[gmx-developers] GROMACS 4.6 error in file src/gromacs/analysisdata/analysisdata.cpp:45:0

[Roland Schulz]

Hi,

you don't need OpenMM for the new GPU feature in 4.6. It has build in
GPU/Cuda support. Also you seem to have downloaded the master branch and
not 4.6. If you got the code by git you can use "git checkout release-4-6"
to get 4.6.
You seem to have found a problem with OpenMM and the master branch. I don't
know whether we are planning to support OpenMM for 5.0 so I'm not sure this
is something important to fix.

Roland

On Thu, Aug 23, 2012 at 6:06 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:

>  Greetings,
>
> I am trying to compile the latest source (v4.6) with cmake. I think I
> managed to set up my laptop GPU (GEFORCE GT 650M) with bumblebee in Fedora
> 17 (I am not 100% sure), and after working out several installation errors,
> I stuck at the point described below. I would describe every step I did in
> detail hence the long text. Hope someone can help me.
>
> # After installing OpenMM4.1.1 and CUDA4.1
> $cd gromacs
> $mkdir build_gromacs_gpu
> $cd build_gromacs_gpu
> $export OPENMM_ROOT_DIR=/home/thomas/Programs/OpenMM4.1.1-Linux64
> $cmake -i ../ -DGMX_OPENMM=ON
> -DCMAKE_INSTALL_PREFIX=`pwd`/installation_dir -DGMX_THREADS=OFF
>
> Would you like to see advanced options? [No]:
> Please wait while cmake processes CMakeLists.txt files....
>
>
>
> Variable Name: BUILD_SHARED_LIBS
> Description: Enable shared libraries (can be problematic with MPI, Windows)
> Current Value: ON
> New Value (Enter to keep current value): OFF
>
> Variable Name: Boost_DIR
> Description: The directory containing a CMake configuration file for Boost.
> Current Value: Boost_DIR-NOTFOUND
> New Value (Enter to keep current value):
>
> Variable Name: CMAKE_BUILD_TYPE
> Description: Choose the type of build, options are: Debug Release
> RelWithDebInfo MinSizeRel.
> Current Value: Release
> New Value (Enter to keep current value):
>
> Variable Name: CMAKE_INSTALL_PREFIX
> Description: Install path prefix, prepended onto install directories.
> Current Value:
> /home/thomas/Programs/gromacs/build_gromacs_gpu/installation_dir
> New Value (Enter to keep current value):
>
> Variable Name: CUDA_BUILD_CUBIN
> Description: Generate and parse .cubin files in Device mode.
> Current Value: OFF
> New Value (Enter to keep current value):
>
> Variable Name: CUDA_BUILD_EMULATION
> Description: Build in Emulation mode
> Current Value: OFF
> New Value (Enter to keep current value):
>
> Variable Name: CUDA_SDK_ROOT_DIR
> Description: Path to a file.
> Current Value: CUDA_SDK_ROOT_DIR-NOTFOUND
> New Value (Enter to keep current value): /opt/cuda
>
> Variable Name: CUDA_TOOLKIT_ROOT_DIR
> Description: Toolkit location.
> Current Value: /opt/cuda
> New Value (Enter to keep current value): q^C
> thomas at thomasASUS:~/Programs/gromacs/build_gromacs_gpu$ cmake -i ../
> -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=`pwd`/installation_dir
> -DGMX_THREADS=OFF
> Would you like to see advanced options? [No]:
> Please wait while cmake processes CMakeLists.txt files....
>
>
>
> Variable Name: BUILD_SHARED_LIBS
> Description: Enable shared libraries (can be problematic with MPI, Windows)
> Current Value: ON
> New Value (Enter to keep current value): OFF
>
> Variable Name: Boost_DIR
> Description: The directory containing a CMake configuration file for Boost.
> Current Value: Boost_DIR-NOTFOUND
> New Value (Enter to keep current value):
>
> Variable Name: CMAKE_BUILD_TYPE
> Description: Choose the type of build, options are: Debug Release
> RelWithDebInfo MinSizeRel.
> Current Value: Release
> New Value (Enter to keep current value):
>
> Variable Name: CMAKE_INSTALL_PREFIX
> Description: Install path prefix, prepended onto install directories.
> Current Value:
> /home/thomas/Programs/gromacs/build_gromacs_gpu/installation_dir
> New Value (Enter to keep current value):
>
> Variable Name: CUDA_BUILD_CUBIN
> Description: Generate and parse .cubin files in Device mode.
> Current Value: OFF
> New Value (Enter to keep current value):
>
> Variable Name: CUDA_BUILD_EMULATION
> Description: Build in Emulation mode
> Current Value: OFF
> New Value (Enter to keep current value):
>
> Variable Name: CUDA_SDK_ROOT_DIR
> Description: Path to a file.
> Current Value: CUDA_SDK_ROOT_DIR-NOTFOUND
> New Value (Enter to keep current value):
> /home/thomas/NVIDIA_GPU_Computing_SDK
>
> Variable Name: CUDA_TOOLKIT_ROOT_DIR
> Description: Toolkit location.
> Current Value: /opt/cuda
> New Value (Enter to keep current value):
>
> Variable Name: CUDA_VERBOSE_BUILD
> Description: Print out the commands run while compiling the CUDA source
> file.  With the Makefile generator this defaults to VERBOSE variable
> specified on the command line, but can be forced on with this option.
> Current Value: OFF
> New Value (Enter to keep current value): ON
>
> Variable Name: GMX_DEFAULT_SUFFIX
> Description: Use default suffixes for GROMACS binaries and libs (_d for
> double, _mpi for MPI; rerun cmake after changing to see relevant options)
> Current Value: ON
> New Value (Enter to keep current value): _cuda
>
> Variable Name: GMX_GSL
> Description: Add support for gsl
> Current Value: OFF
> New Value (Enter to keep current value):
>
> Variable Name: GMX_INTERNAL_BOOST
> Description: Use minimal internal version of boost
> Current Value: OFF
> New Value (Enter to keep current value): ON
>
> Variable Name: GMX_OPENMM
> Description: Accelerated execution on GPUs through the OpenMM library
> (rerun cmake after changing to see relevant options)
> Current Value: ON
> New Value (Enter to keep current value):
>
> Variable Name: GMX_OPENMP
> Description: Enable OpenMP-based mutithreading.
> Current Value: OFF
> New Value (Enter to keep current value):
>
> Variable Name: GMX_X11
> Description: Use X window system
> Current Value: OFF
> New Value (Enter to keep current value):
>
> Variable Name: GMX_XML
> Description: Use libxml2 to parse xml files
> Current Value: ON
> New Value (Enter to keep current value):
>
> Variable Name: OpenMM_PLUGIN_DIR
> Description: OpenMM plugins directory
> Current Value: /home/thomas/Programs/OpenMM4.1.1-Linux64/lib/plugins
> New Value (Enter to keep current value):
>
> Variable Name: OpenMM_ROOT_DIR
> Description: OpenMM installation directory
> Current Value: /home/thomas/Programs/OpenMM4.1.1-Linux64
> New Value (Enter to keep current value):
>
> Variable Name: PTHREADS_INCLUDE_DIR
> Description: Path to a file.
> Current Value: /usr/include
> New Value (Enter to keep current value):
>
> Variable Name: PTHREADS_LIBRARY
> Description: The Portable Threads Library
> Current Value: /usr/lib64/libpthread.so
> New Value (Enter to keep current value):
>
> Please wait while cmake processes CMakeLists.txt files....
>
>
>
> CMake Warning:
>   Manually-specified variables were not used by the project:
>
>     GMX_THREADS
>
>
> CMake complete, run make to build project.
>
>
>
> $ make mdrun
> [  0%] Generating version information
> [  0%] Built target gmx_version
> Scanning dependencies of target libgromacs
> [  0%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.c.o
> [  0%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.c.o
> [  0%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.c.o
> [  0%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.c.o
> [  0%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.c.o
> [  0%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.c.o
> [  1%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/compute_io.c.o
> [  1%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.c.o
> [  1%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.c.o
> [  1%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.c.o
> [  1%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topexcl.c.o
> [  1%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.c.o
> [  1%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.c.o
> [  1%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.c.o
> [  1%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.c.o
> [  2%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.c.o
> [  2%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.c.o
> [  2%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.c.o
> [  2%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.c.o
> [  2%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.c.o
> [  2%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readadress.c.o
> [  2%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.c.o
> [  2%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.c.o
> [  2%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.c.o
> [  4%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.c.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o
> In file included from
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:45:0:
> /home/thomas/Programs/gromacs/src/gromacs/utility/uniqueptr.h:77:12:
> error: ‘std::move’ has not been declared
> /home/thomas/Programs/gromacs/src/gromacs/utility/uniqueptr.h:81:13:
> error: ‘unique_ptr’ in namespace ‘std’ does not name a type
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:92:17:
> error: ‘type’ in ‘struct
> gmx::gmx_unique_ptr<gmx::internal::AnalysisDataHandleImpl>’ does not name a
> type
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:95:29:
> error: ‘HandlePointer’ was not declared in this scope
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:95:42:
> error: template argument 1 is invalid
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:95:42:
> error: template argument 2 is invalid
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:
> In member function ‘void gmx::AnalysisData::setColumnCount(int)’:
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:127:31:
> error: request for member ‘empty’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:
> In member function ‘void gmx::AnalysisData::setMultipoint(bool)’:
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:136:31:
> error: request for member ‘empty’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:
> In member function ‘gmx::AnalysisDataHandle
> gmx::AnalysisData::startData(const gmx::AnalysisDataParallelOptions&)’:
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:146:31:
> error: request for member ‘size’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:148:25:
> error: request for member ‘empty’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:159:5:
> error: ‘HandlePointer’ is not a member of ‘gmx::AnalysisData::Impl’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:159:25:
> error: expected ‘;’ before ‘handle’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:160:21:
> error: request for member ‘push_back’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:160:36:
> error: ‘handle’ was not declared in this scope
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:160:42:
> error: ‘move’ was not declared in this scope
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:161:47:
> error: request for member ‘back’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:
> In member function ‘void
> gmx::AnalysisData::finishData(gmx::AnalysisDataHandle)’:
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:168:32:
> error: expected initializer before ‘i’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:170:10:
> error: ‘i’ was not declared in this scope
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:170:30:
> error: request for member ‘begin’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:170:60:
> error: request for member ‘end’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:177:36:
> error: request for member ‘end’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:180:21:
> error: request for member ‘erase’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:182:25:
> error: request for member ‘empty’ in
> ‘((gmx::AnalysisData*)this)->gmx::AnalysisData::impl_.gmx::PrivateImplPointer<Impl>::operator-><gmx::AnalysisData::Impl>()->gmx::AnalysisData::Impl::handles_’,
> which is of non-class type ‘gmx::AnalysisData::Impl::HandleList {aka int}’
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:
> In member function ‘gmx::AnalysisDataHandle
> gmx::AnalysisData::startData(const gmx::AnalysisDataParallelOptions&)’:
> /home/thomas/Programs/gromacs/src/gromacs/analysisdata/analysisdata.cpp:162:1:
> warning: control reaches end of non-void function [-Wreturn-type]
> make[3]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o]
> Error 1
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make[1]: *** [src/programs/mdrun/CMakeFiles/mdrun.dir/rule] Error 2
> make: *** [mdrun] Error 2
>
>
>


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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