From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jul 22 2014 - 11:56:06 CDT
Aron, when you ahd 9 colvars, maybe they were not assigned a single ABF
bias?
On 22 July 2014 18:30, Aron Broom <broomsday_at_gmail.com> wrote:
> I've used an upwards of 9 colvars at once with no issue, and with a larger
> system size than that. Can you post the *.in file or whatever file
> contains all your colvars definitions? I would suspect something add with
> your colvars. One thing to test might be, when you are at the largest size
> that has worked (I guess 4 colvars?) try just duplicating all those colvar
> blocks and see if it runs. Maybe something is wrong with the 5th colvar
> definition you are entering.
>
>
> On Tue, Jul 22, 2014 at 12:23 PM, Harish Vashisth <
> harish.vashisth_at_gmail.com> wrote:
>
>> Dear All:
>> We have been trying to make use of many CVs (> 20) using abf/colvar
>> options in NAMD2.9. These are all backbone dihedral CVs defined
>> individually in multiple blocks of phi/psi, etc. We are able to run ABF
>> jobs fine up to 5 CVs, but including a sixth one or more does not work. The
>> error reported in the log file right after initialization of colvars module
>> is:
>>
>> FATAL ERROR: Memory allocation failed on processor 0.
>>
>> Looking through previous posts, someone seemed to suggest that it is
>> likely occurring due to large system size as NAMD keeps a copy of the
>> system on processor 0?
>>
>> In our case, the solvated system size is ~40,000 atoms. The error occurs
>> using NAMD2.9 on local workstation, our local CRAYXE6m-200 as well as on
>> Stampede (XSEDE resource.) Is there an upper limit on how many CVs colvar
>> module can handle?
>>
>> Any suggestions would be helpful. Thanks.
>>
>> -Harish
>> --------------
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:01 CST