Re: [AMBER] installing pmemd.cuda (Amber20, WSL2)

From: Lucy Yang <>
Date: Thu, 5 Nov 2020 23:35:54 -0800

Resolved, I have AmberTools20, which was free, and not Amber20, which is
licensed and contains pmemd.

On Thu, Nov 5, 2020 at 8:46 PM Lucy Yang <> wrote:

> Dear all,
> First time "Linux" user so apologies in advance for missing some basics.
> First, I made sure to install WSL2 correctly with NVIDIA drivers and cuda
> toolkit properly working. (This took a lot of troubleshooting and jumping
> between 3-4 different installation guides, but it eventually worked.) I
> successfully installed Amber20 for WSL following a combination of these
> instructions
> <> and
> Googling. I went through the PolyAT tutorial
> <> and
> successfully ran everything except MD Equilibration on the whole system
> (step 5.1.6). This demonstrates that serial CPU amber works. Now, I wanted
> to use the gpu-accelerated version of sander to save time. I followed these
> instructions <> to install the GPU code.
> Specifically:
> make clean
> ./configure -cuda gnu (or intel)
> make install
> make test
> My system passes all the tests (14 file comparisons passed, 0 file comparisons failed, 0 tests experienced errors). This plus the tests I tried with the WSL2/NVIDIA driver (unofficial) guide <> indicates to me that the GPU is working.
> However, when I try a simulation with:
> ${AMBERHOME}/bin/pmemd.cuda -O -i mdin -o mdout -p prmtop -c inpcrd \
> -r restrt -x mdcrd -inf mdinfo
> It tells me that there is no such file or directory. I navigate in an
> explorer window to my home/lucyyang/amber20_src/bin/ I do not see
> pmemd.cuda in there. Did I miss something? cpptraj.cuda , mdx.cuda , and
> pbsa.cuda are all in there. I did not find anything useful via
> Googling/searching this list's archives.
> I have been very close to asking you guys some questions during the entire
> process but eventually a solution after Googling. This time I'm at my wit's
> end, I hope someone can help me
> Lucy
> side note: sander.MPI works but takes the same amount of time to run as
> sander. but maybe that is due to using the relatively small file in the
> tutorial <>.
> Tutorial says 5.1.3 (minimization stage 1) took 146s on a 1.4 GHz Intel i5.
> My system took 65s on a AMD Ryzen 5 6-core 3.60 GHz for both sander and
> sander.MPI. Judging by the CPU usage (~14%) it only used 1 core.
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Received on Fri Nov 06 2020 - 00:00:02 PST
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