From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Tue Jan 29 2019 - 10:37:15 CST
Dear NAMD users and developers,
I have recently attempted to compile namd2.13 nightly build to run multiple
GPU node replica exchange simulations using REST2 methodology.
First, I was able to run the current version of namd 2.13
Linux-x86_64-verbs-smp-CUDA (Multi-copy algorithms on InfiniBand) binaries
with charmrun in our university cluster using multiple node/GPU setup (with
Then, I tried compiling namd 2.13 nightly version to use REST2 (since the
current version have a bug with selecting solute atom IDs as told here -
), with information in NVIDIA site as well as what mentioned in the
release note. But I failed my self miserably as several others had ( as I
can see from the mailing thread). Since the precompiled binaries within the
current version work perfectly, I cannot think of a reason why my attempts
failed other than some issue related to library files and compilers I am
loading when building charm for multiple node GPU setup. I have used
following flags to build the charmm.
*./build charm++ verbs-linux-x86_64 icc smp --with-production *
I have used ifort and Intel/2018 compilers.
One thing I have noticed is that when I use precompiled namd2.13 I did not
have to link LD_LIBRARY_PATH. But I had to do so when I compiled it my
self (otherwise I keep getting missing library files error).
It would be a great help if any of you who have successfully compiled
multiple node GPU namd 2.13 could share your charmm--6.8.2 files along with
information on compilers you used, so I could compile namd by my self. Or
any sort of advice on how to solve this or sharing namd2.13 precompiled
binaries for the nightly version itself is highly appreciated.
-- Aravinda Munasinghe,
This archive was generated by hypermail 2.1.6 : Tue Dec 10 2019 - 23:20:26 CST