[AMBER] some problems when using pmemd.cuda

From: <xueqiaoup.gmail.com>
Date: Mon, 29 Sep 2014 16:05:22 +0800

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.
        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?

Qiao Xue

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Received on Mon Sep 29 2014 - 01:30:02 PDT
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