[gmx-users] compiling issue

[Éric Germaneau]

Dear all,

I'm trying to build GMX on a Intel CentOS release 6.6 machine using icc 
14.0 and CUDA 6.5.
Here are the error I get:

    [  1%] Built target mdrun_objlib
    In file included from /usr/local/cuda/include/crt/device_runtime.h(251),
                      from
    /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h(212):
    /usr/local/cuda/include/crt/storage_class.h(61): remark #7:
    unrecognized token
       #define __storage_auto__device__ @@@ COMPILER @@@ ERROR @@@

    ...//

    /usr/local/cuda/include/crt/host_runtime.h(121): remark #82: storage
    class is not first
       static void ____nv_dummy_param_ref(void *param) { volatile static
    void * *__ref __attribute__((unused)); __ref = (volatile void *
    *)param; }

    ...

    Scanning dependencies of target cuda_tools
    Linking CXX static library ../../../../lib/libcuda_tools.a
    [  1%] Built target cuda_tools
    [  2%] [  2%] Building NVCC (Device) object
    src/gromacs/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o
    Building NVCC (Device) object
    src/gromacs/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/nbnxn_cuda_generated_nbnxn_cuda.cu.o
    /usr/local/cuda/include/crt/host_runtime.h(121): remark #82: storage
    class is not first
       static void ____nv_dummy_param_ref(void *param) { volatile static
    void * *__ref __attribute__((unused)); __ref = (volatile void *
    *)param;

    ...

    /tmp/iccZVwEChas_.s: Assembler messages:
    /tmp/iccZVwEChas_.s:375: Error: suffix or operands invalid for `vpaddd'
    /tmp/iccZVwEChas_.s:467: Error: no such instruction: `vpbroadcastd
    %xmm0,%ymm0'
    /tmp/iccZVwEChas_.s:628: Error: suffix or operands invalid for `vpxor'
    /tmp/iccZVwEChas_.s:629: Error: suffix or operands invalid for
    `vpcmpeqd'
    /tmp/iccZVwEChas_.s:630: Error: no such instruction: `vpbroadcastd
    %xmm0,%ymm0'
    /tmp/iccZVwEChas_.s:709: Error: suffix or operands invalid for
    `vpcmpeqd'
    /tmp/iccZVwEChas_.s:711: Error: suffix or operands invalid for `vpxor'
    /tmp/iccZVwEChas_.s:712: Error: suffix or operands invalid for `vpsubd'
    /tmp/iccZVwEChas_.s:713: Error: suffix or operands invalid for `vpaddd'
    /tmp/iccZVwEChas_.s:1620: Error: no such instruction: `shlx
    %r8d,%eax,%r11d'
    /tmp/iccZVwEChas_.s:2000: Error: no such instruction: `shlx
    %r8d,%eax,%r10d'
    /tmp/iccZVwEChas_.s:2107: Error: no such instruction: `shlx
    %r9d,%eax,%eax'
    /tmp/iccZVwEChas_.s:2485: Error: suffix or operands invalid for `vpaddd'
    /tmp/iccZVwEChas_.s:3255: Error: suffix or operands invalid for `vpaddd'
    /tmp/iccZVwEChas_.s:3650: Error: suffix or operands invalid for `vpaddd'
    /tmp/iccZVwEChas_.s:4154: Error: suffix or operands invalid for `vpaddd'
    CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:264
    (message):
       Error generating file
    /home/eric/soft/science/opensource/gromacs/build-5.0.4/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o


    make[2]: ***
    [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_memtestG80_core.cu.o]
    Error 1
    make[1]: ***
    [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
    make: *** [all] Error 2

The CPU version compile smoothly.
Any hint here ?

    Éric.

-- 
Éric Germaneau (艾海克), Specialist
Center for High Performance Computing
Shanghai Jiao Tong University
Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
M:germaneau at sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn