From: Madhulika Gupta (gmadhulika1909_at_gmail.com)
Date: Wed Nov 18 2015 - 10:31:55 CST
The simulation yielding the exclusion error works perfectly fine with all
the other versions except NAMD2.11. It doesn't run even for the zeroth
step. If I try to minimize the system and then run further, it terminates
with the same exclusion error as soon as minimization completes.
On Nov 18, 2015 8:51 PM, "Jim Phillips" <jim_at_ks.uiuc.edu> wrote:
> 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?
> 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
>> 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
>> (NVIDIA CUDA acceleration)
>> - Linux-x86_64-ibverbs-smp-CUDA
>> (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.
>> Research Scholar
>> Department of Chemistry
>> Indian Institute of Technology, Delhi
>> New Delhi-110016
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