[gmx-developers] GROMACS 4.6 error in file src/gromacs/analysisdata/analysisdata.cpp:45:0
Thomas Evangelidis
tevang3 at gmail.com
Fri Aug 24 00:06:13 CEST 2012
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
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