[gmx-users] further compilation issues on stretch

Michael Brunsteiner mbx0009 at yahoo.com
Thu Feb 15 17:27:47 CET 2018

as compilation of gmx-2018 idn't work for me i went back to 2016.4
after some google-ing i found that the following commands work, and gmx compiles without any complaints...
> cmake .. -DGMX_GPU=on  -DNVML_FOUND=1 -DNVML_LIBRARY=/usr/lib/x86_64-linux-gnu/libnvidia-ml.so.1 -DNVML_INCLUDE_DIR=/usr/include -DCUDA_NVCC_FLAGS='-ccbin clang-3.8'
> make -j 12
however, when i do mdrun see in my log file: 

[...]Build OS/arch:      Linux 4.9.0-4-amd64 x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz
Build CPU family:   6   Model: 62   Stepping: 4
Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:         /usr/bin/cc GNU 6.3.0
C compiler flags:    -mavx     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
C++ compiler:       /usr/bin/c++ GNU 6.3.0
C++ compiler flags:  -mavx    -std=c++0x   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
CUDA compiler:      /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44
CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;-Wno-deprecated-gpu-targets;-D_FORCE_INLINES;-ccbin clang-3.8;-Xcompiler;,-mavx,,,,,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,; 
CUDA driver:        8.0
CUDA runtime:       0.0

NOTE: Error occurred during GPU detection:
      unknown error
      Can not use GPU acceleration, will fall back to CPU kernels.

i have a vanilla version of debian stretch with nvidia drivers and toolkit installed from theofficial debian packages. my graphic card is Geforce GTX 780
my gcc is 6.3 (no 5 in stretch)
i wonder if i installed the nvidia driver/toolkit as provided directly from nvidia would that makethings work .. or rather worse ??
thanks for any suggestions!michael =============================== Why be happy when you could be normal?

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