[CPMD-list] LOOP WAS VECTORIZED

Sat Apr 5 03:05:28 CEST 2008

Dear Dr. Kohlmeyer,

I am sorry for that, I disabled this feature from my email and I appreciate that you spent the effort and time to read it and answer it though. 

I was alarmed when you said that I have to compensate for the dispersion interaction or I will get worse results than those from classical MD, which brings me to you question about the choice of the project; My supervisors published a paper about methane under high pressures but using classical MD, my job is to get better results especially for low temperatures using QM simulation. So it is vital to get better results or else it would be pointless to do a QM simulation. I was warned several times that DFT doesn't represent van der Waal interaction very well but I thought in comparison to other interactions but still better than Classical MD not worse. doesn't CPMD offer the correction for van der Waal interaction through VDW CORRECTION in &VDW section, is that what you mean by compensating for the dispersion interaction? 

I actually tried to do a wavefunction optimization for 32 H2S molecules with Cutoff 100, but after two days I stopped the run. I thought that I must have done something wrong that made it take so long, after all most people in this mailing list work on desktops not all of them have cluster. I also attributed the long time to the fact that having 1G ram wasn't enough because most of the time was spent on r/w from the hard disk and so the processor was idle. but apparently 32 molecules is a little ambitious, my supervisors and I thought that 16 would be too few especially for statistical limit and especially that we read a paper published ten years ago that simulated methane (16 molecules ten years ago, the computational power exponentially increased since then)QM but at very high temp and pressures. 

concerning grid computing, you said it is pointless, I don't understand why , I mean unicore is a grid system that has CPMD on it and people do testing jobs on it. 

I am sorry for the long email. Thank you Dr Kohlmeyer for your help.
Best Regards,
Nora M. Hassan

--- On Thu, 4/3/08, Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote:

> From: Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
> Subject: Re: LOOP WAS VECTORIZED
> To: "Nora Mohamed" <nora221282 at yahoo.com>
> Cc: cpmd-list at cpmd.org
> Date: Thursday, April 3, 2008, 10:35 AM
> On Thu, 3 Apr 2008, Nora Mohamed wrote:
> 
> dear nora,
> 
> please _NEVER_ send html formatted mails to mailing lists.
> 
> most people that recieve a lot of mail prefer using a text
> mode mail program, and there those take significant effort
> to make them readable. as i wrote many times before: the
> easier you make it to answer the more likely you get help.
> 
> NM> Dear Dr. Kolmeyer,
> NM>   I am sorry for the inconvenience, I didn't see
> the first email I 
> NM> sent in my inbox and so thought that the group
> didn't receive it 
> NM> as well and so sent it again. I actually didn't
> receive your 
> 
> mailing lists, and that includes the cpmd list,
> occasionally get
> "stuck" or are taken down for maintenance or ...,
> it is advisable to wait at least a day before resending.
> 
> NM> reply, I only came across it while I am searching in
> the mailing
> NM> list for another problem I had. 
> 
> so you'll have to check your mail setup and or change
> your 
> e-mail provider...
> 
> NM> 1.  Concerning my test run, I get very consistent
> results;
> NM> my total energy is very consistent with the test
> case results. there
> NM> are only differences in the forces. 
> 
> [...]
> 
> NM>   20  2.880E-08   1.243E-09      -9.141771  
> -3.997E-13     18.58
> NM>   21  8.633E-09   7.382E-10      -9.141771  
> -6.750E-14     18.60 
> NM>  
> NM> In the last three lines, there are differences in
> the DETOT, but
> NM> I don't think the differences are major or
> serious. 
> 
> if you read my previous comments about achievable limits of
> accuracy,
> then you should be aware that relative differences of the
> order of 
> 1e-15 are the limit of double precision floating point
> accuracy.
> those differences can be caused by different setting for
> rounding of
> the floating point unit or different compilers, or
> optimization levels.
> in fact, differences cause by all of those can be _much_
> larger.
> 
> NM>    2  B  9.4486  9.4486 13.0108   1.234E-12 
> 4.871E-15  9.479E-04
> NM>    3  H 11.3223  9.4486 11.3384  -3.742E-03 
> 6.548E-16 -7.247E-06
> NM>    4  H  7.5749  9.4486 11.3384   3.742E-03 
> 2.186E-16 -7.247E-06
> NM>    5  H  9.4486 11.4168 14.1063   5.774E-13
> -2.357E-03 -1.100E-03
> NM>    6  H  9.4486  7.4804 14.1063   5.672E-13 
> 2.357E-03 -1.100E-03
> NM>    7  H  9.4486  7.4804  8.5704   5.783E-13 
> 2.357E-03  1.102E-03
> NM>    8  H  9.4486 11.4168  8.5704   5.669E-13
> -2.357E-03  1.102E-03
> 
> 
> NM> the gradients however, there are differences in the
> order of magnitude.
> NM> but I think now that, as you said, if the optimum
> number is zero,then 
> NM> these differences would be considered minor errors. 
> 
> yes. even with very tight convergence on the wavefunction,
> i'd
> be surprised if your forces can be converged to more than
> 1e-7
> absolute.
> 
> NM> performance from OpenMP with small number of
> cpu's, but in one of 
> NM> the messages you mentioned that you could get 80% of
> the MPI 
> NM> performance with OpenMP on a two-socket dual-core
> intel machine, 
> NM> so should I use openMP or I am better off without
> it?  
> 
> MPI is the better solution. there is no other way to find
> the
> best way of how to run jobs on your machine than running
> benchmarks
> and trying out compiler and input flags that are affecting 
> performance systematically.
> 
> NM> I need the best possible performance since I do
> constant pressure
> NM> MD for 32 ch4 molecules and these two machines are
> all I can get.
> 
> did you choose this project or somebody else? the few
> percent
> speedup won't help you much. to run this reasonably,
> you need
> to run on a problem cluster or large multiprocessor machine
> or
> else you'll be waiting for years until you have
> reasonable results.
> 
> also, constant pressure simulations with CPMD add a whole
> new 
> dimension of difficulty (you need a converged stress
> tensor,
> not only converged forces, you need to pick two fictitious
> masses
> that must not couple to anything, you have to consider the
> change of the effective plane wave cutoff with changing box
> size).
> when modeling methane you have to consider a method to
> compensate 
> for the incomplete description of dispersion interactions,
> or else
> your results will be worse than those of classical MD.
> 
> NM> I checked Unicore to see the possibility of doing
> heavy MD, but 
> NM> I am only allowed to testing and not to get final
> results that 
> NM> I can publish later on. 
> 
> grid computing is pointless for these kinds of runs. you
> need
> a proper cluster with a fast network (myrinet, infiniband
> or alike). 
> 
> cheers,
>    axel.
> 
> NM> Thanks a lot Dr. Kohlmeyer.
> NM> Best Regards,
> NM> Nora M. Hassan
> 
> -- 
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu  
> http://www.cmm.upenn.edu
>    Center for Molecular Modeling   --   University of
> Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia,
> PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel:
> 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a
> better idiot.

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