Re: [AMBER] some problems when using pmemd.cuda

From: Jason Swails <>
Date: Mon, 29 Sep 2014 08:15:29 -0400

On Mon, 2014-09-29 at 16:05 +0800, wrote:
> Dear Amber users:
> Hi! When I am using pmemd.cuda on GPU to accelerate MD, I
> suffer some problems.
> First, My node has 2U GPU nvidia M2090, 32 cores CPU(2U), 64G
> memory. But I can only use the first one(CUDA_VISIBLE_DEVICE="0"). I
> can run MD simulations on the first GPU. When I set
> CUDA_VISIBLE_DEVICE="1", the same MD simulations stop without any
> error message. Both of the GPUs are using cuda-4.2.

There is not enough information to help diagnose what is happening. Are
you sure that the second GPU works? Have you run the Amber CUDA tests
on both GPUs? Do other CUDA programs (e.g., from the CUDA samples or
CUDA SDK) work? What version of Amber are you using? Have you updated
to the latest version?

> Secondly, the system contained 8W atoms runs 8 ns/day when
> using 1 GPU. It takes 538M of the GPU memory (5037M total.). Once I
> submit another job on this GPU, they just occupy 1000M GPU memory.
> However, both speeds decrease to 4 ns/day. The node still have enough
> GPU memory, CPU cores and memory. Why the speed of the job decrease so
> much?

Because you are splitting the processing power between two jobs. The
amount of memory has virtually no impact on performance as long as you
have enough to prevent swapping. The speed of the memory bus and the
speed of the processors have a lot more effect. Because pmemd.cuda is
well-optimized, it wastes very few clock cycles. As a result, if you
run 2 jobs on the same GPU, each job will get on average half of the
available clock cycles, meaning it can run half as fast.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Sep 29 2014 - 05:30:03 PDT
Custom Search