undefined reference to `operator new(unsigned long)'
Posted: Tue Feb 23, 2016 1:02 pm
Hi Peter,
I am having build issues on a new server (OS: Scientific Linux release 6.7 (Carbon)) which I hope you can help diagnose. Building and linking without tests completes without error, but there are downstream problems with simbody and MMB that made me take a closer look. When I build with tests, I get this error:
[samuelf@tintin3 build]$ make
[ 1%] Built target ApiWrappers
[ 51%] Built target OpenMM
Linking CXX executable ../../../TestReferenceAndersenThermostat
CMakeFiles/TestReferenceAndersenThermostat.dir/TestReferenceAndersenThermostat.cpp.o: In function `testTemperature()':
TestReferenceAndersenThermostat.cpp:(.text+0x39): undefined reference to `operator new(unsigned long)'
TestReferenceAndersenThermostat.cpp:(.text+0xfd): undefined reference to `operator new(unsigned long)'
TestReferenceAndersenThermostat.cpp:(.text+0x1aa): undefined reference to `operator new(unsigned long)'
TestReferenceAndersenThermostat.cpp:(.text+0x44e): undefined reference to `operator delete(void*)'
TestReferenceAndersenThermostat.cpp:(.text+0x459): undefined reference to `operator delete(void*)'
.. this looks like a c++11 issue .. but I am setting the appropriate flag. OpenMM really doesn't provide all that many cmake options so I am at a loss as to how to proceed. I append my CMakeCache.txt in hopes that you can see something wrong.
Thanks
Sam
[samuelf@tintin3 build]$ cat CMakeCache.txt
# This is the CMakeCache file.
# For build in directory: /home/samuelf/github/openmm/build
# It was generated by CMake: /pica/sw/apps/build/cmake/2.8.11.2_tintin/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUI's for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.
########################
# EXTERNAL cache entries
########################
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BUILD_TESTING:BOOL=ON
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CMAKE_COLOR_MAKEFILE:BOOL=ON
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CMAKE_CXX_FLAGS:STRING=-std=c++11
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//Flags used by the compiler during release minsize builds.
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//Flags used by the compiler during release builds (/MD /Ob1 /Oi
// /Ot /Oy /Gs will produce slightly less optimized but smaller
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//Flags used by the linker during Release with Debug Info builds.
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//Path to a file.
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DOXYGEN_EXECUTABLE:FILEPATH=/usr/bin/doxygen
//Path to a file.
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//Path to a library.
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OPENMM_BUILD_CUDA_LIB:BOOL=OFF
//Build wrappers for C and Fortran
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS:BOOL=ON
//Build Drude implementation for CUDA
OPENMM_BUILD_DRUDE_CUDA_LIB:BOOL=OFF
//Build Drude implementation for OpenCL
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//Build Drude plugin
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//Build example executables
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//Build OpenMMOpenCL library
OPENMM_BUILD_OPENCL_LIB:BOOL=OFF
//Build CPU PME plugin
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//Build wrappers for Python
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//Build RPMD implementation for CUDA
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//Build RPMD plugin
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//ADVANCED property for variable: CUDA_BUILD_CUBIN
CUDA_BUILD_CUBIN-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_BUILD_EMULATION
CUDA_BUILD_EMULATION-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_CUDART_LIBRARY
CUDA_CUDART_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_CUDA_LIBRARY
CUDA_CUDA_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_GENERATED_OUTPUT_DIR
CUDA_GENERATED_OUTPUT_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_HOST_COMPILATION_CPP
CUDA_HOST_COMPILATION_CPP-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_HOST_COMPILER
CUDA_HOST_COMPILER-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_NVCC_EXECUTABLE
CUDA_NVCC_EXECUTABLE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_NVCC_FLAGS
CUDA_NVCC_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_NVCC_FLAGS_DEBUG
CUDA_NVCC_FLAGS_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_NVCC_FLAGS_MINSIZEREL
CUDA_NVCC_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_NVCC_FLAGS_RELEASE
CUDA_NVCC_FLAGS_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_NVCC_FLAGS_RELWITHDEBINFO
CUDA_NVCC_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_PROPAGATE_HOST_FLAGS
CUDA_PROPAGATE_HOST_FLAGS-ADVANCED:INTERNAL=1
//This is the value of the last time CUDA_SDK_ROOT_DIR was set
// successfully.
CUDA_SDK_ROOT_DIR_INTERNAL:INTERNAL=CUDA_SDK_ROOT_DIR-NOTFOUND
//ADVANCED property for variable: CUDA_TOOLKIT_INCLUDE
CUDA_TOOLKIT_INCLUDE-ADVANCED:INTERNAL=1
//This is the value of the last time CUDA_TOOLKIT_ROOT_DIR was
// set successfully.
CUDA_TOOLKIT_ROOT_DIR_INTERNAL:INTERNAL=CUDA_TOOLKIT_ROOT_DIR-NOTFOUND
//ADVANCED property for variable: CUDA_VERBOSE_BUILD
CUDA_VERBOSE_BUILD-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_cublas_LIBRARY
CUDA_cublas_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_cublasemu_LIBRARY
CUDA_cublasemu_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_cufft_LIBRARY
CUDA_cufft_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CUDA_cufftemu_LIBRARY
CUDA_cufftemu_LIBRARY-ADVANCED:INTERNAL=1
//Location of make2cmake.cmake
CUDA_make2cmake:INTERNAL=/pica/sw/apps/build/cmake/2.8.11.2_tintin/share/cmake-2.8/Modules/FindCUDA/make2cmake.cmake
//Location of parse_cubin.cmake
CUDA_parse_cubin:INTERNAL=/pica/sw/apps/build/cmake/2.8.11.2_tintin/share/cmake-2.8/Modules/FindCUDA/parse_cubin.cmake
//Location of run_nvcc.cmake
CUDA_run_nvcc:INTERNAL=/pica/sw/apps/build/cmake/2.8.11.2_tintin/share/cmake-2.8/Modules/FindCUDA/run_nvcc.cmake
//ADVANCED property for variable: CVSCOMMAND
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//ADVANCED property for variable: CVS_UPDATE_OPTIONS
CVS_UPDATE_OPTIONS-ADVANCED:INTERNAL=1
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//ADVANCED property for variable: DART_BUILD_WARNING_REPORT_LIMIT
DART_BUILD_WARNING_REPORT_LIMIT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_ROOT
DART_ROOT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_TESTING_TIMEOUT
DART_TESTING_TIMEOUT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_VERBOSE_BUILD
DART_VERBOSE_BUILD-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DELIVER_CONTINUOUS_EMAIL
DELIVER_CONTINUOUS_EMAIL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DL_LIBRARY
DL_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DOXYGEN_DOT_EXECUTABLE
DOXYGEN_DOT_EXECUTABLE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DOXYGEN_DOT_PATH
DOXYGEN_DOT_PATH-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DOXYGEN_EXECUTABLE
DOXYGEN_EXECUTABLE-ADVANCED:INTERNAL=0
//Single output directory for building all executables.
EXECUTABLE_OUTPUT_PATH:INTERNAL=/home/samuelf/github/openmm/build
//ADVANCED property for variable: FFTW_INCLUDES
FFTW_INCLUDES-ADVANCED:INTERNAL=1
//ADVANCED property for variable: FFTW_LIBRARY
FFTW_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: FFTW_THREADS_LIBRARY
FFTW_THREADS_LIBRARY-ADVANCED:INTERNAL=1
//Details about finding Doxygen
FIND_PACKAGE_MESSAGE_DETAILS_Doxygen:INTERNAL=[/usr/bin/doxygen][v1.6.1()]
//Details about finding PythonInterp
FIND_PACKAGE_MESSAGE_DETAILS_PythonInterp:INTERNAL=[/home/samuelf/bin/python][v3.3.3()]
//ADVANCED property for variable: GITCOMMAND
GITCOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: GUNZIPCOMMAND
GUNZIPCOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HGCOMMAND
HGCOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: JAVACOMMAND
JAVACOMMAND-ADVANCED:INTERNAL=1
//Single output directory for building all libraries.
LIBRARY_OUTPUT_PATH:INTERNAL=/home/samuelf/github/openmm/build
//ADVANCED property for variable: MAKECOMMAND
MAKECOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: MEMORYCHECK_COMMAND
MEMORYCHECK_COMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: MEMORYCHECK_SUPPRESSIONS_FILE
MEMORYCHECK_SUPPRESSIONS_FILE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: OPENCL_INCLUDE_DIR
OPENCL_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: OPENCL_LIBRARY
OPENCL_LIBRARY-ADVANCED:INTERNAL=1
//MODIFIED property for variable: OPENMM_BUILD_EXAMPLES
OPENMM_BUILD_EXAMPLES-MODIFIED:INTERNAL=ON
//MODIFIED property for variable: OPENMM_BUILD_PYTHON_WRAPPERS
OPENMM_BUILD_PYTHON_WRAPPERS-MODIFIED:INTERNAL=ON
//ADVANCED property for variable: OPENMM_PYTHON_STAGING_DIR
OPENMM_PYTHON_STAGING_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: OPENMM_VERSION
OPENMM_VERSION-ADVANCED:INTERNAL=1
//ADVANCED property for variable: PYTHON_EXECUTABLE
PYTHON_EXECUTABLE-ADVANCED:INTERNAL=0
//ADVANCED property for variable: SCPCOMMAND
SCPCOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: SITE
SITE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: SLURM_SBATCH_COMMAND
SLURM_SBATCH_COMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: SLURM_SRUN_COMMAND
SLURM_SRUN_COMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: SVNCOMMAND
SVNCOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: SWIG_VERSION
SWIG_VERSION-ADVANCED:INTERNAL=1
[samuelf@tintin3 build]$
I am having build issues on a new server (OS: Scientific Linux release 6.7 (Carbon)) which I hope you can help diagnose. Building and linking without tests completes without error, but there are downstream problems with simbody and MMB that made me take a closer look. When I build with tests, I get this error:
[samuelf@tintin3 build]$ make
[ 1%] Built target ApiWrappers
[ 51%] Built target OpenMM
Linking CXX executable ../../../TestReferenceAndersenThermostat
CMakeFiles/TestReferenceAndersenThermostat.dir/TestReferenceAndersenThermostat.cpp.o: In function `testTemperature()':
TestReferenceAndersenThermostat.cpp:(.text+0x39): undefined reference to `operator new(unsigned long)'
TestReferenceAndersenThermostat.cpp:(.text+0xfd): undefined reference to `operator new(unsigned long)'
TestReferenceAndersenThermostat.cpp:(.text+0x1aa): undefined reference to `operator new(unsigned long)'
TestReferenceAndersenThermostat.cpp:(.text+0x44e): undefined reference to `operator delete(void*)'
TestReferenceAndersenThermostat.cpp:(.text+0x459): undefined reference to `operator delete(void*)'
.. this looks like a c++11 issue .. but I am setting the appropriate flag. OpenMM really doesn't provide all that many cmake options so I am at a loss as to how to proceed. I append my CMakeCache.txt in hopes that you can see something wrong.
Thanks
Sam
[samuelf@tintin3 build]$ cat CMakeCache.txt
# This is the CMakeCache file.
# For build in directory: /home/samuelf/github/openmm/build
# It was generated by CMake: /pica/sw/apps/build/cmake/2.8.11.2_tintin/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUI's for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.
########################
# EXTERNAL cache entries
########################
//Build the testing tree.
BUILD_TESTING:BOOL=ON
//Path to a program.
BZRCOMMAND:FILEPATH=/usr/bin/bzr
//Path to a program.
CMAKE_AR:FILEPATH=/usr/bin/ar
//Debug or Release build
CMAKE_BUILD_TYPE:STRING=Release
//Enable/Disable color output during build.
CMAKE_COLOR_MAKEFILE:BOOL=ON
//CXX compiler.
CMAKE_CXX_COMPILER:FILEPATH=/sw/comp/gcc/5.1.0_tintin/bin/gcc
//Flags used by the compiler during all build types.
CMAKE_CXX_FLAGS:STRING=-std=c++11
//Flags used by the compiler during debug builds.
CMAKE_CXX_FLAGS_DEBUG:STRING= -std=c++11 -g
//Flags used by the compiler during release minsize builds.
CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG
//Flags used by the compiler during release builds (/MD /Ob1 /Oi
// /Ot /Oy /Gs will produce slightly less optimized but smaller
// files).
CMAKE_CXX_FLAGS_RELEASE:STRING=-std=c++11 -O3 -DNDEBUG
//Flags used by the compiler during Release with Debug Info builds.
CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG
//C compiler.
CMAKE_C_COMPILER:FILEPATH=/sw/comp/gcc/5.1.0_tintin/bin/gcc
//Flags used by the compiler during all build types.
CMAKE_C_FLAGS:STRING=
//Flags used by the compiler during debug builds.
CMAKE_C_FLAGS_DEBUG:STRING=-g
//Flags used by the compiler during release minsize builds.
CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG
//Flags used by the compiler during release builds (/MD /Ob1 /Oi
// /Ot /Oy /Gs will produce slightly less optimized but smaller
// files).
CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
//Flags used by the compiler during Release with Debug Info builds.
CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG
//Flags used by the linker.
CMAKE_EXE_LINKER_FLAGS:STRING=' '
//Flags used by the linker during debug builds.
CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//Enable/Disable output of compile commands during generation.
CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=OFF
//Where to install OpenMM
CMAKE_INSTALL_PREFIX:PATH=/home/samuelf/openmm
//Path to a program.
CMAKE_LINKER:FILEPATH=/usr/bin/ld
//Path to a program.
CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/gmake
//Flags used by the linker during the creation of modules.
CMAKE_MODULE_LINKER_FLAGS:STRING=' '
//Flags used by the linker during debug builds.
CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//Path to a program.
CMAKE_NM:FILEPATH=/usr/bin/nm
//Path to a program.
CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy
//Path to a program.
CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump
//Value Computed by CMake
CMAKE_PROJECT_NAME:STATIC=OpenMM
//Path to a program.
CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib
//Flags used by the linker during the creation of dll's.
CMAKE_SHARED_LINKER_FLAGS:STRING=' '
//Flags used by the linker during debug builds.
CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//If set, runtime paths are not added when installing shared libraries,
// but are added when building.
CMAKE_SKIP_INSTALL_RPATH:BOOL=NO
//If set, runtime paths are not added when using shared libraries.
CMAKE_SKIP_RPATH:BOOL=NO
//Path to a program.
CMAKE_STRIP:FILEPATH=/usr/bin/strip
//If true, cmake will use relative paths in makefiles and projects.
CMAKE_USE_RELATIVE_PATHS:BOOL=OFF
//If this value is on, makefiles will be generated without the
// .SILENT directive, and all commands will be echoed to the console
// during the make. This is useful for debugging only. With Visual
// Studio IDE projects all commands are done without /nologo.
CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE
//Path to program used to compress files for transfer to the dart
// server
COMPRESSIONCOMMAND:FILEPATH=/bin/gzip
//Path to the coverage program that CTest uses for performing coverage
// inspection
COVERAGE_COMMAND:FILEPATH=/sw/comp/gcc/5.1.0_tintin/bin/gcov
//Extra command line flags to pass to the coverage tool
COVERAGE_EXTRA_FLAGS:STRING=-l
//How many times to retry timed-out CTest submissions.
CTEST_SUBMIT_RETRY_COUNT:STRING=3
//How long to wait between timed-out CTest submissions.
CTEST_SUBMIT_RETRY_DELAY:STRING=5
//Compile device code in 64 bit mode
CUDA_64_BIT_DEVICE_CODE:BOOL=ON
//Attach the build rule to the CUDA source file. Enable only when
// the CUDA source file is added to at most one target.
CUDA_ATTACH_VS_BUILD_RULE_TO_CUDA_FILE:BOOL=ON
//Generate and parse .cubin files in Device mode.
CUDA_BUILD_CUBIN:BOOL=OFF
//Build in Emulation mode
CUDA_BUILD_EMULATION:BOOL=OFF
//"cudart" library
CUDA_CUDART_LIBRARY:FILEPATH=CUDA_CUDART_LIBRARY-NOTFOUND
//"cuda" library (older versions only).
CUDA_CUDA_LIBRARY:FILEPATH=CUDA_CUDA_LIBRARY-NOTFOUND
//Directory to put all the output files. If blank it will default
// to the CMAKE_CURRENT_BINARY_DIR
CUDA_GENERATED_OUTPUT_DIR:PATH=
//Generated file extension
CUDA_HOST_COMPILATION_CPP:BOOL=ON
//Host side compiler used by NVCC
CUDA_HOST_COMPILER:FILEPATH=/sw/comp/gcc/5.1.0_tintin/bin/gcc
//Path to a program.
CUDA_NVCC_EXECUTABLE:FILEPATH=CUDA_NVCC_EXECUTABLE-NOTFOUND
//Semi-colon delimit multiple arguments.
CUDA_NVCC_FLAGS:STRING=
//Semi-colon delimit multiple arguments.
CUDA_NVCC_FLAGS_DEBUG:STRING=
//Semi-colon delimit multiple arguments.
CUDA_NVCC_FLAGS_MINSIZEREL:STRING=
//Semi-colon delimit multiple arguments.
CUDA_NVCC_FLAGS_RELEASE:STRING=
//Semi-colon delimit multiple arguments.
CUDA_NVCC_FLAGS_RELWITHDEBINFO:STRING=
//Propage C/CXX_FLAGS and friends to the host compiler via -Xcompile
CUDA_PROPAGATE_HOST_FLAGS:BOOL=ON
//Path to a file.
CUDA_SDK_ROOT_DIR:PATH=CUDA_SDK_ROOT_DIR-NOTFOUND
//Compile CUDA objects with separable compilation enabled. Requires
// CUDA 5.0+
CUDA_SEPARABLE_COMPILATION:BOOL=OFF
//Path to a file.
CUDA_TOOLKIT_INCLUDE:PATH=CUDA_TOOLKIT_INCLUDE-NOTFOUND
//Toolkit location.
CUDA_TOOLKIT_ROOT_DIR:PATH=CUDA_TOOLKIT_ROOT_DIR-NOTFOUND
//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.
CUDA_VERBOSE_BUILD:BOOL=OFF
//"cublas" library
CUDA_cublas_LIBRARY:FILEPATH=CUDA_cublas_LIBRARY-NOTFOUND
//"cublasemu" library
CUDA_cublasemu_LIBRARY:FILEPATH=CUDA_cublasemu_LIBRARY-NOTFOUND
//"cufft" library
CUDA_cufft_LIBRARY:FILEPATH=CUDA_cufft_LIBRARY-NOTFOUND
//"cufftemu" library
CUDA_cufftemu_LIBRARY:FILEPATH=CUDA_cufftemu_LIBRARY-NOTFOUND
//Path to a library.
CUDA_nvrtc_LIBRARY:FILEPATH=CUDA_nvrtc_LIBRARY-NOTFOUND
//Path to a program.
CVSCOMMAND:FILEPATH=/usr/bin/cvs
//Options passed to the cvs update command.
CVS_UPDATE_OPTIONS:STRING=-d -A -P
//Limit of reported errors, -1 reports all.
DART_BUILD_ERROR_REPORT_LIMIT:BOOL=OFF
//Limit of reported warnings, -1 reports all.
DART_BUILD_WARNING_REPORT_LIMIT:BOOL=OFF
//If you have Dart installed, where is it located?
DART_ROOT:PATH=DART_ROOT-NOTFOUND
//Maximum time allowed before CTest will kill the test.
DART_TESTING_TIMEOUT:STRING=1500
//Show the actual output of the build, or if off show a . for each
// 1024 bytes.
DART_VERBOSE_BUILD:BOOL=OFF
//Should Dart server send email when build errors are found in
// Continuous builds?
DELIVER_CONTINUOUS_EMAIL:BOOL=Off
//Path to a library.
DL_LIBRARY:FILEPATH=/usr/lib64/libdl.so
//Graphviz Dot tool for using Doxygen
DOXYGEN_DOT_EXECUTABLE:FILEPATH=/usr/bin/dot
DOXYGEN_DOT_PATH:FILEPATH=/usr/bin
//Doxygen documentation generation tool (http://www.doxygen.org)
DOXYGEN_EXECUTABLE:FILEPATH=/usr/bin/doxygen
//Path to a file.
FFTW_INCLUDES:PATH=/usr/include
//Path to a library.
FFTW_LIBRARY:FILEPATH=/usr/lib64/libfftw3f.so
//Path to a library.
FFTW_THREADS_LIBRARY:FILEPATH=/usr/lib64/libfftw3f_threads.so
//Path to a program.
GITCOMMAND:FILEPATH=/usr/bin/git
//Path to gunzip executable
GUNZIPCOMMAND:FILEPATH=/bin/gunzip
//Path to a program.
HGCOMMAND:FILEPATH=/usr/bin/hg
//Path to java command, used by the Dart server to create html.
JAVACOMMAND:FILEPATH=/usr/bin/java
//Command to build the project
MAKECOMMAND:STRING=/usr/bin/gmake -i
//Path to the memory checking command, used for memory error detection.
MEMORYCHECK_COMMAND:FILEPATH=/usr/bin/valgrind
//File that contains suppressions for the memory checker
MEMORYCHECK_SUPPRESSIONS_FILE:FILEPATH=
//Path to a file.
OPENCL_INCLUDE_DIR:PATH=OPENCL_INCLUDE_DIR-NOTFOUND
//Path to a library.
OPENCL_LIBRARY:FILEPATH=OPENCL_LIBRARY-NOTFOUND
//Build OpenMMAmoebaCuda library for Nvidia GPUs
OPENMM_BUILD_AMOEBA_CUDA_LIB:BOOL=OFF
//Build Amoeba plugin
OPENMM_BUILD_AMOEBA_PLUGIN:BOOL=ON
//Build optimized CPU platform
OPENMM_BUILD_CPU_LIB:BOOL=ON
//Build CUDA runtime compiler plugin
OPENMM_BUILD_CUDA_COMPILER_PLUGIN:BOOL=OFF
//Build OpenMMCuda library for Nvidia GPUs
OPENMM_BUILD_CUDA_LIB:BOOL=OFF
//Build wrappers for C and Fortran
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS:BOOL=ON
//Build Drude implementation for CUDA
OPENMM_BUILD_DRUDE_CUDA_LIB:BOOL=OFF
//Build Drude implementation for OpenCL
OPENMM_BUILD_DRUDE_OPENCL_LIB:BOOL=OFF
//Build Drude plugin
OPENMM_BUILD_DRUDE_PLUGIN:BOOL=ON
//Build example executables
OPENMM_BUILD_EXAMPLES:BOOL=OFF
//Build OpenMMOpenCL library
OPENMM_BUILD_OPENCL_LIB:BOOL=OFF
//Build CPU PME plugin
OPENMM_BUILD_PME_PLUGIN:BOOL=ON
//Build wrappers for Python
OPENMM_BUILD_PYTHON_WRAPPERS:BOOL=OFF
//Build RPMD implementation for CUDA
OPENMM_BUILD_RPMD_CUDA_LIB:BOOL=OFF
//Build RPMD implementation for OpenCL
OPENMM_BUILD_RPMD_OPENCL_LIB:BOOL=OFF
//Build RPMD plugin
OPENMM_BUILD_RPMD_PLUGIN:BOOL=ON
//Whether to build shared OpenMM libraries
OPENMM_BUILD_SHARED_LIB:BOOL=ON
//Whether to build static OpenMM libraries
OPENMM_BUILD_STATIC_LIB:BOOL=OFF
//Whether to create API documentation using Doxygen
OPENMM_GENERATE_API_DOCS:BOOL=OFF
//Temporary staging area for Python API wrappers
OPENMM_PYTHON_STAGING_DIR:PATH=/home/samuelf/github/openmm/build/python
//This is the version of OpenMM which will be built.
OPENMM_VERSION:STRING=6.3.0
//Dependencies for the target
OpenMMAmoebaReference_LIB_DEPENDS:STATIC=general;OpenMM;general;OpenMMAmoeba;
//Dependencies for the target
OpenMMAmoeba_LIB_DEPENDS:STATIC=general;/usr/lib64/libdl.so;general;OpenMM;
//Dependencies for the target
OpenMMCPU_LIB_DEPENDS:STATIC=general;OpenMM;general;pthread;
//Dependencies for the target
OpenMMDrudeReference_LIB_DEPENDS:STATIC=general;OpenMM;debug;OpenMMDrude;optimized;OpenMMDrude;
//Dependencies for the target
OpenMMDrude_LIB_DEPENDS:STATIC=general;/usr/lib64/libdl.so;general;OpenMM;
//Dependencies for the target
OpenMMPME_LIB_DEPENDS:STATIC=general;OpenMM;general;pthread;general;/usr/lib64/libfftw3f.so;general;/usr/lib64/libfftw3f_threads.so;
//Dependencies for the target
OpenMMRPMDReference_LIB_DEPENDS:STATIC=general;OpenMM;general;OpenMMRPMD;
//Dependencies for the target
OpenMMRPMD_LIB_DEPENDS:STATIC=general;/usr/lib64/libdl.so;general;OpenMM;
//Value Computed by CMake
OpenMM_BINARY_DIR:STATIC=/home/samuelf/github/openmm/build
//Dependencies for the target
OpenMM_LIB_DEPENDS:STATIC=general;/usr/lib64/libdl.so;general;pthread;
//Value Computed by CMake
OpenMM_SOURCE_DIR:STATIC=/home/samuelf/github/openmm
//Path to a program.
PYTHON_EXECUTABLE:FILEPATH=/home/samuelf/bin/python
//Path to scp command, used by CTest for submitting results to
// a Dart server
SCPCOMMAND:FILEPATH=/usr/bin/scp
//Name of the computer/site where compile is being run
SITE:STRING=tintin2.uppmax.uu.se
//Path to the SLURM sbatch executable
SLURM_SBATCH_COMMAND:FILEPATH=/usr/bin/sbatch
//Path to the SLURM srun executable
SLURM_SRUN_COMMAND:FILEPATH=/usr/bin/srun
//Path to a program.
SVNCOMMAND:FILEPATH=/usr/bin/svn
//Path to a program.
SWIG_EXECUTABLE:FILEPATH=/usr/bin/swig
//Swig version
SWIG_VERSION:STRING=1.3.40
########################
# INTERNAL cache entries
########################
//MODIFIED property for variable: BUILD_TESTING
BUILD_TESTING-MODIFIED:INTERNAL=ON
//ADVANCED property for variable: BZRCOMMAND
BZRCOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_AR
CMAKE_AR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CMAKE_BUILD_TOOL
CMAKE_BUILD_TOOL-ADVANCED:INTERNAL=1
//What is the target build tool cmake is generating for.
CMAKE_BUILD_TOOL:INTERNAL=/usr/bin/gmake
//MODIFIED property for variable: CMAKE_BUILD_TYPE
CMAKE_BUILD_TYPE-MODIFIED:INTERNAL=ON
//This is the directory where this CMakeCache.txt was created
CMAKE_CACHEFILE_DIR:INTERNAL=/home/samuelf/github/openmm/build
//Major version of cmake used to create the current loaded cache
CMAKE_CACHE_MAJOR_VERSION:INTERNAL=2
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[samuelf@tintin3 build]$