[AMBER] calculation parallel

From: xiaojiong <xiaojiong.zju.edu.cn>
Date: Sun, 29 Apr 2012 08:59:56 +0800

Dear sir/madam,

I am a user of AMBER in China. I have a question with the calculation in parallel. I noticed that in the QM calculation software GAUSSIAN, it is available for users to define the numebers of CPU in the input file.
But it seems that we could only carry out the calculation in parallel in AMBER with "mpirun". To my comprehension, the difference is: N CPUs deal with one process in GAUSSIAN while N CPUS deal with N processes in AMBER.
And I found that it is much slower with GAUSSIAN when I use mpirun instead of defining the CPU numbers in the input file directly. So my question is:

Is it available for AMBER to define the CPU numbers in the input file? Or in other words, is it possiable that when I execute "top" in linux, I could see N CPUs running one sander/pmemd rather than N CPUs running N sander/pmemd?

Thanks for your time!

Cao Yang,
Zhejiang University, China
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Received on Sat Apr 28 2012 - 18:30:03 PDT
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