This looks like it is working, but I had to wait for the first ~5-7 mins
before starting the sander SP job.
Submitting the sander job earlier caused it to finish prematurely (probably
there were only 1-2 snapshots written in the traj file before this point in
time and the sander finished with them quickly).
If I'm understanding this correctly, the exact wait time would depend on
the system size and interval at which the MD traj is being written by the
GPU code (besides other factors that I might be missing).
Please do let me know if this sounds ok and what might be other things that
I should watch for here.
thank you very much and best regards.
On Sat, Feb 6, 2021 at 2:44 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it sounds like this is something you can try and see if it works. I don't
> believe that the files are locked.
>
> On Fri, Feb 5, 2021 at 11:39 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
>> Dear All,
>> Do the Amber MD codes lock the files that are in use or being written?
>> I'm running MD (pmemd.cuda) on GPU, then estimating SP energies with
>> sander
>> on CPU.
>> Now since sander on CPU is slower than the GPU MD code (is it true for SP
>> sander vs MD on GPU? I think it is slower but not by a very large margin).
>> Is it possible to read an MD trajectory using sander (with -y option) to
>> estimate SP Es, while it is being written by the GPU code?
>> If this is possible, then what are the chances that sander will catch up
>> with the GPU code while reading trajectories that GPU code writes.
>>
>> Although this is not absolutely necessary, it might just save a few hours
>> of time, since one wouldn't have to wait for the GPU MD to finish before
>> starting the sander SP calculations.
>> Looking forward to valuable insights and suggestions from the list.
>> thank you and best regards.
>>
>> --
>>
>> Regards,
>>
>> Dr. Vaibhav A. Dixit,
>>
>> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
>> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
>> AND
>> Assistant Professor,
>> Department of Pharmacy,
>> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
>> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
>> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
>> India.
>> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
>> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
>> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
>> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>>
>> ORCID ID: https://orcid.org/0000-0003-4015-2941
>>
>> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>>
>> P Please consider the environment before printing this e-mail
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>>
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
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Received on Sat Feb 06 2021 - 05:30:02 PST
