Re: NAMD2.11 source code not compiling

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Nov 18 2015 - 09:21:13 CST

The build error means exactly what it says. If you really want to you can
remove the "exit -1" command from the error message in the config script.

Did your simulation that is yielding the exclusion error work for a
non-CUDA build or NAMD 2.10? Is there anything unusual about it? Do you
get the error on the first timestep or later in the run?

Jim

On Wed, 18 Nov 2015, Madhulika Gupta wrote:

> Dear All,
> I am trying to compile NAMD2.11 Source code on the central computing
> facility at our institute and I get the error as listed below. I have tried
> compiling both MPI version and Infiniband version but both result in the
> same error. The earlier versions worked just fine on the same machine.
>
> ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64 --with-cuda
> --cuda-prefix /home/soft/cuda-7.0/
>
> Selected arch file arch/Linux-x86_64-g++.arch contains:
>
> NAMD_ARCH = Linux-x86_64
> CHARMARCH = multicore-linux64
>
> CXX = g++ -m64 -std=c++0x -O3
> CXXOPTS = -fexpensive-optimizations -ffast-math
> CC = gcc -m64 -O3
> COPTS = -fexpensive-optimizations -ffast-math
>
>
> ERROR: CUDA builds require non-MPI SMP or multicore Charm++ arch for
> reasonable performance.
>
> Consider ibverbs-smp or verbs-smp (InfiniBand), gni-smp (Cray), or
> multicore (single node).
> -------------------------------------------------------------------------
>
> I have also tried using namd binaries under the following
>
>
> - Linux-x86_64-multicore-CUDA
> <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1357>
> (NVIDIA CUDA acceleration)
> - Linux-x86_64-ibverbs-smp-CUDA
> <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1356>
> (NVIDIA CUDA with InfiniBand)
>
> but they result in the following error:
> Exclusions: detected 16049 expected 16709
> FATAL ERROR: Incorrect number of exclusions detected
>
> Please pay heed to the issue and please help me to resolve the same.
>
> Regards
> Madhulika
> Research Scholar
> Department of Chemistry
> Indian Institute of Technology, Delhi
> New Delhi-110016
>

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