Re: AW: A larger protein data bank for performance benchmark

From: linux freaker (linuxfreaker_at_gmail.com)
Date: Tue May 14 2013 - 01:28:23 CDT

I tried running this command:

Solvate ubq.psf ubq.pdb -t 5 -o ubq_wb

It threw error:

Unable to load file ubq.psf file type psf
On 14 May 2013 11:17, "Norman Geist" <norman.geist_at_uni-greifswald.de> wrote:

> Hi,****
>
> ** **
>
> agree with the last poster. You got to inform about NAMD a little more and
> about HPC. I’m specialist for IT, too, so I know what I’m talking about.
> There are several configuration options that will have huge impact on NAMDs
> scaling behavior (magnitudes of 2 or 4, means some hundred percent). This
> will range from compile stage over the OS settings to the configuration of
> NAMD itself. This is not unique to NAMD but is valid for HPC in general, as
> every computational problem and its parallelization has a own nature. I
> agree with the others, that there are several benchmark systems out there,
> that are used frequently and are kind of representative for NAMDs
> performance on different platforms, two of these are Apoa1 (small-middle
> sized) or stmv (huge size) and should be a good choice. Usually NAMD scales
> well out of the box, when running on one node only (CPU version) and the
> distributed memory version is usually faster than smp (also valid for other
> HPC applications). To get reliable results, you should bind the namd
> processes to the “real” physical cores, instead of letting the OS decide,
> if you have HT or MagnyCores. Otherwise, you will not measure the best
> performance. You will notice less impact of memory bandwidth when using
> NAMD, but if you have many cores per node, check if you get the best
> performance with all physical cores used, or less, care about the
> distribution of processes over multiple CPU sockets here. Also people use
> different settings for “fullelectfrequency”, what controls how often the
> long range electrostatic forces are updated (PME) which is one of the most
> expensive parts of the computation. So you should ship the settings you
> used for the benchmark with the results. Like mentioned on the net when
> googling for “namd tuning” you will also find some information about how to
> improve scaling over large number of processors (some 100). If you plan to
> benchmark multiple node performance also, there are some more things to
> care about, especially with the networks. Let me know and I’ll tell you.**
> **
>
> ** **
>
> So far, how to start a precompiled namd:****
>
> ** **
>
> charmrun +p4 namd2 ++idlepoll apoa1.namd****
>
> ** **
>
> Be sure your machine is prepared to logon to 127.0.0.1, localhost, its own
> ipadress aswell as its hostname without password and without asking for
> saving the ssh fingerprint.****
>
> ** **
>
> Charmrun is the tool for the parallel startup of the Charm++ parallel
> programming model (more often you will find MPI and mpirun in HPC instead).
> ****
>
> The “idlepoll” parameter will cause the namd processes to fill up idle CPU
> time with polling for messages (OpenMPI does by default). This reduces
> latency for inter process communication and therefore usually improves
> scaling. The only additional thing is a namd configuration file. This is a
> plain text file, containing namd tcl commands. So it won’t harm you to read
> the file and the manual and find out what which parameter controls. You
> will also notice, that you can increase the runtime by increasing the
> number of molecular dynamics steps to do (numsteps or run xxx). For very
> big molecular systems and without a high speed file system, you can also
> run into bottlenecks when having to low output frequencies for DCD and
> restart file. Depending on how serious these benchmarks should be, or on
> the reason why you want to do this (a special customer?) you could find
> some more parameters to modify and to measure the scaling impact on.****
>
> ** **
>
> Regards****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Aron Broom
> *Gesendet:* Dienstag, 14. Mai 2013 05:57
> *An:* linux freaker
> *Cc:* Rebecca Swett; Ajasja Ljubetič; Namd Mailing List
> *Betreff:* Re: namd-l: A larger protein data bank for performance
> benchmark****
>
> ** **
>
> I think you may need to read a bit more about what NAMD does, how it runs
> and what its inputs are. But the short answer to your question is no, you
> can't just supply the coordinates. The user manual and tutorials on the
> main site are particularly good sources of information.
>
> As has already been mentioned there already exist benchmarking systems
> that you can use which cover a range of sizes, and which would allow you to
> compare against other hardware. These are ready to use so would save some
> time.****
>
> Have you opened the src/alanin file that you ran to see what the input
> was? Moreover, how do you even know the run completed successfully? The
> 0.0085 seconds could be the time it took to fail from an inappropriate
> input. ****
>
> ** **
>
> On Mon, May 13, 2013 at 10:02 PM, linux freaker <linuxfreaker_at_gmail.com>
> wrote:****
>
> Rebecca,****
>
> I appreciate your response.
> Actually I am into High Performance Computing Team where I need to
> benchmark different kinds of processor family using NAMD.****
>
> I just installed it and able to see that running ./namd src/alanin took
> 0.0085 sec. It finishes up in no seconds.
>
> ****
>
> As I am quite new, I need to know if I actually need to build it to supply
> like alanin running directly like:****
>
> ./namd2 src/x.pdb ****
>
> just works or I need to build pdb format? Please suggest.****
>
> It would be great if you can send me one or two PDBs which are large in
> size and should take sometime for namd to finish.
> Also, it should run directly like ./namd2 src/?.pdb.****
>
> ** **
>
> On Tue, May 14, 2013 at 7:22 AM, Rebecca Swett <rswett_at_chem.wayne.edu>
> wrote:****
>
> I think you are being somewhat unclear. Are you looking for the PDB
> structure of a large protein? or are you looking for a large set of PDB's?
> The acronym PDB stands for protein data bank, www.pdb.org is the
> repository of known crystal structures. Used as a file extension, it
> represents
> crystallographic coordinates saved in the standardized protein data bank
> format. www.pdb.org is where you would find most known structure files in
> the downloadable format
> of numbers and letters. For example 2aa1.pdb is the structure of the day
> today and is a large toxin. If you are looking for a collection of
> structure files in pdb format, you may want to look at some of the search
> and download options on that site. However I strongly suggest doing some
> more reading. It is imperative to good science that users understand the
> files and formats they are working with.
>
> ****
>
> R.J. Swett****
>
> Wayne State University****
>
> 357 Chemistry****
>
> Detroit, MI 48201****
>
> ** **
>
> Lab Phone 313-577-0552****
>
> Cell Phone 906-235-0768****
>
> On 5/13/2013 8:51 PM, linux freaker wrote:****
>
> Hi All,****
>
> I looked into pdb.org but couldnt get large size protein data bank. As I
> am new to NAMD, please suggest me larger PDB.
> http://chemistry.gsu.edu/Glactone/PDB/Amino_Acids/aa.html is the link I
> tried looking into but those are samll size PDBs.****
>
> Can you please paste the link for large size PDB?****
>
> Also, is it possible to accomunlate and run ./namd2 src/* for selecting
> various PDBs?****
>
> ** **
>
> On Mon, May 13, 2013 at 11:42 PM, linux freaker <linuxfreaker_at_gmail.com>
> wrote:****
>
> Which shall I choose? can you suggest me a pdb just like alanin which I
> can use directly?****
>
> On 13 May 2013 22:43, "Ajasja Ljubetič" <ajasja.ljubetic_at_gmail.com> wrote:
> ****
>
> Here is a ready to run benchmark (apo1) ****
>
> http://www.ks.uiuc.edu/Research/namd/performance.html (Direct download<http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz>
> )****
>
> ** **
>
> ** **
>
> ** **
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> ** **
>
> ** **
>
> On 13 May 2013 18:52, Cesar Millan <pachequin_at_gmail.com> wrote:****
>
> www.pdb.org ****
>
> ** **
>
> On Mon, May 13, 2013 at 11:49 AM, linux freaker <linuxfreaker_at_gmail.com>
> wrote:****
>
> I installed namd on linux machine.I ran src/alanin on 4 processor and it
> completed in no time.I need it to take some 5-10 minutes running so that I
> can benchmark.where I can download pdb from which is larger in size?****
>
> ** **
>
> ** **
>
> ** **
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> ** **
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> ** **
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo****
>

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