I used to be happy that my bioinformatics boxes had ~800GB total storage (not including the overhead that RAID/mirroring adds).
Now we are dropping in a 4TB storage area network and that is just to lay the foundation for an unknown future amount of massive expansion. It seems that every new genomics/proteomics/(insert buzzword here) has a nasty multiplyer effect on the total storage a research computing group needs. Makes for some fun infrastructure projects though.
That being said, I wouldn't touch Sun storage products:) Actually I wouldn't use sun servers for any type of hardcore technical computing or sequence analysis work. When it comes to raw integer performance you just can't beat the price/performance that a nice AlphaServer will give you.
(just my $.02) But it's not that funny....PCR takes a small amount of DNA and makes lots more. Has nothing to do with DNA fingerprinting except in that you might use PCR to increase your sample size. So -- weak humor attempt plus lame OJ Simpson reference makes me think that someone was just going for some cheapo karma...
The 'sucka VCs' line was great. I actually just tried to register the suckaVC.com domain name. If I get it and anyone wants an @suckaVC.com mail alias then drop me an email:)
Actually this is great. Losers who bite other peoples resources, copyrights & bandwith for their own websites cannot complain when the item they direct link to suddenly becomes something else entirely. Although there are better ways of preventing this at the webserver level the quick and dirty approach is pretty funny and certainly gets results...
Re:good luck trying to get a quote on this stuff
on
New Mega Alphas
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· Score: 1
This is not meant to be a sales pitch or anything but I buy a significant amount of Alphaserver hardware each year and am *very* happy with the reseller that I use. I've recommended them to others who have also been pleased. Your milage may very but if you are interested in a reseller with good engineers who can get quotes out the door quickly I'd recommend Pioneer Standard (http://www.pios.com). I've been using them for years. My rep has been trying to sell me the DS10L systems for a while so I know that they are familiar with them.
My impression is that it is a marketing term aimed at a bunch of the ease-of-install and ease-of-management stuff that they have added to the systems. This includes the ability to power down parts of the system without bringing the whole machine down as well as a bunch of features aimed at the "limited access" crowd (think co-located servers in secure racks/rooms) -- the systems can be installed and configured/run remotely and have all sorts of sensors and environment monitors that can report sensor status to remote management tools.
please don't feed the trolls...getting angry responses is what they live for (sad huh?)
The 1U unit is called the 'DS10L'
on
New Mega Alphas
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· Score: 2
I saw a few of these in a Compaq SAN interoperability lab a few weeks ago. I assume they are ready now with Tru64 Unix...not sure about getting them preinstalled with linux though.
The Compaq product info page is here. The 64bit OS plus the high internal bandwith means it should be a very great clustering unit, especially as you can now fit 40 of them into a single rack.
Here are the specs:
1U Form factor for rackmount version
466 MHz Alpha 21264 64-bit processor
Desktop or rack-mount, with up to 40 systems in a rack
The primary reason for the success of Celera's mapping effort was the simply incredible technological advancements in the DNA Sequencing hardware and procedures that made the process faster and cheaper than anyone thought was possible.
10 years ago the state of the art was pretty poor. The HGP estimates were based on that technology.
Celera's relationship with PE allowed them to get their hands on tons of the new 6700 series DNA sequencers. Without them Celera's effort would have been impossible.
So-- Ventor does deserve some credit -- he was smart enough to realize that the revolution in sequencing (plus a cozy relationship with PE) had changed things enough to make a a large-scale private effort possible.
Celera is using an obscene amount of AlphaServers from Compaq. They are doing large scale clustering as well as compute farms and "farms of farms". Lots of their process involves big compute but the biggies seem to be the actual assembly process plus the analysis of the finished data.
I did hear at one point that they were going to gang together 400 or so 4processor AlphaServer ES40's specifically to handle either the assembly or analysis portion. The 400 servers X 4 600mhz EV6 Alpha chips would give you 1200+ cpu's in the cluster...the final version of this system is what they claim will be the 2nd fastest civillian owned supercomputer on earth.
I don't work for Celera so mistakes made above are my own. I'm just a bioinformatics hardware geek and a big supporter of Alpha-for-life-science-research type projects. From a infrastructure geek's perspective what Celera is doing is just amazing...
Ewan Birney, bio.perl.org hacker extrordinaire is heading up a new effort called ensEMBL which is intended to provide a free and open "baseline" annotation of the human genome. You can find more info at http://ensembl.ebi.ac.uk.
not that I want to defend the show or anything. ack. I think you got the question wrong...
The question from the AOL user was "How do I get credit card numbers" _not_ "How do I get passwords". Different question totally and the talk show people basically said that "those types of questions are simply not asked..."
Perhaps they could have educated the newbie a bit more but given all the other bad stuff in the show the talk show segement was not all that horrible...
If previous patterns hold true than the knowledge and technologies developed just to get the space station off the ground and running will spin off into the civilian world and drive all kinds of wild new innovations.
It's easy to diss the potential value of the pure research projects that will go on up there but I think just the technical achievements involved in getting the station up and running & supporting life will have all kinds of useful applications down on earth.
Look into the fields of bioinformatics, genomics and computational biology. You get to work at the cutting edge of many disciplines -- high performance technical computing, genetics, molecular biology etc. etc.
Right now the field is pretty hot -- companies and labs are desperate for biologists who can code and techies who have a basic mol. bio background.
We even have our own Open Source projects to play around with:) Take a look at http://bio.perl.org.
Sorry, no raw performance numbers:) I'm also not a networking guru...
Back when I was looking into things, I found a Lisa98 presentation by Curtis Preston called "Using Gigabit Ethernet to Backup 6 Terabytes" -- in his presentation he referred to gigabit ethernet as really being "200Base-T" based on the results he saw. Much depends on your TCP stack and support for jumbo frames, etc. etc.
The ATM vs gigabit ethernet debate totally depends on what "situation" you are talking about. ATM has alot of advantages and seems to be the fastest shipping bandwith available now (OC-48,etc.) It also has nifty billing/accounting/garanteed bandwith abilities and can easily handle both delay sensitive (isochronous) data like streaming media as well as more traditional computer network traffic.
I guess it all comes down to how you want to use it -- I chose Gigabit ethernet for my DNA crunching alphaservers because I knew I was going to have a small number of hosts carrying IP traffic only -- no need for extensive WAN or MAN interconnects or thousands of circuits, no need to deal with isochronous data alongside computer traffic and no real urgent need for the accounting/management features of ATM.
The biggest reason for my choice of gigabit over ATM was inhouse experience -- my group of biogeeks and the corporate IS people have tons of ethernet experience and no real ATM experience. This is why I think gigabit is going to _really_ take off in the LAN/intranet space-- being able to use your ethernet-aware people AND your existing Cat.5 copper wiring is very very attractive.
We need to get this stuff into the mainstream media instead of preaching to the converted on this and other sites. It looks like this may start to happen.
Katz mentioned previously that reporters were trawling this site looking for people and stories. A nice followup article would be to analyze any resulting press to see how well they grasped the issues. Might let us know how well we do at communicating our views 'out there'.
I think the zeroknowledge example code has been around for a while now. The real news today centers around the discovery of Intel getting the antivirus people to declare the zeroknowledge stuff malicious.
The bioperl project depends on the perl.org DNS server for our box bio.perl.org.
(we do have bioperl.org just in case)
I sent an email to the boston-pm gurus but if anyone out there can assure me that DNS for the perl.org domains will be transitioned smoothly I would _greatly_ appreciate it.
On the upside it is great to see the perl user groups (pm.org) taking off.
Bias alert:) I'm licensed to carry in Massachusetts, own 1 firearm (Glock 17) and head to the range often enough that it makes economic sense for me to make/load my own 9mm ammunition.
I shoot for target/sport only, I do not hunt, I do not conceal carry and I do not keep weapons in my home for self defense.
jslag said: The 2nd scenario is more threatening, because, all else being equal, the person who is angry at me and has weapons could more easily act on his anger by harming me.
I can understand where jslag was coming from with this -- although I would argue that by the time someone gets worked up enough to entertain thoughts of premeditated physical harm it really doesn't make much sense to single out the gun owner vs. the non-gun owner...someone in that state is going to cause trouble regardless. It is absolutly trivial for anyone, anywhere to make, buy, improvise or steal any number of possible/potential deadly weapons.
I groaned to myself when I read that Wired article -- I personally believe that it was too big of a leap for someone on one end of a (public no less!) email flame war to jump to the conclusion that because ESR owns weapons, he represented a physical threat. My impression was that Bruce acted a bit to quickly in advance of better judgement -- it was a quick and dirty way to generate some press and attack a critic by playing on stereotypes that all firearm owners are lunatics or not in full control of their faculties.
Mind you this is just my $.02:) As individuals we are responsible for much of our own security and I don't want to knock Bruce for doing what any normal person would do if he/she felt threatened. I just personally feel that in this case it was a bit of stretch to reach that judgement and it brought a whole new negative light onto the whole deal.
Slashdot Mirror
very very true.
:) Actually I wouldn't use sun servers for any type of hardcore technical computing or sequence analysis work. When it comes to raw integer performance you just can't beat the price/performance that a nice AlphaServer will give you.
I used to be happy that my bioinformatics boxes had ~800GB total storage (not including the overhead that RAID/mirroring adds).
Now we are dropping in a 4TB storage area network and that is just to lay the foundation for an unknown future amount of massive expansion. It seems that every new genomics/proteomics/(insert buzzword here) has a nasty multiplyer effect on the total storage a research computing group needs. Makes for some fun infrastructure projects though.
That being said, I wouldn't touch Sun storage products
just my $.02
saw 'shaft' last night and it was basically pretty horrible. There is only so much disbelief I can suspend for one movie
(just my $.02) But it's not that funny....PCR takes a small amount of DNA and makes lots more. Has nothing to do with DNA fingerprinting except in that you might use PCR to increase your sample size. So -- weak humor attempt plus lame OJ Simpson reference makes me think that someone was just going for some cheapo karma...
Interesting...donated hardware or hosting perhaps?
The 'sucka VCs' line was great. I actually just tried to register the suckaVC.com domain name. If I get it and anyone wants an @suckaVC.com mail alias then drop me an email :)
Actually this is great. Losers who bite other peoples resources, copyrights & bandwith for their own websites cannot complain when the item they direct link to suddenly becomes something else entirely. Although there are better ways of preventing this at the webserver level the quick and dirty approach is pretty funny and certainly gets results...
hmmm. bioinformatics/computational biology perhaps :)
This is not meant to be a sales pitch or anything but I buy a significant amount of Alphaserver hardware each year and am *very* happy with the reseller that I use. I've recommended them to others who have also been pleased. Your milage may very but if you are interested in a reseller with good engineers who can get quotes out the door quickly I'd recommend Pioneer Standard (http://www.pios.com). I've been using them for years. My rep has been trying to sell me the DS10L systems for a while so I know that they are familiar with them.
My impression is that it is a marketing term aimed at a bunch of the ease-of-install and ease-of-management stuff that they have added to the systems. This includes the ability to power down parts of the system without bringing the whole machine down as well as a bunch of features aimed at the "limited access" crowd (think co-located servers in secure racks/rooms) -- the systems can be installed and configured/run remotely and have all sorts of sensors and environment monitors that can report sensor status to remote management tools.
please don't feed the trolls...getting angry responses is what they live for (sad huh?)
I saw a few of these in a Compaq SAN interoperability lab a few weeks ago. I assume they are ready now with Tru64 Unix...not sure about getting them preinstalled with linux though.
The Compaq product info page is here. The 64bit OS plus the high internal bandwith means it should be a very great clustering unit, especially as you can now fit 40 of them into a single rack.
Here are the specs:
Ewan is heading up just such an open source project you mention. Check out www.ensembl.org.
In a more general way we are also working on tools over at bio.perl.org
10 years ago the state of the art was pretty poor. The HGP estimates were based on that technology.
Celera's relationship with PE allowed them to get their hands on tons of the new 6700 series DNA sequencers. Without them Celera's effort would have been impossible.
So-- Ventor does deserve some credit -- he was smart enough to realize that the revolution in sequencing (plus a cozy relationship with PE) had changed things enough to make a a large-scale private effort possible.
just my $.02
I did hear at one point that they were going to gang together 400 or so 4processor AlphaServer ES40's specifically to handle either the assembly or analysis portion. The 400 servers X 4 600mhz EV6 Alpha chips would give you 1200+ cpu's in the cluster...the final version of this system is what they claim will be the 2nd fastest civillian owned supercomputer on earth.
I don't work for Celera so mistakes made above are my own. I'm just a bioinformatics hardware geek and a big supporter of Alpha-for-life-science-research type projects. From a infrastructure geek's perspective what Celera is doing is just amazing...
Ewan Birney, bio.perl.org hacker extrordinaire is heading up a new effort called ensEMBL which is intended to provide a free and open "baseline" annotation of the human genome. You can find more info at http://ensembl.ebi.ac.uk.
not that I want to defend the show or anything. ack. I think you got the question wrong...
The question from the AOL user was "How do I get credit card numbers" _not_ "How do I get passwords". Different question totally and the talk show people basically said that "those types of questions are simply not asked..."
Perhaps they could have educated the newbie a bit more but given all the other bad stuff in the show the talk show segement was not all that horrible...
It's easy to diss the potential value of the pure research projects that will go on up there but I think just the technical achievements involved in getting the station up and running & supporting life will have all kinds of useful applications down on earth.
just my $.02
Right now the field is pretty hot -- companies and labs are desperate for biologists who can code and techies who have a basic mol. bio background.
We even have our own Open Source projects to play around with :) Take a look at http://bio.perl.org.
speaking as a biocomputing geek, the NCBI website is a great starting point...
All vendor/consortium links I'm afraid...
Sorry, no raw performance numbers :) I'm also not a networking guru...
Back when I was looking into things, I found a Lisa98 presentation by Curtis Preston called "Using Gigabit Ethernet to Backup 6 Terabytes" -- in his presentation he referred to gigabit ethernet as really being "200Base-T" based on the results he saw. Much depends on your TCP stack and support for jumbo frames, etc. etc.
The ATM vs gigabit ethernet debate totally depends on what "situation" you are talking about. ATM has alot of advantages and seems to be the fastest shipping bandwith available now (OC-48,etc.) It also has nifty billing/accounting/garanteed bandwith abilities and can easily handle both delay sensitive (isochronous) data like streaming media as well as more traditional computer network traffic.
I guess it all comes down to how you want to use it -- I chose Gigabit ethernet for my DNA crunching alphaservers because I knew I was going to have a small number of hosts carrying IP traffic only -- no need for extensive WAN or MAN interconnects or thousands of circuits, no need to deal with isochronous data alongside computer traffic and no real urgent need for the accounting/management features of ATM.
The biggest reason for my choice of gigabit over ATM was inhouse experience -- my group of biogeeks and the corporate IS people have tons of ethernet experience and no real ATM experience. This is why I think gigabit is going to _really_ take off in the LAN/intranet space-- being able to use your ethernet-aware people AND your existing Cat.5 copper wiring is very very attractive.
just my $.02
We need to get this stuff into the mainstream media instead of preaching to the converted on this and other sites. It looks like this may start to happen.
Katz mentioned previously that reporters were trawling this site looking for people and stories. A nice followup article would be to analyze any resulting press to see how well they grasped the issues. Might let us know how well we do at communicating our views 'out there'.
I think the zeroknowledge example code has
been around for a while now. The real news today centers around the discovery of Intel
getting the antivirus people to declare the
zeroknowledge stuff malicious.
-chris
The bioperl project depends on the perl.org
DNS server for our box bio.perl.org.
(we do have bioperl.org just in case)
I sent an email to the boston-pm gurus but if
anyone out there can assure me that DNS for the
perl.org domains will be transitioned smoothly
I would _greatly_ appreciate it.
On the upside it is great to see the perl user groups (pm.org) taking off.
-chris
I shoot for target/sport only, I do not hunt, I do not conceal carry and I do not keep weapons in my home for self defense.
jslag said:
The 2nd scenario is more threatening, because, all else being equal, the person who is angry at me and has weapons could more easily act on his anger by harming me.
I can understand where jslag was coming from with this -- although I would argue that by the time someone gets worked up enough to entertain thoughts of premeditated physical harm it really doesn't make much sense to single out the gun owner vs. the non-gun owner...someone in that state is going to cause trouble regardless. It is absolutly trivial for anyone, anywhere to make, buy, improvise or steal any number of possible/potential deadly weapons.
I groaned to myself when I read that Wired article -- I personally believe that it was too big of a leap for someone on one end of a (public no less!) email flame war to jump to the conclusion that because ESR owns weapons, he represented a physical threat. My impression was that Bruce acted a bit to quickly in advance of better judgement -- it was a quick and dirty way to generate some press and attack a critic by playing on stereotypes that all firearm owners are lunatics or not in full control of their faculties.
Mind you this is just my $.02 :) As individuals we are responsible for much of our own security and I don't want to knock Bruce for doing what any normal person would do if he/she felt threatened. I just personally feel that in this case it was a bit of stretch to reach that judgement and it brought a whole new negative light onto the whole deal.