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

From: Lucy Yang <lucyyang.uw.edu>
Date: Thu, 5 Nov 2020 20:46:31 -0800

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
Googling. I went through the PolyAT tutorial
<https://ambermd.org/tutorials/basic/tutorial1/section5.php> 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 <https://ambermd.org/GPUHowTo.php> to install the GPU code.

    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


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 <https://ambermd.org/tutorials/basic/tutorial1/section5.php>.
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 Thu Nov 05 2020 - 21:00:03 PST
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