undefined reference to `operator new(unsigned long)'

[Samuel Flores]

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
########################

//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=

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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.
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//If set, runtime paths are not added when installing shared libraries,
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CMAKE_SKIP_INSTALL_RPATH:BOOL=NO

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CMAKE_SKIP_RPATH:BOOL=NO

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CMAKE_USE_RELATIVE_PATHS:BOOL=OFF

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// .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

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COMPRESSIONCOMMAND:FILEPATH=/bin/gzip

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//Extra command line flags to pass to the coverage tool
COVERAGE_EXTRA_FLAGS:STRING=-l

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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
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CUDA_ATTACH_VS_BUILD_RULE_TO_CUDA_FILE:BOOL=ON

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CUDA_BUILD_CUBIN:BOOL=OFF

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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

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// With the Makefile generator this defaults to VERBOSE variable
// specified on the command line, but can be forced on with this
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//"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
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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
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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
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//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

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OPENCL_LIBRARY-ADVANCED:INTERNAL=1
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OPENMM_BUILD_EXAMPLES-MODIFIED:INTERNAL=ON
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OPENMM_BUILD_PYTHON_WRAPPERS-MODIFIED:INTERNAL=ON
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SWIG_VERSION-ADVANCED:INTERNAL=1

[samuelf@tintin3 build]$

[Peter Eastman]

Never seen anything like that, but I haven't tried that particular compiler. Try removing "-std=c++11" from the build flags: we don't use any C++11 features, and that might be causing problems. Does it make a difference?

[Samuel Flores]

Interestingly, leaving out this flag induces the error even sooner:

Building CXX object platforms/reference/tests/CMakeFiles/TestReferenceCustomCompoundBondForce.dir/TestReferenceCustomCompoundBondForce.cpp.o
Linking CXX executable ../../../TestReferenceCMMotionRemover
CMakeFiles/TestReferenceCMMotionRemover.dir/TestReferenceCMMotionRemover.cpp.o: In function `testMotionRemoval()':
TestReferenceCMMotionRemover.cpp:(.text+0x169): undefined reference to `operator new(unsigned long)'
TestReferenceCMMotionRemover.cpp:(.text+0x1d7): undefined reference to `operator new(unsigned long)'
TestReferenceCMMotionRemover.cpp:(.text+0x29e): undefined reference to `operator new(unsigned long)'
TestReferenceCMMotionRemover.cpp:(.text+0x338): undefined reference to `operator new(unsigned long)'



In any case, will the resulting binaries still be compatible with third party code that requires the c++11 flag?

[Samuel Flores]

For reference, I am having similar issues for simbody:



Building CXX object SimTKcommon/tests/CMakeFiles/BNTTest.dir/BNTTest.cpp.o
[ 10%] Building CXX object SimTKcommon/tests/CMakeFiles/SpatialAlgebraTest.dir/SpatialAlgebraTest.cpp.o
Linking CXX executable ../../SFMTTest
CMakeFiles/SFMTTest.dir/SFMTTest.cpp.o: In function `main':
SFMTTest.cpp:(.text.startup+0x33): undefined reference to `operator new[](unsigned long)'
SFMTTest.cpp:(.text.startup+0x60): undefined reference to `operator delete[](void*)'
SFMTTest.cpp:(.text.startup+0x75): undefined reference to `__cxa_begin_catch'
SFMTTest.cpp:(.text.startup+0x88): undefined reference to `std::cout'
SFMTTest.cpp:(.text.startup+0x90): undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)'



There I am using gcc 4.9.2 and blas that should be compatible, as well as lapack which I am less sure is compatible:

/sw/comp/gcc/4.9.2_tintin/bin/gcc

/sw/libs/scalapack/2.0.2_tintin_pgi13_openmpi1.6/libscalapack.a

/sw/libs/openblas/0.2.14a/tintin/lib/libopenblas.so.0
/sw/mf/tintin/libraries/scalapack/2.0.2:

module-whatis loads the ScaLAPACK environment
conflict scalapack
prepend-path LIBRARY_PATH /sw/libs/scalapack/2.0.2_tintin_pgi13_openmpi1.6
setenv SCALAPACKDIR /sw/libs/scalapack/2.0.2_tintin_pgi13_openmpi1.6
setenv SCALAPACKLIBS /sw/libs/scalapack/2.0.2_tintin_pgi13_openmpi1.6/libscalapack.a
setenv LD_FLAGS -L /sw/libs/scalapack/2.0.2_tintin_pgi13_openmpi1.6 -lscalapack -lacml
-------------------------------------------------------------------

[samuelf@tintin1 build]$ module show openblas/0.2.14a
-------------------------------------------------------------------
/sw/mf/tintin/libraries/openblas/0.2.14a:

module-whatis Loads OpenBLAS Library environment.
conflict openblas
setenv OPENBLAS /sw/libs/openblas/0.2.14a/tintin
prepend-path LD_LIBRARY_PATH /sw/libs/openblas/0.2.14a/tintin/lib
prepend-path LD_RUN_PATH /sw/libs/openblas/0.2.14a/tintin/lib
prepend-path CPATH /sw/libs/openblas/0.2.14a/tintin/include
prepend-path LD_LIBRARY_PATH /sw/comp/gcc/4.9.2_milou/lib64
prepend-path LD_LIBRARY_PATH /sw/comp/gcc/4.9.2_milou/lib
append-path CMAKE_MODULE_PATH /sw/libs/openblas/0.2.14a/tintin/lib/cmake/openblas
-------------------------------------------------------------------

I append my CMakeCache.txt in case that helps..

Hope you have some sort of insight!

Sam


[samuelf@tintin3 build]$ cat CMakeCache.txt
# This is the CMakeCache file.
# For build in directory: /home/samuelf/github/simbody/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
########################

//Path to a library.
BLAS_Accelerate_LIBRARY:FILEPATH=/sw/libs/openblas/0.2.14a/tintin/lib/libopenblas.so.0

//Path to a library.
BLAS_acml_LIBRARY:FILEPATH=BLAS_acml_LIBRARY-NOTFOUND

//Path to a library.
BLAS_acml_mp_LIBRARY:FILEPATH=BLAS_acml_mp_LIBRARY-NOTFOUND

//Path to a library.
BLAS_atlas_LIBRARY:FILEPATH=

//Path to a library.
BLAS_blas_LIBRARY:FILEPATH=/usr/lib64/libblas.so

//Path to a library.
BLAS_complib.sgimath_LIBRARY:FILEPATH=BLAS_complib.sgimath_LIBRARY-NOTFOUND

//Path to a library.
BLAS_cxml_LIBRARY:FILEPATH=BLAS_cxml_LIBRARY-NOTFOUND

//Path to a library.
BLAS_dxml_LIBRARY:FILEPATH=BLAS_dxml_LIBRARY-NOTFOUND

//Path to a library.
BLAS_essl_LIBRARY:FILEPATH=BLAS_essl_LIBRARY-NOTFOUND

//Path to a library.
BLAS_f77blas_LIBRARY:FILEPATH=

//Path to a library.
BLAS_goto2_LIBRARY:FILEPATH=BLAS_goto2_LIBRARY-NOTFOUND

//Path to a library.
BLAS_scsl_LIBRARY:FILEPATH=BLAS_scsl_LIBRARY-NOTFOUND

//Path to a library.
BLAS_sgemm_LIBRARY:FILEPATH=BLAS_sgemm_LIBRARY-NOTFOUND

//Path to a library.
BLAS_sunperf_LIBRARY:FILEPATH=BLAS_sunperf_LIBRARY-NOTFOUND

//Path to a library.
BLAS_vecLib_LIBRARY:FILEPATH=BLAS_vecLib_LIBRARY-NOTFOUND

//The Simbody build (not the install) puts all the libraries and
// executables together here (with /Release, etc. appended on some
// platforms).
BUILD_BINARY_DIR:PATH=/home/samuelf/github/simbody/build

//g++ Debug build compile flags
BUILD_CXX_FLAGS_DEBUG:STRING=-g -m

//g++ MinSizeRel build compile flags
BUILD_CXX_FLAGS_MINSIZEREL:STRING=-DNDEBUG -Os -m

//g++ Release build compile flags
BUILD_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -O3 -funroll-loops -fno-tree-vrp -fno-strict-aliasing -fno-guess-branch-probability -m

//g++ RelWithDebInfo build compile flags
BUILD_CXX_FLAGS_RELWITHDEBINFO:STRING=-DNDEBUG -O3 -g -funroll-loops -fno-tree-vrp -fno-strict-aliasing -fno-guess-branch-probability -m

//gcc Debug build compile flags
BUILD_C_FLAGS_DEBUG:STRING=-g -m

//gcc MinSizeRel build compile flags
BUILD_C_FLAGS_MINSIZEREL:STRING=-DNDEBUG -Os -m

//gcc Release build compile flags
BUILD_C_FLAGS_RELEASE:STRING=-DNDEBUG -O3 -funroll-loops -fno-tree-vrp -fno-strict-aliasing -fno-guess-branch-probability -m

//gcc RelWithDebInfo build compile flags
BUILD_C_FLAGS_RELWITHDEBINFO:STRING=-DNDEBUG -O3 -g -funroll-loops -fno-tree-vrp -fno-strict-aliasing -fno-guess-branch-probability -m

//Control building of Simbody example programs.
//\n To actually build examples, one
//\n or both of BUILD_TESTS_AND_EXAMPLES_STATIC and
//\n BUILD_TESTS_AND_EXAMPLES_SHARED must be ON.
BUILD_EXAMPLES:BOOL=OFF

//CPU instruction level compiler is permitted to use (default:
// let compiler decide).
BUILD_INST_SET:STRING=

//This is the platform and ABI we're building for. Not changeable
// here; use a different CMake generator instead.
BUILD_PLATFORM:STRING=Linux:x64

//Build '_static' versions of libraries in addition to dynamic
// libraries?
BUILD_STATIC_LIBRARIES:BOOL=FALSE

//Build the testing tree.
BUILD_TESTING:BOOL=ON

//If building test or example programs, include dynamically-linked
// ones?
BUILD_TESTING_SHARED:BOOL=ON

//If building static libraries, build static test and example programs
// too?
BUILD_TESTING_STATIC:BOOL=ON

//If BUILD_TESTING or BUILD_EXAMPLES, build dynamically-linked
// ones?
BUILD_TESTS_AND_EXAMPLES_SHARED:BOOL=ON

//If BUILDING_STATIC_LIBRARIES and BUILD_TESTING or BUILD_EXAMPLES,
// build
//\n statically-linked test and example programs too? On Windows,
//\n statically-linked tests may be easier to debug than DLL-linked
// tests.
//\n Statically-linked examples are never installed.
BUILD_TESTS_AND_EXAMPLES_STATIC:BOOL=ON

//Build library names, and assume dependency names, with no version
// numbers?
BUILD_UNVERSIONED_LIBRARIES:BOOL=TRUE

//All library names will be prefixed with 'xxx_' if this is set
// to xxx.
BUILD_USING_NAMESPACE:STRING=

//If you have your own Lapack and Blas, put library basenames here,
// separated by semicolons. See LAPACK_BEING_USED to see what's
// actually being used.
BUILD_USING_OTHER_LAPACK:STRING=

//Build library names, and assume dependency names, with version
// numbers?
BUILD_VERSIONED_LIBRARIES:BOOL=FALSE

//Control building of the visualizer component
BUILD_VISUALIZER:BOOL=ON

//Path to a program.
BZRCOMMAND:FILEPATH=/usr/bin/bzr

//Path to a program.
CMAKE_AR:FILEPATH=/usr/bin/ar

//Debug, RelWithDebInfo (recommended), 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/g++

//Flags used by the compiler during all build types.
CMAKE_CXX_FLAGS:STRING=-std=c++11

//Can't change here -- see BUILD_CXX...
CMAKE_CXX_FLAGS_DEBUG:STRING='-g '

//Can't change here -- see BUILD_CXX...
CMAKE_CXX_FLAGS_MINSIZEREL:STRING='-DNDEBUG -Os '

//Can't change here -- see BUILD_CXX...
CMAKE_CXX_FLAGS_RELEASE:STRING='-DNDEBUG -O2 '

//Can't change here -- see BUILD_CXX...
CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING='-DNDEBUG -O2 -g '

//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=

//Can't change here -- see BUILD_C...
CMAKE_C_FLAGS_DEBUG:STRING='-g '

//Can't change here -- see BUILD_C...
CMAKE_C_FLAGS_MINSIZEREL:STRING='-DNDEBUG -Os '

//Can't change here -- see BUILD_C...
CMAKE_C_FLAGS_RELEASE:STRING='-DNDEBUG -O2 '

//Can't change here -- see BUILD_C...
CMAKE_C_FLAGS_RELWITHDEBINFO:STRING='-DNDEBUG -O2 -g '

//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=ON

//user executables (bin)
CMAKE_INSTALL_BINDIR:PATH=bin

//read-only architecture-independent data (DATAROOTDIR)
CMAKE_INSTALL_DATADIR:PATH=

//read-only architecture-independent data root (share)
CMAKE_INSTALL_DATAROOTDIR:PATH=share

//documentation root (DATAROOTDIR/doc/PROJECT_NAME)
CMAKE_INSTALL_DOCDIR:PATH=share/doc/simbody

//C header files (include)
CMAKE_INSTALL_INCLUDEDIR:PATH=include

//info documentation (DATAROOTDIR/info)
CMAKE_INSTALL_INFODIR:PATH=

//object code libraries (lib64)
CMAKE_INSTALL_LIBDIR:PATH=lib64

//program executables (libexec)
CMAKE_INSTALL_LIBEXECDIR:PATH=libexec

//locale-dependent data (DATAROOTDIR/locale)
CMAKE_INSTALL_LOCALEDIR:PATH=

//modifiable single-machine data (var)
CMAKE_INSTALL_LOCALSTATEDIR:PATH=var

//man documentation (DATAROOTDIR/man)
CMAKE_INSTALL_MANDIR:PATH=

//C header files for non-gcc (/usr/include)
CMAKE_INSTALL_OLDINCLUDEDIR:PATH=/usr/include

//Install path prefix.
CMAKE_INSTALL_PREFIX:STRING=/home/samuelf/SimTK

//system admin executables (sbin)
CMAKE_INSTALL_SBINDIR:PATH=sbin

//modifiable architecture-independent data (com)
CMAKE_INSTALL_SHAREDSTATEDIR:PATH=com

//read-only single-machine data (etc)
CMAKE_INSTALL_SYSCONFDIR:PATH=etc

//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=Simbody

//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

//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

//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 program.
GITCOMMAND:FILEPATH=/usr/bin/git

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//Value Computed by CMake
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//Value Computed by CMake
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//Path to a library.
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//Path to a file.
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//Path to a file.
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//Path to a file.
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//Path to a library.
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//Path to a library.
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