[gmx-developers] make install-mdrun

Carsten Kutzner ckutzne at gwdg.de
Wed Oct 24 17:59:55 CEST 2012 

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…
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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>> 
>> 
>> 
>> 
>> 
>> 
>> -- 
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>> 
>> 
> 
> 
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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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