[gmx-users] compiling issue

[Éric Germaneau]

Actually I can't figure where my setting is wrong.
Here is my cmake command:

    CC=$IMPI_PATH/mpiicc CXX=$IMPI_PATH/mpiicpc
    CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin\
       $CMAKE \
        -DFFTW_INCLUDE_DIR=$FFTW3DIR/include \
        -DFFTW_LIBRARY=$FFTW3DIR/lib \
        -DGMX_MPI=ON \
        -DGMX_GPU=ON [-DCUDA_TOOLKIT_ROOT_DIR=$CUDAPATH] \
        -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
        -DGMX_X11=OFF ../$APP \
        -DGMX_THREADS=OFF \
        -DGMX_OPENMP=ON \
        -DBUILD_SHARED_LIBS=ON \
        -DGMX_PREFER_STATIC_LIBS=OFF

Anyone has experienced this issue already?

On 01/10/2015 09:00 AM, Éric Germaneau wrote:
> 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
>>> -- 
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
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>>>
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>>>
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>>> send a mail to gmx-users-request at gromacs.org.
>>>
>

-- 
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