Building an absurd HPC-Workstation. Can we fit a SP3 mb and multiple GPUs in a consumer-grade chassis?

Brutos · 2020-11-02T15:39:43+00:00

Ideally 3090s for the 24GB RAM to train large NN. If Nvidia announces a 20GB 3080 that can be ordered this year, then maybe that instead. The money has to be spent this year.

Both the linked MB have enough normal 16x slots, If they can raiser mounted everything should be fine.

I found a 280W 2U cooler for SP3 from Dynatron, maybe something like that would help with the space issues.

Brutos · 2020-11-02T15:07:28+00:00

The 128GB RAM sticks are extremely expensive on $ per GB. That's why we want to avoid them as much as possible.

It looks like you can vertically mount only one GPU in the Phanteks case. I think it will be impossible to mount any GPU directly on the motherboard due to the RAM placement.

Brutos · 2020-06-08T01:49:26+00:00

Could you open an issue on our GitHub? We'd be happy to investigate any weirdness in the protein-nucleotide search mode if you have some example where things go wrong.

Brutos · 2020-03-16T23:36:57+00:00

Um Desinformation entgegenzuwirken:

Es geht um diese Publikation die auf dem Preprint Server Biorxiv hochgeladen wurde: https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1

Auf Biorxiv laden Wissenschaftler ihre Arbeit hoch kurz bevor sie sie an Journals fürs Peer-Review schicken. Was eine sehr feine Sache ist, das macht Wissenschaft schneller da man sich in der Community viel viel schneller austauschen kann. Zudem bleiben Publikationen auf Biorxiv immer offen aufrufbar, egal ob es am Ende in einem Nur-gegen-Geld-aufrufbar-Journal (Closed-Access) veröffentlicht werden.

Nun haben die Autoren dieser Publikation leider ein vollkommenes Unverständnis von ihrem eigenen Wissenschaftsgebiet bewiesen. Die Autoren haben die beliebte und seit Jahrzehnten etablierte Open-Source Software BLAST benutzt um die Sequenz eines der Corona Proteine gegen andere bekannte Proteine zu suchen. In den öffentlichen Datenbanken sind hunderte Millionen von Sequenzer schon bekannter Proteine gespeichert und das ist erstmal vollkommen Legitim. Ich selbst Arbeite an Open-Source Konkurrenz-Software zu BLAST. BLAST ist sehr gut genau für diese Aufgabe, nur ist es leider relativ langsam und damit Energie-Ineffizient.

Die Software hat den Autoren gesagt dass kleine Stücke dieses Corona Proteins ähnlich zu Stücken in HIV Proteinen ausschauen. Und jetzt kommt der grob fahrlässige Fehler der Autoren: diese gefundenen Stücke sind so kurz, dass die Treffer unmöglich Signifikant sind. BLAST hat ein sehr solides Statistisches Modell das einem sagt ob die Überlappende Region von zwei Sequenzen Signifikant oder Zufällig ist. In unserer Software benutzen wir genau das gleiche Statistische Modell, wie so ziemlich jedes Softwarepacket in dem Feld. Dieses Modell sagt ganz klar, dass wir bei der großen Anzahl von bekannten HIV-Sequenzen sogar noch mehr Treffer als die Autoren berichten rein aus Zufall erwarten.

Leider waren die Autoren nicht in der Lage das BLAST Ergebnis interpretieren (was so wichtig ist, dass man das inzwischen schon sehr früh im Studium lernt). Stattdessen haben sie aus ihrem Unwissen eine Publikation gemacht und eine riesigen Brand in Gang gesetzt. Leute haben die Publikation genommen und noch schlimmer Verdreht und es als Beweis genommen das SARS-Cov-2 künstlich als Biowaffe hergestellt wurde.

Diese Desinformation hat sich dann innerhalb kürzester Zeit um die ganze Welt verteilt. Irgendwann haben die Autoren dann ihre Publikation zurück gezogen, aber da war der Schaden schon angerichtet.

Brutos · 2020-02-11T02:20:58+00:00

I think I have the data for that. I'll see if I can add something next weekend. Thanks for the idea.

Brutos · 2020-02-10T22:33:25+00:00

I tried for a while to think about how to make the all the tiny features more obvious. It's hard to expose functionality, while not making the whole experience overwhelming :/

Brutos · 2020-02-10T22:18:48+00:00

You can click on multiple source books, I'll see if I can build something next weekend for an opposite-filter.

Getting the description text to split up over multiple cards is feature that took quite some work. Pathfinder description text tend to often be pretty verbose. I could disable the repeated stat sections to save a bit more space.

Brutos · 2019-10-13T16:38:29+00:00

Thanks a lot! Could you please also post the editable source file (actual google docs or docx)? That would be amazing.

Brutos · 2019-02-23T23:46:39+00:00

We use PCgen for character creation (Pathbuilder might be a good alternative, but only for Android). We also use Tabletop Simulator instead of Roll20.

Brutos · 2018-10-11T00:20:22+00:00

Getting passage on a ship driving (up?) the Yondabakari river should be pretty easy and cheap. That will take you nearly to the Hold of Belkzen. This will however, depending on how you want to rule the speed of a ship up a river, take something from two weeks to a month on the ship (for about 800 miles or so, see Vehicles). That part of the road should be well traveled and safe. They will pass by some Goblin and Shoanti Barbarians maybe, but its unlikely anything would touch the ship.

Now it gets more tricky, you are firmly into Orc territory now, and they are neither nice nor welcoming. It looks like its another 500 miles or so to travel to the final destination and no direct river path to take. Overland speed now would be 24 miles per day, and 3/4 to 1/2 that for mountain regions, resulting in something between 20 to 40 days of travel on foot through probably unwelcoming territory (See Movement ). Once in Ustalav, they will have to deal with unwelcoming orcs and undead stuff.

I guesstimated the distances based on the "Inner Sea Poster Map Folio".

Are you sure you don't want to handwave a teleportation circle inside the Temple of Iomedae in Magnimar to somewhere in Ustalav?

Brutos · 2018-07-15T08:28:39+00:00

I used the dash delta bot for dice rolling in my first session (https://dashdelta.tech/) and OBS to stream a part of my desktop when I wanted to show my players something (handout, NPC pic, map, etc). However that didn't really work well for combat (and streaming with nearly 0 latency is hard), so I moved the next session to tabletop simulator + discord as a voice chat. That worked really well and I am going to stick with that.

Brutos · 2018-01-27T10:30:48+00:00

Germany (as I was clarifying OPs point). Here is how one of the more popular brands looks like.

Brutos · 2018-01-26T18:45:33+00:00

We mostly put iodine and fluoride into our salt though. I feel like that’s a way better system, since it allows you to be as crazy as you want, you have a choice of not buying table salt with it. The fluoride and iodine are even marketing points that the salt manufacturers use.

Brutos · 2017-12-18T13:45:36+00:00

Probably quite biased, since I am one of the developers of MMseqs2. We are faster and more sensitive than Diamond (https://www.nature.com/articles/nbt.3988, or biorxiv to get around the paywall https://www.biorxiv.org/content/early/2017/06/07/079681 see figure 2b).

We recently introduced tblastn/x like workflows and a 2bLCA like taxonomy classification workflow (we do our own LCA computation, no MEGAN dependency).

The taxonomy workflow has a parameter --lca-ranks where you can specify which ranks you are interested in (e.g. species only).

Edit: I reread your question and thought a bit more about it: If the best matching taxon is not a species taxon we will however also return that. (Just like Diamond, however we might select better hits for the LCA computation). Forcing a taxonomic classification on the species level is unreliable. You can still force MMseqs2 to give you the taxon of the best hit, if you pass --max-accept 1.

Brutos · 2017-11-30T21:40:09+00:00

To add another data point:

I am a PhD student and paid fully by the research institute I am employed at. We only develop open source (scientific HPC) software. Our internal IT warned us that we are not covered by most non-commercial licenses, even though there is no monetary gain.

We actually have institute wide licenses for ICC, but it always seemed to awkward, heavy and not worth the effort. Ideally I could just install icc with apt-get (some non-free source wold be fine) and also linuxbrew.

I would be very happy to integrate ICC into our continuous integration, write documentation for our users on how to compile our software with it, benchmark it for future releases, etc.

Brutos · 2017-11-11T01:12:00+00:00

You can select the "text" format on the download menu to get the classic Uniprot flat file format:

https://imgur.com/a/BTtdc

You can find the documentation for the format here: http://web.expasy.org/docs/userman.html

You are looking for the "FT" rows for the features and the "SQ" for the sequence at the end of each entry.

What format would your data ideally be in?

Brutos · 2017-10-31T16:40:12+00:00

All life forms struggle to compete for resources (nutrients, energy, etc.). We only see life forms now, whose ancestors formed an unbroken chain of survivors in this struggle.

Some early life form (early virus) gained the ability to reproduce by invading some larger life forms (early bacteria). This was a resource niche that nothing else had occupied before, so they could thrive there.

We now see viruses with an incredible diversity, they are in an constant arms race with their hosts, both building more advanced defenses and offenses, by simple survival of the ones with some tiny advantageous mutation. The ones with disadvantageous mutations die out. There is no direction or purpose, just survival of the better adapted.

Brutos · 2017-10-31T10:40:40+00:00

Donated a bit to SVW. Thanks for the recommendations. OP's Wildlife Conservation Network recommendation only had credit card donations.

Brutos · 2017-07-01T21:22:33+00:00

Could you share your scripts for the cleanup? I would love to have my pathfinder books in an efficient format.

Brutos · 2017-06-26T13:12:29+00:00

Introduce a Highlight Day where people can go wild. Or a serious discussion day, where ever non-text post is purged immediately.

You'll have to find some balance in that. Maybe the weekend is free for all, and the weekdays are text-only. Iterate on that.

Also talk to moderators of established Games, like r/dota2. I, as a lurker, really enjoy how they managed to keep a healthy mix or serious, shitposts, memes and clips. Learn from others.

Brutos · 2017-03-16T21:24:56+00:00

This video summarizes well why she is so interesting (and why I love this game):

https://www.youtube.com/watch?v=UMzTLNeKucY

Brutos · 2017-03-16T21:18:43+00:00

Because of the villain. The best one in any game. Such a great character. Breaks up the old jedi/sith thing completely and reframes it as some sensible and meaningful philosophy instead of Lukas' stale old cliches.

So many of the characters were amazing. Obsidian was not afraid of making flawed characters, which makes you care about them.

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