Hi Bob,
>Does this happen to you with Amber 11, and while using CUDA/CUDA.MPI? if you run non-CUDA pmemd.mpi , can you get it to happen?Sounds to me like you are talking small cluster systems, in-lab, correct?
Yes, I use just several individual desktop machines and Amber11. I tried again right now and the problem is the same when using both pmemd.cuda.MPI and pmemd.MPI, as well as when I use the serial version.
It is very strange. I noticed this problem one year ago but because I never used restart files I report it now here.
All the best,
Filip
________________________________
From: "Duke, Robert E Jr" <rduke.email.unc.edu>
To: filip fratev <filipfratev.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Sunday, December 25, 2011 9:03 PM
Subject: Re: [AMBER] Restart file for pmemd not showing all information
Thanks filip,
So the question for everyone with pmemd restart file problems becomes this: Does this happen to you with Amber 11, and while using CUDA/CUDA.MPI? The other question would be, "if you run non-CUDA pmemd.mpi (amber11 or amber10), can you get it to happen?". We then can distinguish between something specific to a version/build type of pmemd vs. a possible OS problem. Sounds to me like you are talking small cluster systems, in-lab, correct? (ie., you are not running at one of the big supercomputer centers with some sort of super-optimized parallel file system).
Best Regards - Bob Duke
________________________________________
From: filip fratev [filipfratev.yahoo.com]
Sent: Sunday, December 25, 2011 3:30 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Restart file for pmemd not showing all information
Hi all,
Marry Christmas and
happy New Year!
I have the same
problem - some atoms missing and no any information about the box. I never obtained
full restart file during the simulations. I use pmemd.CUDA and CUDA.MPI compiled with
gcc4.3, 4.5 and 4.6 on different systems under Suse11.3, 11.4 and 12.1. The
only proper restart files are those obtained after the end of the simulation.
What might be
the problem and how to solve it?
All the best,
Filip
________________________________
From: Bill Ross <ross.cgl.ucsf.EDU>
To: amber.ambermd.org
Sent: Saturday, December 24, 2011 11:26 PM
Subject: Re: [AMBER] Restart file for pmemd not showing all information
> If memory serves, really the only way we could flush the buffers during
> a run was an actual close and reopen cycle
How about flush()?
http://gcc.gnu.org/onlinedocs/gcc-4.1.2/gfortran/FLUSH.html
Though I think close/open would be easier to trust.
Bill
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Received on Sun Dec 25 2011 - 13:00:02 PST
