going to go through the same sh_tshow next time you update the client.
8) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93167)
Posted 3 Apr 2020 by JoshuaScholar
What do I do to clean my system since the damn antivirus program "restored" some of rosetta's files to a previous state, assuming that Rosetta 4.12 is a ransomware program?

I tried aborting the WU's currently being calculated but one finished.
9) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93106)
Posted 2 Apr 2020 by JoshuaScholar
Bitdefender thinks that rosetta_4.12_windows_intelx86.exe "exhibits ransomeware behavior"
I thinks that it encrypted
[a bunch similar like it]
I'm guessing that rng means random number generator and that it reinitialized a bunch of random number files, the program detected the maximum entropy and assumed that the files are encrypted.

I can make that program an exception, but I don't know what's ruined because the damn program restored some of the files to their previous state.
10) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93072)
Posted 2 Apr 2020 by JoshuaScholar
Oh you're right.
I just looked at my task list.
Time per WU has jumped from 8 hours to 16 hours!
The cores are running cooler than the last version too, suggests a bottleneck.
Note 2, I just noticed that the most recent few are fast again.
Maybe there was just a run of WU for a harder problem.
11) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93066)
Posted 2 Apr 2020 by JoshuaScholar
That might be because of the bugs I noticed.
Make sure that every thread is really allocated in its own hyperhthread, because BOINC doesn't leave it up to the OS.
12) Message boards : Cafe Rosetta : Rosetta volunteers in conversation (Message 93060)
Posted 2 Apr 2020 by JoshuaScholar
It looks like everyone will be exposed eventually. But we can slow down the spread so that the hospitals are not overloaded with patients all at once.

The trick will be managing that intelligently. Some governments are better at it than others.

The sheltering in place that countries are doing will keep most people from being exposed until after the sheltering ends ... which starts the problem up again. We're not just flattening the curve, we're also keeping people from getting exposed at all. We're going to have to do a lot of social distancing after the sheltering is over or reinstate sheltering over and over to prevent more peaks.

One solution is a vaccine if we ever get one.

Another solution is anti-viral drugs so that vulnerable people can survive the disease.

The current experience is that anti-viral drugs work well, but ONLY if used when symptoms are mild. While that sounds useless, a closer look suggests it's not useless, only expensive because everyone's symptoms are mild if you catch them instantly after having their first symptoms.

There is one doctor claiming success treating people this way. He treated people so fast that he treated anyone who was elderly or otherwise vulnerable who had any symptoms suggesting COVID-19 BEFORE getting tests back verifying the illness, reasoning that the extra days could cause fatal damage.

And, as I said, he's claiming preliminary success. None of his nearly 700 hundred of patients died and only 2 needed hospitalization, but he hasn't been treating them for very long.

Keep in mind that by the time people are on ventilators, in this disease, the damage to their lungs is so great that they'd probably have a 40%-50% chance of dying even if the virus was magically gone from their bodies.
13) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93058)
Posted 2 Apr 2020 by JoshuaScholar
I know this affects so few people that it won't matter much but:
I have an older 2 socket Xeon system (Sandy Bridge era e5-2690s).

Let me tell you what DOESN'T work properly with the Windows client on my Windows 10 pro setup:
1) NUMA.
Having two sockets, the most common way to run Windows is with each processor accessing the memory that's attached to it directly preferentially. This is called NUMA, and it's slightly faster.
But with NUMA enabled, the client picks the proper number of threads as if it's going to use both sockets, but then it runs all of the threads on only ONE of the sockets.

2) Hyperthreading with NUMA off. [NUMA off is called "uniform memory access", by the way.] With NUMA off and Hyperthreading enabled, the client creates the right number of threads for using both sockets BUT it allocates both threads to the SAME hyperthread in each core. So each core has one empty hyperthread and one hyperthread shared by two threads.

So on this old 2 socket Xeon system running Windows 10 pro, the only efficient way to run the BOINC client is to turn off NUMA and also turn off hyperthreading.

Then it works properly.

On a machine this old, on a highly parallel workload, turning off hyperthreading is about a 20% throughput hit. On a newer processor it would be a greater hit.

I'm not sure if there's any real hit to turning off NUMA, but it isn't a big one.

Josh Scholar
14) Message boards : News : Rosetta's role in fighting coronavirus (Message 92879)
Posted 1 Apr 2020 by JoshuaScholar
Nothing to crunch and it's been over 2 days now which is a good sign more folks are signing up. All's not lost though I'm crunching Smash Childhood Cancer at the World Community Grid until more R@H work units are released.

That's weird, I've done 200 WU in 4 days.
15) Message boards : News : Rosetta's role in fighting coronavirus (Message 92867)
Posted 1 Apr 2020 by JoshuaScholar
I'm running both Rosetta and Folding@home. But Folding is overwhelmed by new volunteers and they don't have enough storage so work units don't come very often.
16) Message boards : Cafe Rosetta : I'm new here and I notice that we're almost out of WU, is that normal? (Message 92684)
Posted 31 Mar 2020 by JoshuaScholar
I've been running for 3 and a half days and I notice that my work queue is now short and that it says that there are only 4,880 work units waiting on the server, so we'll be through them shortly.

Does this happen often? Have we finished all the jobs they had scheduled?

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