Re: [gmx-users] compiling issue

Éric Germaneau Sat, 10 Jan 2015 03:05:07 -0800

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 notbeing able

to assemble SIMD sounds like you haven't set up the whole compiler

environment properly. Odds are excellent that gcc will run fasteranyway...


Mark
On Jan 9, 2015 1:24 AM, "Éric Germaneau" <german...@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 usingicc

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) { volatilestatic

    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) { volatilestatic

    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:german...@sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn
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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:german...@sjtu.edu.cn Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn
--
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] compiling issue

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