[gmx-users] gromacs 4.6.4 query

[Szilárd Páll]

On Tue, Feb 11, 2014 at 6:12 AM, Chaitali Chandratre
<chaitujoshi at gmail.com> wrote:
> Dear Sir,
>
> Below is error message for gromacs-4.6.4 gpu enabled install:
> ---------------------------------------------------------------------------------------------------------------------------
> make error :
>
> "[chaitalij at gpu4 build-gpu]$ make
> [  0%] Building NVCC (Device) object
> src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
> /opt/CUDA-5.5/include/host_config.h(72): catastrophic error: #error
> directive: -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64
> is supported!
>  #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is
> supported!
>   ^

The error is right there, explained quite clearly in the above
message. What you can do is to:
- complain to NVIDIA  AND

- remove the limitation which is mostly a safety measure (AFAIK the
nvcc + icc 13 is not fully tested and/or compatible) by either editing
the above mentioned header or if you can't do that (no root access)
creating a copy of to edit it and appending its path in
CUDA_NVCC_FLAGS (i.e. adding ";-I/path/to/my/cuda-host-config-h").
OR
- use another compiler, e.g. gcc 4.8 will probably be faster than icc 13.

> CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message):
>  Error generating
>   path/to/gromacs/gromacs-4.6.4/build-gpu/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
>
>
> make[2]: ***
> [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
> Error 1
> make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2
> make: *** [all] Error 2
> "
> -------------------------------------------------------------------------------------------------------------------------
>
> Below is config command :
> ----------------------------------------------------------------------------------------------------------------------
> "
> /path/to/cmake-2.8.12.1/bin/cmake  -DGMX_FFT_LIBRARY=mkl
> -DMKL_LIBRARIES="/path/to//mkl/lib/intel64"
> -DMKL_INCLUDE_DIR="/path/to//mkl/include" -D
> CMAKE_INSTALL_PREFIX=/path/to//gromacs-4.6.4/build-gpu/  -DGMX_MPI=ON
> -DGMX_GPU=ON -DCUDA_HOST_COMPILER=/path/to/intel64/icc
> -DCUDA_TOOLKIT_ROOT_DIR=/opt/CUDA-5.5/ /path/to/gromacs-4.6.4/
> "
> ------------------------------------------------------------------------------------------------------------------------
> Icc details :
> icc version 13.0.1 (gcc version 4.4.6 compatibility)
>
> OpenMM is not available in environment.
>
>
>
>
> On Mon, Feb 10, 2014 at 6:15 PM, Szilárd Páll <pall.szilard at gmail.com>wrote:
>
>> On Mon, Feb 10, 2014 at 1:27 PM, Chaitali Chandratre
>> <chaitujoshi at gmail.com> wrote:
>> > Dear Sir,
>> >
>> > I have question w.r.t gromacs-4.6.4 installation with GPU support.
>> > I have installed non-GPU vesion(for 4.6.4) and it works fine.
>> >
>> > But while compiling with gpu (-DGMX_GPU=ON
>> > -DCUDA_TOOLKIT_ROOT_DIR=/opt/CUDA-5.5)
>> > It gives compilation error. The node is having gpu card fermi and
>> cuda5.5.
>> >
>> > Do I need to set some more things?
>>
>> Yes, perhaps you could tell us what the error is. :)
>>
>> --
>> Szilárd
>>
>> >
>> > Thanks.
>> >
>> > --
>> > With Regards,
>> >    Chaitali
>> >
>> > "I know everything happens for a reason...But sometimes I wish I knew
>> what
>> > the reason was !! "
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
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>> posting!
>> >
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>> >
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>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
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>
>
>
> --
> With Regards,
>    Chaitali
>
> "I know everything happens for a reason...But sometimes I wish I knew what
> the reason was !! "
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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