AW: NAMD 2.9 CUDA compilation

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Mar 12 2013 - 01:57:00 CDT

Hi Francesco,

the usual path for the cuda runtime is "/usr/local/cuda" I guess. If your installation does not have this path, you have to use the configure option to specify the location on you system. Also IMHO it is not enough to just include the the folder to your includes, as it will also need nvcc and other stuff maybe. I guess the best to try is to supply the right location to you cuda installation at configure stage.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Francesco Pietra
> Gesendet: Montag, 11. März 2013 16:57
> An: NAMD
> Betreff: Fwd: namd-l: NAMD 2.9 CUDA compilation
>
> 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
>
>
> Thanks
>
> francesco
>
> ---------- 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>
>
>
> Hello:
> 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\"
> -DNAMD -DREMOVE_PROXYRESULTMSG_EXTRACOPY
> -DNODEAWARE_PROXY_SPANNINGTREE -DUSE_NODEPATCHMGR
> -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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