[gmx-users] compiling issue
Mark Abraham
mark.j.abraham at gmail.com
Mon Jan 12 18:34:39 CET 2015
Hi,
The problem does not seem like it is within the sphere of GROMACS CMake
settings. To use the non-MPI Intel compilers you have to have already
sourced the right magic scripts, and if you had not then you might observe
the finding C++ standard libraries from wherever the system can get them...
Combining icc with MPI and CUDA seems likely to have more such constraints,
but you'll have to check out the docs for the toolchain you're trying to
use. It's hard to see who would have had the interest in actively
supporting and documenting that particular combination, though..
Mark
On Sat, Jan 10, 2015 at 12:04 PM, Éric Germaneau <germaneau at sjtu.edu.cn>
wrote:
> 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
>>>>
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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
> --
> Gromacs Users mailing list
>
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