Fwd: NAMD 2.9 CUDA compilation

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 11 2013 - 10:56:51 CDT

I recognize now that I was previously using namd 2.9 binary, which was
not activated during the compilation below. Therefore ,

-DNAMD_FFTW -DNAMD_CUDA -I. -I/usr/local/encap/cuda-4.0/include

will not find the runtime. What should be installed for the runtime?

>From "apt-cache search cuda";

libcublas4 - NVIDIA CUDA BLAS runtime library
libcudart4 - NVIDIA CUDA runtime library
libcufft4 - NVIDIA CUDA FFT runtime library
libcuinj4 - NVIDIA CUDA INJ runtime library
libcupti-dev - NVIDIA CUDA Profiler Tools Interface development files
libcupti-doc - NVIDIA CUDA Profiler Tools Interface documentation
libcupti4 - NVIDIA CUDA Profiler Tools Interface runtime library
libcurand4 - NVIDIA CUDA Random Numbers Generation runtime library
libcusparse4 - NVIDIA CUDA Sparse Matrix runtime library
libnpp4 - NVIDIA Performance Primitives runtime library
nvidia-cuda-dev - NVIDIA CUDA development files
nvidia-cuda-doc - NVIDIA CUDA and OpenCL documentation
nvidia-cuda-gdb - NVIDIA CUDA GDB
nvidia-cuda-toolkit - NVIDIA CUDA toolkit
nvidia-visual-profiler - NVIDIA Visual Profiler
libcuda1 - NVIDIA CUDA runtime library
libcuda1-ia32 - please switch to multiarch libcuda1:i386
libnvcuvid1 - NVIDIA CUDA nvcuvid runtime library
libnvidia-compiler - NVIDIA runtime compiler library



---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Mon, Mar 11, 2013 at 4:40 PM
Subject: namd-l: NAMD 2.9 CUDA compilation
To: NAMD <namd-l_at_ks.uiuc.edu>

I am attempting to compile namd 2.9 with cuda on Debian GNU/Linux
amd64. Configured;

./config Linux-x86_64-g++ --with-cuda

The output of "make depends", followed by "make"

ended with error:

g++ -m64 -O3 -I.rootdir/charm-6.4.0/multicore-linux64/include
-DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/include -DSTATIC_PLUGIN
-I.rootdir/tcl-threaded/include -DNAMD_TCL -I.rootdir/fftw/include
-DNAMD_FFTW -DNAMD_CUDA -I. -I/usr/local/encap/cuda-4.0/include
-DNAMD_VERSION=\"2.9\" -DNAMD_PLATFORM=\"Linux-x86_64-multicore-CUDA\"
-fexpensive-optimizations -ffast-math -o obj/ComputeNonbondedCUDA.o
-c src/ComputeNonbondedCUDA.C
src/ComputeNonbondedCUDA.C:6:26: fatal error: cuda_runtime.h: No such
file or directory
compilation terminated.
make: *** [obj/ComputeNonbondedCUDA.o] Error 1

Actually, /src does not include cuda-related files. Was the
configuration command malformed?

Thanks. Please inform me if more information is needed. I tried to be concise.

francesco pietra

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