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

From: linux freaker (linuxfreaker_at_gmail.com)
Date: Tue May 14 2013 - 01:30:42 CDT

Where can I find 1-1-build directory?
On 14 May 2013 11:58, "linux freaker" <linuxfreaker_at_gmail.com> wrote:

> 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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