[gmx-developers] make install-mdrun

Carsten Kutzner ckutzne at gwdg.de
Mon Oct 29 13:05:41 CET 2012 

On Oct 24, 2012, at 5:59 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
> On Oct 24, 2012, at 5:08 PM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
> 
>> What's your icc version? Perhaps the issue is related to this:
>> http://software.intel.com/en-us/articles/use-intel-cc-compilers-v1201107-or-higher-version-to-resolve-error-when-preprocessing-and-then-compiling-c-language-code-which-included-mathh-or-mathimfh-header
> Ah, that is likely. We have 12.0.0 -> upgrading tomorrow…
Yes, with icc 13.0.1 it works fine. (if the gnu c compiler is not 4.1.2!).

Carsten 

> Thanks a lot!!
> 
> Carsten
> 
>> --
>> Szilárd
>> 
>> 
>> On Wed, Oct 24, 2012 at 2:46 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
>> On 10/24/2012 02:21 PM, Roland Schulz wrote:
>>> 
>>> 
>>> On Wed, Oct 24, 2012 at 7:45 AM, Mirco Wahab <mirco.wahab at chemie.tu-freiberg.de> wrote:
>>> Am 24.10.2012 13:02, schrieb Szilárd Páll:
>>>> On 10/20/2012 07:46 PM, Szilárd Páll wrote:
>>>>> On Sat, Oct 20, 2012 at 5:43 PM, Mirco Wahab <wahab-mail at gmx.de> wrote:
>>>>> 
>>>>>        icc 13.0.0 CUDA5        build fail,    -
>>>>> 
>>>>> 
>>>>>    That should work out of the box -- unless you're using an fftw
>>>>>    that is older than 3.3.1. What error are yo getting?
>>>> 
>>>>    is icc 13 required for building 4.6 with GPU support or should icc
>>>>    12 do as well?
>>>> 
>>>> I'm ont entirely sure about the officially supported versions, but both
>>>> 12 and 13 work fine.
>>> 
>>> I retestet CUDA5 + icc13 on x64-Linux (OpenSuSE) and it builds
>>> perfectly, as you expected. My error from test before may have
>>> resulted from a unlucky combination of GMX_PREFER_STATIC_LIBS
>>> and BUILD_SHARED_LIBS in my build script.
>>> Any combination of these flags should work. Let us know if you have some combination which reproducible fails.
>> Hi,
>> 
>> I cannot get it compiled at all with icc, see below.
>> 
>> Best,
>>  Carsten
>> 
>> 
>> mkdir build
>> cd build
>> source /usr/local/intel/ics/compilerpro-12.0.0.084/bin/iccvars.sh intel64
>> export ICC=/usr/local/intel/ics/composerxe-2011.0.084/bin/intel64/icc
>> export ICPC=/usr/local/intel/ics/composerxe-2011.0.084/bin/intel64/icpc
>> module add MPIBPC/cuda-5.0.35
>> 
>> cmake .. \
>> -DCMAKE_C_COMPILER=$ICC \
>> -DCMAKE_CXX_COMPILER=$ICPC
>> 
>> 
>> [  0%] Building NVCC (Device) object src/gmxlib/cuda_tools/./cuda_tools_generated_pmalloc_cuda.cu.o
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(235): error: omission of exception specification is incompatible with previous function "__isinff"                                     
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6073): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(236): error: omission of exception specification is incompatible with previous function "__isinf"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6087): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(238): error: omission of exception specification is incompatible with previous function "__isinfl"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6410): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(245): error: omission of exception specification is incompatible with previous function "__isnanf"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6074): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(246): error: omission of exception specification is incompatible with previous function "__isnan"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6086): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(248): error: omission of exception specification is incompatible with previous function "__isnanl"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6411): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(275): error: omission of exception specification is incompatible with previous function "__finitef"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6084): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(276): error: omission of exception specification is incompatible with previous function "__finite"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6083): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(278): error: omission of exception specification is incompatible with previous function "__finitel"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6409): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(285): error: omission of exception specification is incompatible with previous function "__signbitf"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6090): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(286): error: omission of exception specification is incompatible with previous function "__signbit"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6085): here
>> 
>> /sw/cluster/intel/ics/composerxe-2011.0.084/compiler/include/math.h(288): error: omission of exception specification is incompatible with previous function "__signbitl"
>> /usr/local/cuda/cuda50/toolkit/5.0.35/include/math_functions.h(6403): here
>> 
>> /usr/include/c++/4.1.2/bits/cpp_type_traits.h(358): error: expected an identifier
>> 
>> /usr/include/c++/4.1.2/bits/cpp_type_traits.h(371): error: expected an identifier
>> 
>> 14 errors detected in the compilation of "/tmp/tmpxft_00000dbc_00000000-9_pmalloc_cuda.compute_30.cpp1.ii".
>> CMake Error at CMakeFiles/cuda_tools_generated_pmalloc_cuda.cu.o.cmake:256 (message):
>>  Error generating file
>>  /home/ckutzne/installations/gromacs/build/src/gmxlib/cuda_tools/./cuda_tools_generated_pmalloc_cuda.cu.o
>> 
>> 
>> make[2]: *** [src/gmxlib/cuda_tools/./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
>> 
>> 
>> 
>> 
>>> Roland 
>>> 
>>> So all is ok now. Thanks!
>>> 
>>> M.
>>> 
>>> --
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>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>> 
>>> 
>> 
>> 
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> 
> 
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> 
> -- 
> gmx-developers mailing list
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner

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