smaerd
International Hazard
Posts: 1262
Registered: 23-1-2010
Member Is Offline
Mood: hmm...
|
|
Anyone have access to a computer cluster?
I'll keep it brief.
Does anyone have access to a computer cluster?  Edit- Or a wicked hot-iron home
computer/server with GAMESS on it  .
I have a few computational experiments I am keen on running but they exceed my hard-drive space and take days on my computer. I couldn't even do the
geometry optimization on the one molecule. It ate up my diskspace almost completely.
edit -
I guess in return I'll end up sharing one of my ideas which has some pretty solid experimental evidence behind it. Which ya is pretty meaningless but
its a cool project with potential real world applications etc... All it really lacks is a computation FT-IR or H1-NMR. Well ideally I'd have a 2-D
experimental NMR (TOECSY, ROESY, NOESY, etc) but I wasn't able to accomplish those in the time-frame that I did my project in due to having a limited
instrument. I don't think I'll be publishing the idea even though I could. It might be more badass to make it public or something.
[Edited on 3-7-2015 by smaerd]
|
|
|
careysub
International Hazard
Posts: 1339
Registered: 4-8-2014
Location: Coastal Sage Scrub Biome
Member Is Offline
Mood: Lowest quantum state
|
|
I have an 8 core, 4 GHZ, 32 GB RAM data crunching machine running Spark currently. How much storage did you eat up?
|
|
|
Zombie
Forum Hillbilly
Posts: 1700
Registered: 13-1-2015
Location: Florida PanHandle
Member Is Offline
Mood: I just don't know...
|
|
I have a similar set up, and am willing to volunteer time to do what you need. I have a few 1TB hard drives that are empty, and it takes a second to
install them.
A cold beer is payment enough. I'll collect that if your ever in carrabelle.
They tried to have me "put to sleep" so I came back to return the favor.
Zom.
|
|
|
smaerd
International Hazard
Posts: 1262
Registered: 23-1-2010
Member Is Offline
Mood: hmm...
|
|
Doing a geometry optimization I ate up 200+GB which made the calculation impossible. I'm not sure if RAM was an issue it looked like it was okay with
250k words. Keep in mind geometry optimization is just the first thing so I can get a vibrational analysis. I'm new to GAMESS in general, so I may
need some input on good basis set's and configurations etc.
"EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Wed May 6 15:39:17 2015
24946128 WORDS OF DYNAMIC MEMORY USED"
Aye Careysub now that's a beastly computer! Zombie I'm afraid the data storage may end up in the TB range. I don't know though, I think there is a way
to get GAMESS to predict that but I am new. So not sure.
Right now I'm in contact with a member who has access to a cluster. If they are allowed, and can run the file then it'll be solved. If not I am going
to have to take either of you up on the offer. Either way I think I'm going to make the project public.
Just because I'd like people to build off of the idea, and I'd love some face-to-face criticism of my work. There are a few things I was uncertain of.
Edit-
Also I wanted to thank everyone who PM'd me offering advice and other things. It means a lot. I want to put the project to rest but my mind will
always look back and wonder unless I can get a little bit more information. Which otherwise I may never have the opportunity too. Also Dr. Bob helped
supply me with some things that made it possible, so it would only be right to post it here.
[Edited on 3-7-2015 by smaerd]
|
|
|
Polverone
Now celebrating 21 years of madness
Posts: 3186
Registered: 19-5-2002
Location: The Sunny Pacific Northwest
Member Is Offline
Mood: Waiting for spring
|
|
I am posting here because smaerd said it was ok to discuss in the public thread. He is looking at a cyclodextrin derivative.
The disk space issue is caused by intermediate integrals taking up too much space. You can get around that by running a direct calculation that
recomputes integrals as needed instead of storing them, but that will be slower and this is already going to be quite slow even on an 8 core machine.
The desire is to do geometry optimization and then a vibrational analysis, to predict IR spectrum, possibly followed by NMR shielding prediction.
A cyclodextrin is a fairly large molecule by the standards of ab initio quantum chemistry. Predictions made by electronic structure methods are not
directly comparable to typical condensed phase conditions at the laboratory bench. Computational chemistry assumes, by default, an isolated molecule
in vacuum. You can run calculations with implicit solvation to partially correct the problem, but it's only a partial fix and it increases the
computational cost. You also need to account for electron correlation to produce reasonably accurate geometries. That means a rather more expensive
calculation than simple Hartree-Fock if you stick with ab initio methods.
There is a recent Nature Protocols paper, which you can find in References, guiding researchers how to produce computational NMR predictions that are
actually useful at the bench level: http://www.nature.com/nprot/journal/v9/n3/abs/nprot.2014.042...
The steps can be mimicked with free software instead of the expensive commercial products they recommend, but it will be a fair bit of work for a
molecule this size. You need to find multiple conformers and run property calculations on each of them.
I have recommended to smaerd that he obtain MOPAC2012, since it is free for academic use: http://openmopac.net/
The semi-empirical geometry optimization and vibrational analysis with PM7 or PM6 will run much faster than ab initio calculations with GAMESS. Those
calculations can run with implicit solvation via COSMO if desired. Structures from MOPAC optimization can be used for NMR shielding calculations in
GAMESS if enough computing power is available for that kind of job.
PGP Key and corresponding e-mail address
|
|
|
paulr1234
Hazard to Self
Posts: 51
Registered: 30-8-2010
Member Is Offline
Mood: No Mood
|
|
Scarily smart people on this forum. I was happy to correctly calculate the density of sulfur in my Chem 101 class last night!
|
|
|
Zombie
Forum Hillbilly
Posts: 1700
Registered: 13-1-2015
Location: Florida PanHandle
Member Is Offline
Mood: I just don't know...
|
|
I understood "sulfur".
The bottom right corner shows what I have. I can set the computations to run thru the graphics card at a much faster rate. (similar to Bit Coin
mining).
If you need help... It's here.
They tried to have me "put to sleep" so I came back to return the favor.
Zom.
|
|
|
Northern
Harmless
Posts: 1
Registered: 12-3-2004
Member Is Offline
Mood: holy crap i signed up in 2004 and just now am using the site?!?!?!
|
|
Get an Amazon web services account and purchase computer time in units as needed. For data storage they can handle literally anything essentially
anything whether you want a relation db (*think sql), something like Mongo that uses a NoSQL key-value pair engine, or just flat file storage which is
provided by there S3 service.
I swear i dont work for them but by god have i been using the hell out of their free tier since its well free and I have some spare time to play with
all of there toys.
|
|
|
smaerd
International Hazard
Posts: 1262
Registered: 23-1-2010
Member Is Offline
Mood: hmm...
|
|
Thanks Northern,
Hmmm. I'll have to see if they are capable of handling what I need. By what you describe it doesn't sound like they would be able too.
Recently I have migrated to a larger university with a few clusters hanging around. I now know someone who can introduce me to someone whose bread and
butter is gaussian and other types of calculations. So I'm going to try that out.
|
|
|
![[*]](images/xpblue/default_icon.gif){kind=icon}
