* Posts by Chemist

2677 publicly visible posts • joined 24 Mar 2010

German Foreign Office kills desktop Linux, hugs Windows XP

Chemist

businesses will never take OSS seriously

Having worked for one of the world's largest pharmaceuticals companies for 38 years I can tell you that OSS was taken very seriously from Linux servers to large Linux compute farms to the 3D desktop workstations that computational chemists used. Even though some of the desktop software we used was some of the most expensive I've ever heard of the use of Linux and Xeons gave the stability and power to run molecular dynamics or protein modeling flat out for days at a stretch without expensive proprietary Unix/hardware. This wasn't just now this was 6-8 years ago

Chemist

Re : A genuine question

OpenSUSE and KDE

Welcome to the Petabyte Club

Chemist

There's big data ..

and there's the LHC - in a different league

The Large Hadron Collider will produce roughly 15 petabytes (15 million gigabytes) of data annually

Nissan readies ultra-low CO2 petrol engine for Micra

Chemist
Joke

You forgot...

the brewers. Panic now

Watson? Commercial – not super – computer

Chemist

Should have been ...

Mycroft , who was Sherlock Holmes' smarter brother

Intel seeks connected home for Atom

Chemist

But

IF this ever came to pass it would have an ARM or even just a PIC in it and NOT a mobile link. For that matter the tracker device in my motorhome has GPS/mobile link and doesn't cost that much.

Chemist

Hint

Vodafone

Oracle gives 21 (new) reasons to uninstall Java

Chemist

"Openoffice depends on it"

Turning Java requirements off is an official way of speeding-up OpenOffice startup

SGI plunks Windows on big Altix UV supers

Chemist

On the other hand ..

You, supported by no-one, have ranted on without any evidence and totally ignored any real references to actual hardware and systems. I think you should attempt to get yourself up-to-date with the whole area.

Blacklight, the World’s Largest Coherent Shared-Memory Computing System, is Up and Running at the Pittsburgh Supercomputing Center

PITTSBURGH, PA., October 11, 2010 — Researchers are making productive use of Blacklight. This new system, which the Pittsburgh Supercomputing Center (PSC) acquired in July (aided by a $2.8M award from the National Science Foundation) features SGI’s (NASDAQ:SGI) newest scalable, shared-memory computing platform and associated disks. Called Blacklight, the SGI® Altix® UV1000 system’s extremely large, coherent shared-memory opens new computational capability for U.S. scientists and engineers.

Featuring 512 eight-core Intel Xeon 7500 (Nehalem) processors (4,096 cores) with 32 terabytes of memory, Blacklight is partitioned into two connected 16-terabyte coherent shared-memory systems — creating the two largest coherent shared-memory systems in the world.

These days, the Top500 list of the world's most powerful supercomputers is dominated by cluster designs assembled from many independent computing nodes. But there's still a place in the world for an earlier approach, as evidenced by a new machine called Blacklight at the Pittsburgh Supercomputing Center.

http://insidehpc.com/2010/08/03/the-rich-report-the-16-terabyte-pc-sgi-bets-on-exascale/

i

nsideHPC: And that’s a single system image for all those cores?

Dr. Eng Lim Goh: Yes. It runs as a Single System Image on the Linux operating system, either SuSe or Red Hat, and we are in the process of testing Windows on it right now. So when you get Windows running on it, it’s really going to be a very big PC. It will look just like a PC. We have engineers that are compiling code on their laptops and the binary just works on this system. The difference is that their laptops have two Gigabytes of memory and the Altix UV has up to 16 Terabytes of memory and 2000+ physical cores.

So this is going to be a really big PC. Imagine trying to load a 1.5 Terabyte Excel spreadsheet and then working with it all in memory. That’s one way of using the Altix UV.

(I may be a chemist but my involvement in computing goes back almost 30 years from SC/MP, 6502, 6809, 68000 and PICs., PDP-11/34, Evans and Sutherland vector graphics systems, VAX/VMS all the way to SMP workstations and 1024 cpu Linux Clusters.)

Chemist

Oh good grief !

I repeat the PSC Blacklight is an Altix® UV1000 with 4096 cores and 2 copies of LInux

http://www.psc.edu/publicinfo/news/2010/101110_Blacklight.php

Chemist

You seem to be under the wrong impression..

A multiprocessor system that runs ONE copy of the OS is not a cluster - how can it be ?

You seem to think that a multiprocessor NUMA system is a cluster - it's not

I repeat the PSC Blacklight is an Altix® UV1000 with 4096 cores and 2 copies of LInux

http://www.psc.edu/publicinfo/news/2010/101110_Blacklight.php

A computer cluster is a collection of computers that are highly interconnected via a high-speed network or switching fabric. Each computer runs under a separate instance of an Operating System (OS).

A multiprocessing computer is a computer, operating under a single OS and using more than one CPU, wherein the application-level software is indifferent to the number of processors. The processors share tasks using Symmetric multiprocessing (SMP) and Non-Uniform Memory Access (NUMA).

Chemist

FYI

http://www.psc.edu/publicinfo/news/2010/101110_Blacklight.php

has 4096 cores running 2 Linux kernel images

Chemist

So ..

you are saying that SGI don't know what they are manufacturing and don't care that customers will notice that it's all snakeoil. Yeah, right.

The fact, by the way, that you can read (any) comments in the kernel source is a strength. Who knows what nightmare is in the Windows source.

From an Intel paper software.intel.com/sites/oss/pdfs/mclinux.pdf

2.6 Linux kernels (which have better SMP scalability compared to 2.4 kernels)

From a MIT paper pdos.csail.mit.edu/papers/linux:osdi10.pdf

"First we measure scalability of the MOSBENCH

applications on a recent Linux kernel (2.6.35-rc5, released

July 12, 2010) with 48 cores...."

"FreeBSD, Linux, and Solaris [54], and find that Linux

scales better on some microbenchmarks and Solaris scales

better on others. We ran some of the MOSBENCH appli-

cations on Solaris 10 on the 48-core machine used for

this paper. While the Solaris license prohibits us from re-

porting quantitative results, we observed similar or worse

scaling behavior compared to Linux; however, we don’t

know the causes or whether Solaris would perform better

on SPARC hardware. We hope, however, that this paper

helps others who might analyze Solaris."

From The Register http://www.theregister.co.uk/2010/11/10/redhat_rhel_6_launch/

On 64-bit x64 platforms, it can scale to 128 cores/threads and 2TB of main memory using one set of kernel extensions and to 4,096 cores/threads and 64TB of main memory. (Not that anyone can build a system with that many processors or that much memory yet.)

These are NOT clusters - I used a 1024 node cluster YEARS ago - these are for single image machines. I notice you've had the same arguments with different people all over the net. They all told you you were wrong.

Chemist

Oh and by the way

Your comment "unstable toy OS with low code quality" REALLY shows up your lack of knowledge

That's why Linux is used for >90 of the worlds top supercomputers ?

Chemist
Flame

Suggest you ..

read what SGI say about it.

http://www.sgi.com/products/servers/altix/uv/

" whereas Altix UV 100 and Altix UV 1000 are all about scaling a single system image to a maximum of 2048 cores"

"Because of SGI's collaboration with the Linux community, Altix UV runs completely unmodified Linux, including standard distributions from both Novell and Red Hat"

Latest boffinry: Feeding TNT to sheep

Chemist

"if it's not being ingested then the TNT"

It's being eaten - the TNT gets into the grass, the sheep eat the grass but then the bacteria in their gut breaks down the TNT to, presumably, safer and/or more biodegradable products. These may well be absorbed/excreted/exhaled

DEC: The best of systems, the worst of systems

Chemist

I don't think it could have been

It was sometime in the early 80s and I was more interested in what could be done with it.

We had some fine kit in the next few years. I seem to recall an Evans and Sutherland colour vector graphics display run by a bit-slice processor and with a PDP11 as its file store.

By the time I retired we had stereo-graphics equipped dual xeon workstation running Linux with access to 1024 machine Linux clusters for the 'hard' stuff. Some of the easier protein modeling took a weekend to run on dual xeon machines

Chemist

PDP11/34

First computer I used that with a few add-ons could display molecules being rotated and manipulated in real-time.

Rare metals found in Cornish tin mine

Chemist

Great wit

His songs were brilliant. "The Masochism Tango" was one of his ?and "Poisoning Pigeons in the Park"

US gov says it can't build an interstellar starship

Chemist

Very reasonable plan

Let's get the spanners out Gromit !

Linux vulnerable to Windows-style autorun exploits

Chemist

FUD

You seem to have had bad experiences. I don't know why. I use OpenSUSE 11.2 on 5 quite different machines and have had no problems - they are all rock solid. My ultra-low power file-server is only rebooted for updates.

Chemist

Ah, the A1000

Ditto

Chemist

Futher comment

To reply to some comments down the forum :

Even if the usb stick didn't automount the same/similar vulnerability would be triggered if the user then mounted it and used whatever flawed application.

The main problem here is that the file manager opened the usb stick automatically - that should never be allowed and indeed I don't think it is in most distributions.

Chemist

Well in a general sense I agree, Big Yin

but it doesn't allow anything that isn't predefined. No scripts or executables.

Chemist

To add

Certainly using OpenSUSE 11.2 and usb stick or any removable device *automounts* but ONLY puts up a requester asking for reasonable option to deal with the device ( Do nothing or file manager or picture viewer whatever for a USB stick)

Chemist

Oh good grief !

Are we really supposed to take this seriously ?

HP rocks Redmond with webOS PC play

Chemist

What is WebOS?

Linux

Super-thin materials could POWER our WORLD

Chemist

"I was taught that the benzene molecule had two conformations"

No it's planar - cyclohexane has chair & boat conformers. Benzene has delocalised electrons that convert the bonding from sp3 (tetrahedral) found in alkanes to sp2 ( trigonal) so kinked versus planar. The conformation of benzene was contentious for along time but it's been fixed for many decades. It can be seen in any x-ray derived structure that has a benzene ring or derivative.

Download the excellent SwissPDB ( Mac & Windows) and get yourself a structure to view.

http://spdbv.vital-it.ch/download.html

http://www.pdb.org/pdb/home/home.do

I used to wear a white coat but it's been virtual for a while

Chemist

I have the feeling that ..

The original way of getting monolayers of graphene involved little more than graphite and sellotape

Chemist

Not too suprising ..

Given that there are ~~8e19 carbon atoms in a 1mg of graphene

Chemist

Re : Yes, planar

Oh sure, there's plenty to be pedantic about. The real measurement is distance and that's on an atomic scale - in this sense a 'molecule' is meaningless going from a molecular weight of 2 for a hydrogen molecule to essentially anything you like such as billions for polymers.

This is all about, let's call them pseudo 2D structures, that have an 'average' thickness in the order of (at the most) atom-atom bond lengths.

Chemist

Re : Not necessarily →

True. A benzene molecule, for example, is a flat ring with 6 carbons in a plane but is only 1 carbon atom thick

'Tree Octopus' proves journos no smarter than 13-year-old Americans

Chemist

Great

Wonderful description - I haven't a copy to hand at the moment but the Chancellor's (or what ever he was ) assertion that meta-analysis WAS the only scientific method was priceless.

I also liked the mayor's conclusion that the Chancellor had seems a consumate donkey but was really rather a clever politician in that he's had talks for days with the scientists who were the governors of Terminus but all he'd said and promised when analysed by symbolic logic amounted to nothing - that everything he'd said had eventually been canceled out by other statements and NOBODY (except the mayor ) has noticed. I often think of this when listening to politicians.

Chemist

Think this needs rephrasing

I know what you means but there really is something very wrong with :

"used to prove the link between vaccination and autism."

Aussie advertisers call for more bloat in web ads

Chemist

"Then Edimax added offical support for Linux...."

"I will now go to Edimax first"

Me too.

Official: PhD in 'Essential Oils' or 'Natural Toiletries' = 'a Scientist'

Chemist

"western medicine bases it cures on herbs and natural substances"

I take your point but to a great extent it's not true. I spent 38 years doing pharmaceutical research and only worked around natural products on 2 occasions.

Chemist

"happy to recognise them as scientists if they have PhDs"

Academic qualifications are NOT necessary. Practicing the scientific method, contributing and peer review are the key items.

I've worked with several great chemists, the most notable, who had published widely and was one of the world experts on LogP calculation, did not have a PhD.

For that matter Einstein didn't have too many serious qualifications until after Relativity.

Chemist

".. label "scientist" would be those who practice ... the scientific method."

Agreed.

Boffins hope for dimensional portal event at LHC by 2013!

Chemist

Obvious answer is ...

Strange projects but they're up and down about them

Cold call scareware scammers aim to bring Mac fans into the fold

Chemist

I had one of these recently....

Foreign accent telling me I had serious malware problem and what version of Windows was I using. I told her that all my machines ran only Linux and that she was obviously running a con. She rabbited on and I did what I usually do and left the phone to its own devices for a few minutes. Blow me after I put the phone 'back on the hook' she rang again !

Hubble squints at most distant galaxy

Chemist

Re : Mathematics

Even more interesting ( or mind-boggling ) is the set of inflation hypotheses that suggest that in the first ~1e-32 s after the big bang our 'universe' expanded from less than the size of a proton to ~10 cm across (or much more). This was an inflation of spacetime - no FTL rules were broken.

The current expansion seems quite staid by comparison

Gates, Woz, and the last 2,000 years of computing

Chemist

Sinclair Research

Well I had a Science of Cambridge Mk14 but that was the only Sinclair machine I had. 6809 man for many years with a homebrew Forth system that still runs albeit with a virtual screen/keyboard/disk drive in recent years.

Extension of flexibility 'may help solve retirement problems'

Chemist

"..this week's strategic suggestion from the very expensive.."

In my area it was ~every 10 years.

Bot attacks Linux and Mac but can't lock down its booty

Chemist

"..that Linux users never reboot their machines.."

Oh really. I leave my ultra-low power fileserver on all the time. But if I left the other 6 on I'd pay a fortune for electricity. As someone said it's hardly likely the fileserver is going to go off browsing on its own

Chemist

Even using Linux exclusively..

.. I don't browse without NoScript

HBase: Shops swap MySQL for open source Google mimic

Chemist

"..yanking dud valves out.."

Oddly enough I was taught Physics by someone who had worked as a graduate student on the Manchester Baby. He had a photo of himself, stripped to the waist, working in a room stacked with chassis. No A/C of course and precious little ventilation

Who are the biggest electric car liars - the BBC, or Tesla Motors?

Chemist

"..eliminating the need for hiring cars or using taxis.."

So you think that the real cost of hauling a tonne+ of car by train will be cheaper than a taxi ?.

Chemist

"...have to be overhead lines like a real bumper car..."

Overtaking would be tricky !

Ubuntu - yes, Ubuntu - poised for mobile melee

Chemist

"Play flash full screen?"

It works fine on my old single-core celerion laptop. Mind I'm using OpenSUSE 11.2 not ubuntu. Kubuntu runs flash full screen without any problems on my Asus 901as well.

Lane Fox promises sub-£100 PCs

Chemist

"..from the web she doesn't already get from the telly.."

You ageist Anonymous Coward !!