[gmx-users] compiling issue

[Mark Abraham]

Picking up standard library includes from the system gcc and not being able
to assemble SIMD sounds like you haven't set up the whole compiler
environment properly. Odds are excellent that gcc will run faster anyway...

Mark
On Jan 9, 2015 1:24 AM, "Éric Germaneau" <germaneau at sjtu.edu.cn> wrote:

> So sorry, I forgot to mention I use *GMX 5.0.4*.
>
> On 01/09/2015 08:21 AM, Éric Germaneau wrote:
>
>> 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
> --
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