[gmx-users] compiling issue

[Éric Germaneau]

alright, thank you.
Will check this.

On 01/09/2015 10:17 PM, Mark Abraham wrote:
> 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 (???), 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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>>
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>>

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