[gmx-developers] make install-mdrun

Szilárd Páll szilard.pall at cbr.su.se
Mon Oct 29 13:28:05 CET 2012 

On Mon, Oct 29, 2012 at 1:05 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:

> 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!).
>

I guess you mean the gcc compatibility mode icc works in. You can set that
with -gcc-version=XYZ.

--
Szilárd


>
> 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.
> >>>
> >>> --
> >>> gmx-developers mailing list
> >>> gmx-developers at gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> >>> Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-developers-request at gromacs.org.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> >>> 865-241-1537, ORNL PO BOX 2008 MS6309
> >>>
> >>>
> >>
> >>
> >> --
> >> gmx-developers mailing list
> >> gmx-developers at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-developers
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> >>
> >> --
> >> 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
> >
> > --
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-developers-request at gromacs.org.
>
>
> --
> 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
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
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>
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