TA GENOME@HOME MEMBERS ,ATTENTION NEEDED!

[Assimilator1]

I was just having a quick read of the welcome sticky thread & noticed there was nothing about the G@H project there.If you want a bit more exposure I suggest you PM the mod & give him a brief description of G@H + any links for joining & stats etc.

Btw I see Nexus9 is in that team ,anyone seen him lately?

 

[Assimilator1]

*ahem* is G@H TA dead?

 

[Rattledagger]

The last first... Nexus9 haven't returned anything in Genome since 28.11.2001.

I'm probably not the right to write a description, but let's try anyway...

Genome@Home
is together with Folding@Home run by PandeGroup at Stanford.
The goal of Genome@home is to design new genes that can form working proteins in the cell. The 4 main applications is:
Engineering new proteins for medical therapy, Designing new pharmaceuticals, Assigning functions to the dozens of new genes being sequenced every day, Understanding protein evolution.

Link to Genome@Home project and client download

Anandtech Stats

Client-setup:
Download&install to whatever directory you want...
Run ghclient.exe
1st time run, you'll have to input a...
User Name: CasesENsitiVe...choose that you want
Team account number: 604374405
Server, leave at default if you don't need a proxy-server... There's currently little support for this...
Port, probably leave at default. Note, Genome uses port 10100, and this must therefore be open somethere...
Firewall yes/no... if yes, you'll have to input some more info...

If no problem, the client will now download a wu from Stanford and start crunching...

Make sure the info in ghclient.cfg is correct... If something wrong, you can edit this here. The important is...
email=YourUserName
account=604374405
Note, in Genome, all results returned to a username/group will forever stay in this group with this username. Mistakes in account-number will either be credited to another group, or to no group at all.

Normal running...
Just let it keep on crunching. Normally, it will upload/download then done with wu. If for any reason it can't connect, it will retry a couple of times, and after 5? minutes restart current wu.

Genome will on every restart first upload/download. If you've got a partially done wu, it will download an extra wu if you've not already got an extra wu.
Afterwards, it will Filter. This is just a pre-process on the wu, there it counts up from 1 to aa. (see below for aa)
Now the actual prosessing starts. It will count 10%-20% ... 100% and afterwards...
Sequence nn completed. A wu contains 30 sequences. Genome only saves after a sequence is completed...

Smp or dublicating the same install to multiple machines...
If you've got multi-cpu, you'll have to run multiple instances of genome. Just put them in different directories. There's no special switch for smp.
If you're copying an already made install, MAKE SURE to DELETE id.dat on all new copies. Also delete the wu with genome -clear

Nonetting, sneakernetting...
Genome's biggest advantage over other projects is that it can re-run the same wu. Genome is using a random number for every re-run, and should therefore not normally make doublets. For this reason, it's very easy to put genome on machines without net-connection, and let them crunch away for days/weeks before uploading the results... If you're running without net-connection, use genome -nonet
Then you will upload, you should move the whole directory to a net-machine... Or if you will keep running, copy the directory (except lock.gah that is locked...), delete csum.#####, output.chi.#####, str.##### (##### is a number, the same for one result) from the no-netteded machine. On the networked machine, run genome -upload

Wu-score
aa stands for AminoAcid, and is how many there's in a wu. This number is showing up then filtering, and it's the number of letters printed after every sequence is done... But the easiest way to find the number of AminoAcids is to look at the number on the 1st line in input.inp
The score to a wu is calculated by:
wu-score = 0.05 * aa + 0.0025 * aa * aa
This is more or less following the cpu-time, but there's some disrepancies.
As a comparison, a machine running Seti will in the same time manage to produce 10x in Genome... Well, an Intel-machine will manage this. AMD is a little faster, so 11x-12x is nearer...

misc info
In Genome, it's the raw cpu-speed that's counting. Cache-size, memory-speed, cpu-multiplier is important in Seti, but not for Genome. The only difference is that AMD Athlon/duron/palomino is faster than Intel for the same MHz. There's no performance-hit running multiple instances on smp-machines.

Stats is updated every 3 hours, but due to checking it can take a couple of updates before results is showing up.

Genome-switches, run genome -help

Service-install... Use either FireDaemon or srvany.exe.

Genome is in windows running at priority 4, the same as Seti. A combination with seti will therefore give 50-50-split.

Currently the only clients is win32-cmd and linux.

Huh, sure it got long-winded. Someone should probably put the useful bits up somewhere.

 

[Assimilator1]

Thanks Rattledagger ,lots of info
I hope you don't mind but I going to make a few grammatical corrections & trim it down very slightly
[edit]I've just had another look at the sticky welcome thread & each project has a short description of what it is (about 6-7 lines) ,& the links to the client & stats.It looks like most of the info here needs to go to TeamAnandtech.com

Virge ,grab the info below for the TA site,thanks
**********************************************************************

Genome@Home along with Folding@Home is run by PandeGroup at Stanford.

The goal of Genome@home is to design new genes that can form working proteins in the cell. The 4 main applications are:
Engineering new proteins for medical therapy, designing new pharmaceuticals, assigning functions to the dozens of new genes being sequenced every day, & understanding protein evolution.

Genome@Home project and client download

Team Anandtech stats

Client-setup:
Download & install to whichever directory you want...
Run ghclient.exe
On the 1st run you'll have to input a user Name: Case sENsitiVe...choose whatever you want
Team account number - 604374405
Server - leave at default if you don't need a proxy-server.There's currently little support for this.
Port - probably leave at default. Note, Genome uses port 10100, and this must therefore be open somewhere.
Firewall- yes/no... if yes, you'll have to input some more info.
If there's no problem the client will now download a wu from Stanford and start crunching...

Make sure the info in ghclient.cfg is correct, if something is wrong you can edit it here. The important things are :-
email=YourUserName
account=604374405
Note in Genome, all results returned to a username/group will stay with this group & username forever. Mistakes in account-number will either be credited to another group or to no group at all.

Normal running
Just let it keep on crunching. Normally, it will upload/download when done with a WU. If for any reason it can't connect, it will retry a couple of times, and after about 6 minutes restart the current WU.

Genome will on every restart first upload/download. If you've got a partially done WU it will download an extra one if you've not already got a spare WU.
Afterwards it will Filter. This is just a pre-process on the WU, where it counts up from 1 to aa. (see below for aa)
Now the actual prosessing starts. It will count 10%-20% ... 100% and afterwards,sequence nn completed. A WU contains 30 sequences. Genome only saves after a sequence is completed.

Smp or dublicating the same install to multiple machines...
If you've got multi-cpu, you'll have to run multiple instances of genome. Just put them in different directories. There's no special switch for smp.
If you're copying an already made install, MAKE SURE to DELETE id.dat on all new copies. Also delete the wu with genome -clear

Nonetting, sneakernetting
Genome's biggest advantage over other projects is that it can re-run the same WU. Genome uses a random number for every re-run, and should therefore not normally make duplicates. For this reason it's very easy to put genome on machines without net-connection and let them crunch away for days/weeks before uploading the results.If you're running without net-connection, use genome -nonet
When you need to upload, you should move the whole directory to a net-machine.Or if you want to keep it running, copy the directory (except lock.gah that is locked), delete csum.#####, output.chi.#####, str.##### (##### is a number, the same for one result) from the un-netteded machine. On the networked machine, run genome -upload

WU-score
aa stands for AminoAcid, and its how many there are in a WU. This number is shown when filtering, and it's the number of letters printed after every sequence is done.But the easiest way to find the number of AminoAcids is to look at the number on the 1st line in input.inp
The score to a WU is calculated by: WU-score = 0.05 * aa + 0.0025 * aa * aa
This is more or less following the cpu-time, but there are some discrepancies.
As a comparison, an Intel machine running Seti will in the same time manage to produce 10x the WU's in Genome.AMD is a little faster, about 11x-12x

Misc info
In Genome, it's the raw cpu-speed that counts.Cache size, memory speed, cpu multiplier is important in Seti, but not for Genome.
The only difference is that AMD Athlon/duron/palomino is faster than Intel for the same MHz. There's no performance-hit running multiple instances on smp-machines.
Stats are updated every 3 hours, but due to checking it can take a couple of updates before results show up.
Genome-switches, run genome -help
Service-install, use either FireDaemon or srvany.exe.
Genome in windows runs at priority 4, the same as Seti CLi. A combination with Seti will therefore give 50-50-split.
Currently the only clients are win32-cmd and linux.

 

[Assimilator1]

Rattledagger
If you could read through the above & check that I havent actually altered any info about G@H (particularly WU score) that would be appriecated
I suggest what actually goes into the Welcome thread is this :-

Genome@Home along with Folding@Home is run by PandeGroup at Stanford

The goal of Genome@home is to design new genes that can form working proteins in the cell. The 4 main applications are:
Engineering new proteins for medical therapy, designing new pharmaceuticals, assigning functions to the dozens of new genes being sequenced every day, & understanding protein evolution.

Genome@Home project and client download

Team Anandtech stats

Currently TA G@H is fairly small but has still managed to reach No 28 in the team listings and needs your help!

Once you've obtained the client, you'll simply need to unzip, install, and then start it up. A readme is included with the parameters. When installing for the first time, you'll need to enter your account info and here's the important part, join TA by entering the team number when asked:

604374405


***********************************************************
The rest of the info needs to be put at TeamAnandetch.com or some other site

Any other G@H members want to add something?

 

[Poof]

Thanks Assimilator1 & Rattledagger for stirring this up!

I know that Smokeball and I had some stuff on all the TeAms back in October in a sticky (and then a new one was posted that missed the G@H info). I did manage to find the old PM message that Smokeball and I had exchanged that included an abreviated version of what you guys have. Here's what we had in the original TeAm sticky:

Interested in helping Team Anandtech to help Stanford University's biomolecular research?
Then join us in running Genome@Home or Folding@Home and help propel TA up the ranks!

Here are the projects and info to get you started:

G@H

Info on the project.

Sign up for an account and download a client.

Once you've obtained the client, you'll simply need to unzip, install, and then start it up. A readme
is included with the parameters. When installing for the first time, you'll need to enter your account info and here's the important part, join TA by entering the team number when asked:

604374405

You can get your stats fix here.

Download Electron Microscope of G@H

 

[Assimilator1]

There is life in G@H TA then?

Unless anyone else wants to add anything I'll PM Smokeball & get him to add my cut down message to the sticky thread.
We could still do with a site for the rest of the info though.Could it be added to TeamAnandtech.com?

 

[Poof]

There is life in G@H TA then?

Of course!

I'm "Blazer" on the TeAm list! I think all these little projects go through ups and downs over time.

Not sure if Smokeball can edit the current sticky since a Moderator put that thread up there. Also not sure who is managing the TA site... Maybe ViRGE knows for sure.

 

[Rattledagger]

Assimilator1, it looks ok from here. Grammatical corrections... as expected.

As for the 5 minutes to restart, I don't remember... But taking a quick look, it seems that "The client will attempt to get new work more often than previous versions. After three failed attempts, it will try to rerun any current work units. The wait-time between get work attempts and put work attempts has been reduced to two minutes." Ok, maybe it's 6 minutes then. I'm always using -nonet.

 

[Assimilator1]

Ok cool ,I'll PM Smokeball for the info to the welcome thread
I'll see if I can get Virge to add anything to the TA site

Poof
I have edited my short description to include part of yours,Smokeball is going to get it added to the Welcome thread

Rattledagger
Virge tells me he should hopefully be able to add the full description to the TeamAnandtech website at the weekend

 

[Smoke]

Take a look and let me know if the G@H info is OK.

/and no, I'm not a MOD! LOL

 

[Poof]

Looks good!!! Thanks guys!!!

 

[Assimilator1]

Rattledagger
Hey! hey! ,Virge has added your info that I edited to the TeamAnandtech site

Poof
I expect payment in kindness for the help I've given to TA G@H!:Q[img]i/expressions/face-icon-small-happy.gif[/img] ,especially considering I don't even do G@H![img]i/expressions/face-icon-small-tongue.gif[/img]

Virge
Thanks for putting the page up so quickly,fits in nicely & looks good

Smokeball
Thanks for that ,looks good
1 thing though that might want altering (which is my fault) ,the very last line I said 'and they need your help!'
I think it should of been 'and we need your help!'

Another thought! ,now that we have the more detailed info about G@H on the TA.com FAQ page a link to that in the welcome thread would be a good idea ,use the link above ,thanks Smokeball

 

[Poof]

:Q



I didn't start the team! You have to go find dewedge, imhotepmp, & smp for your payment!!!!!!!!!!!

Thanks for the kick-start though.

 

[Assimilator1]

No thanks:,I'd rather have you Poof! hehe ,you're still an active G@H member

No worries

 

[Poof]

You're still my honey Assim1. :Q

 

[Smoke]

Yuck

 

[Assimilator1]

Hey Smoke ,did you see what I said about a link to TA.com FAQ?

 

[Smoke]

Done

 

[Rattledagger]

I see the info is up.

Another thing, what about a cool graphic at the genome-stats-page?

 

[Assimilator1]

That would be down to G@H wouldn't it? ,thats the only stats I know of is at there site(aside from your stats the other day)

Thanks Smokie
(you missed the smilie off though ,nm)

 

[Rattledagger]

Yes, it's on Genome@home's stats-page, but the founder of the team can include a picture. The picture is also a link to example the teams own home-page or thatever...
There's only to start at the top groups of the team-stats to get an idea of the result...

 

[Assimilator1]

I see what you mean ,I looked at MURCS team stats page ,maybe a few more of the G@H people will wake & stir to sort TA's out!

Btw I see your close to Jorden ,give him a nudge from me hehe

Btw2 I've just looked at Nexus9's SETI stats & he restarted doing SETI a few days before he stopped G@H ,looks like he switched back ,though he went flatline again 14/2/02 .Though his SETI output has just been barely ticking over since 8/01.
I wonder what he's doing now? F@H perhaps?