Re: The limit of atom number on Blue Gene/L

From: Fred (Rui FENG) (fengruifree_at_gmail.com)
Date: Mon Jan 19 2009 - 20:41:51 CST

Hi Peter,

Oh it's my fault. The wiki says "This function is already integrated
into the code", so I just thought the binary has the function. I have
submitted an application to the cvs version. Do you know when will the
NAMD 2.7 release? Thanks!

Have a good night!

Fred

On Mon, Jan 19, 2009 at 7:40 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Fred,
> where does it say on the wiki that this functionality has been
> incorporated into the released binaries? As noted on the wiki, you need
> to compile from source (and you'll need to get the cvs version, at least
> until 2.7 releases start showing up).
> Best,
> Peter
>
> Fred (Rui FENG) wrote:
>> Hi Peter,
>>
>> Thank you for your reply.
>>
>> I tried to generate the compressed PSF but failed. I downloaded a
>> binary version for AMD64 and added the "genCompressedPsf on" in the
>> configuration file. When I ran the command ./namd abc.txt (the conf
>> file name), an error occurred:
>>
>> ERROR: The following variables were set in the
>> ERROR: configuration file but are NOT VALID
>> ERROR: genCompressedPsf
>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>
>> It seems that the pre-compiled version of NAMD doesn't support the
>> parameter "genCompressedPsf", but in the wiki it says the function has
>> been integrated in the binary. Do you think it's necessary to compile
>> the source code? Thank you!
>>
>> Fred
>>
>>
>>
>> On Mon, Jan 19, 2009 at 8:41 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>>> Hi Fred,
>>> you should be able to simulate meaningful systems that are a bit larger
>>> by using NAMD's compressedPsf features; please follow the directions at
>>> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction
>>>
>>> Fred (Rui FENG) wrote:
>>>> Hi All,
>>>>
>>>> Is there anyone who tested the limit of atom number on Blue Gene/L? My
>>>> answer is 1 million (no bonds) on 512/1024/2048 nodes, no matter the
>>>> scale of partitions. For example, when I submit a job that has more
>>>> than 1 million particles (say, 1.1 million) on 512 nodes with VN mode,
>>>> the NAMD crashes. But When I submit the same job on 1024 nodes or 2048
>>>> nodes, it still crashes.
>>>>
>>>> Can you give me some experience about how to run millions of particles
>>>> (no bonds) on Blue Gene/L? Is there any compile option or argument I
>>>> can set? Thank you so much!
>>>>
>>>> Have a nice day!
>>>>
>>>> Fred
>

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