[gmx-users] Building Gromacs

Justin Lemkul jalemkul at vt.edu
Tue Nov 13 01:04:39 CET 2018

On 11/12/18 6:57 PM, paul buscemi wrote:
> This may be entirely misleading, but I have Gromacs 2018.3 loaded onto a SSD.  This seems to be quite portable between machines I have access to ( during some builds ) ranging from an i5 4core, I7-8 core, i7-12 core and AMD 16 core 32 threads  - all with expected scaling in speed and all cores used during MD.  So I am not sure why you must rebuild.

If the architecture is different between nodes, you can get 
incompatibilities, missing libraries, or poor performance due to 
suboptimal compilation. I've ported binaries between machines of similar 
construction, but we also have some hybrid clusters that do not work 
with this approach (e.g. head node different from compute nodes - if the 
code is compiled on the head node, it will either not work or work 
poorly on the compute node).


> Paul
>> On Nov 12, 2018, at 3:45 PM, Jasper Jordan <hoseknows at gmail.com> wrote:
>> I was sure that a month ago when I started down the path of building and
>> making Gromacs available for our user community, that I read a statement
>> that whenever there is a hardware change, you need to rebuild Gromacs. I
>> took this quite literally. So I assume that if hardware isn't identical
>> (make, model, etc) a rebuild is required.
>> Well, now I can't find the statement, and we're attempting to deploy to AWS
>> where we might have 1 core, or 8, and we may have no GPUs, or 1, 8, or 16
>> per instance. So people are asking why I need to rebuild, and I can't give
>> them an answer because I can't find the statement any more.
>> Can somebody tell me if it is required? Was it required? Or is it just a
>> misremembery that I need to just discard?
>> -- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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