Re: AW: compress PSF into INTER

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Jun 07 2012 - 08:11:49 CDT

I just successfully tried your configuration file but with a different PSF file, coordinate file, and parameter files (obviously), and it worked fine with the standard NAMD 2.9 build (NOT memopt) on one processor. I'm not sure what else to suggest, except trying it A) with different input files and B) on a different computer.

Info: TIME FOR READING PSF FILE: 36.7447
Bond sigs: 264
Angle sigs: 861
Dihedral sigs: 1499
Improper sigs: 74
Crossterm sigs: 45
Atom's sigs: 1656
Exclusion signatures: 2210
Finished compressing molecule information, which takes 23.8148(s)
Program finished.

On Jun 7, 2012, at 7:02 AM, Cruz-Chu Eduardo Roberto wrote:

> Hi;
>
> I am still trying to generate the INTER file. That is, just the first step before running anything, only switching the structure file using "genCompressedPsf on".
>
> Not need of "useCompressedPsf on" yet, just the INTER file.
>
> So I moved to a small system of about 9000 atoms, just to check the thing is working. Unfortunately, I was not able to obtain the INTER file.
>
> I did three attemps:
>
> 1.- NAMD, binary downloaded from website.
> 2.- NAMD, normal compilation.
> 3.- NAMD, compiled with "-with-memopt" flag.
>
> The log files are attached below, and also the configuration file.
>
> If you had done it before (Chris?), please just send me your namd config file, even outside the list, so I can see what I am doing wrong.
>
> Regards;
>
> Eduardo
>
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of JC Gumbart [gumbart_at_ks.uiuc.edu]
> Sent: Thursday, June 07, 2012 12:26 PM
> To: Norman Geist
> Cc: Namd Mailing List
> Subject: Re: AW: namd-l: compress PSF into INTER
>
> I have generated compressed psfs before and can assure you that there should be more in the log file than what Eduardo listed. I also trust that he would have checked his directory for additional files after exit.
>
>
> On Jun 7, 2012, at 5:15 AM, Norman Geist wrote:
>
>>> -----Ursprüngliche Nachricht-----
>>> Von: Norman Geist [mailto:norman.geist_at_uni-greifswald.de]
>>> Gesendet: Donnerstag, 7. Juni 2012 12:12
>>> An: 'Cruz-Chu Eduardo Roberto'
>>> Cc: Namd Mailing List (namd-l_at_ks.uiuc.edu)
>>> Betreff: AW: namd-l: compress PSF into INTER
>>>
>>> Hi,
>>>
>>> I'm sorry to tell you that you haven't followed the tutorial very
>>> carefully. The keyword "genCompressedPsf on" does only generate a new
>>> compressed psf when running namd and than exits. To use the new
>>> compressed psf afterwards, you need to specify "useCompressedPsf on"
>>> and remove the "genCompressedPsf on" from the conf. Also use
>>> structure.inter instead of structure in the conf. Also you should use
>>> bincoordinates instead of coordinates which means that you have to
>>> convert your non binary pdb or coor to a binary one (using vmd).
>>>
>>> So the bottom line is it's two steps:
>>>
>>> 1. Generate a compressed psf with namd and genCompressedPsf on" and a
>>> binary coordinate file with vmd.
>>> 2. Run memopt namd with "useCompressedPsf on"
>>
>> and structure.inter
>>
>> I forgot to mention.
>>
>>>
>>> I hope I got it right.
>>>
>>> Good luck.
>>>
>>> For more information look at
>>> http://www.ks.uiuc.edu/Research/namd/wiki/?NamdMemoryReduction
>>>
>>> Norman Geist.
>>>
>>>
>>>> -----Ursprüngliche Nachricht-----
>>>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>>>> Auftrag von Cruz-Chu Eduardo Roberto
>>>> Gesendet: Donnerstag, 7. Juni 2012 11:21
>>>> An: Norman Geist
>>>> Cc: Namd Mailing List
>>>> Betreff: RE: namd-l: compress PSF into INTER
>>>>
>>>> Hi Norman;
>>>>
>>>> NAMD just halts after reading the PSF file, then NAMD crashes. The
>>>> last line of the log file are:
>>>>
>>>> Info: 0 VDW_PAIRS
>>>> Info: 0 NBTHOLE_PAIRS
>>>> Info: TIME FOR READING PSF FILE: 34.5907
>>>>
>>>> My desktop has 16 GB of memory, so it should handle the PSF/COOR
>>> files,
>>>> which are less than 2GB of data.
>>>>
>>>> Below I am attaching the log file.
>>>>
>>>> Have you (or anyone) successfully used the "genCompressedPsf on"
>>> option
>>>> to generate an INTER file?. I pay a beer for any positive answer.
>>>>
>>>> Regards;
>>>>
>>>> Eduardo
>>>> ________________________________________
>>>> From: Norman Geist [norman.geist_at_uni-greifswald.de]
>>>> Sent: Thursday, June 07, 2012 8:24 AM
>>>> To: Cruz-Chu Eduardo Roberto
>>>> Cc: Namd Mailing List
>>>> Subject: AW: namd-l: compress PSF into INTER
>>>>
>>>>> -----Ursprüngliche Nachricht-----
>>>>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>>>>> Auftrag von Cruz-Chu Eduardo Roberto
>>>>> Gesendet: Mittwoch, 6. Juni 2012 20:38
>>>>> An: namd-l_at_ks.uiuc.edu
>>>>> Betreff: namd-l: compress PSF into INTER
>>>>>
>>>>> Hi;
>>>>>
>>>>
>>>> Hi
>>>>
>>>>>
>>>>> I am trying to run a 6 million atom system. For that, I need to
>>>>
>>>> Wow, that's heavy. My biggest system has 1.5 million ^^
>>>>
>>>>> compress the PSF file into a INTER file. The NAMD wiki provide
>>> some
>>>>> brief explanation.
>>>>>
>>>>>
>>>>>
>>>>
>>> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReductio
>>>>> n
>>>>>
>>>>>
>>>>> that is "b) add a field "genCompressedPsf on" in the configuration
>>>>> file".
>>>>>
>>>>>
>>>>> well, I did it using NAMD 2.8 and also NAMD 2.9. I also compiled
>>> NAMD
>>>>> with --with-memopt flag, and no success.
>>>>
>>>> What exactly does "no success" mean? Is namd crashing with an error
>>> or
>>>> something?
>>>> We need some detail to identify the problem.
>>>>
>>>> Regards
>>>>
>>>> Norman
>>>>
>>>>>
>>>>>
>>>>> Does anyone has an example?, a namd configuration file I can use as
>>>>> guide?.
>>>>>
>>>>>
>>>>> Below, I am attaching my namd configuration, the one that did not
>>>> work.
>>>>>
>>>>>
>>>>> Any help, it would be really appreciated.
>>>>>
>>>>>
>>>>> Regards;
>>>>>
>>>>>
>>>>> Eduardo
>>>>>
>>>>>
>>>>
>>
>>
>
>
> <eg07PSF4.namd><03_memOptcompiled.log><02_compiled.log><01_download.log>

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