Guys,
I am compiling simbody on a server I haven't used in a while. I am having some odd issues finding lapack:
CMake Warning at CMakeLists.txt:510 (message):
Could not find blas/lapack
I figured out it is lapack and not blas that is the problem.
Here are my Lapack related cmake settings:
LAPACK_Accelerate_LIBRARY LAPACK_Accelerate_LIBRARY-NOTFOUND
LAPACK_BEING_USED
LAPACK_goto2_LIBRARY LAPACK_goto2_LIBRARY-NOTFOUND
LAPACK_lapack_LIBRARY /usr/lib64/liblapack.so.3.2.1
LAPACK_vecLib_LIBRARY LAPACK_vecLib_LIBRARY-NOTFOUND
I have gotten away with not setting vecLib, goto2, and Accelerate on other Linux systems. I have tried copying liblapack.so.3gf, libf77blas.so.3gf, libatlas.so.3gf, and other libs to my build directory, and specifying these in LAPACK_BEING_USED, but that did not work. The workings of find_package(LAPACK) are pretty opaque to me. I would much appreciate any help.
Many thanks
Sam
Odd issue with Lapack
-
Christopher Dembia
- Posts: 506
- Joined: Fri Oct 12, 2012 4:09 pm
Re: Odd issue with Lapack
Hey Sam:
You can set `BUILD_USING_OTHER_LAPACK`. CMake should also be able to find LAPACK if its libraries are on your `LD_LIBRARY_PATH`.
The variable `LAPACK_BEING_USED` is internal and should not be set manually. It is automatically filled in from `BUILD_USING_OTHER_LAPACK`. CMake does not search your build directory for dependencies (unless it is also on your LD_LIBRARY_PATH, CMAKE_PREFIX_PATH, etc.). So while placing them in the build directory may allow your executable to find them at runtime, CMake doesn't know about that.
Hope that helps.
You can set `BUILD_USING_OTHER_LAPACK`. CMake should also be able to find LAPACK if its libraries are on your `LD_LIBRARY_PATH`.
The variable `LAPACK_BEING_USED` is internal and should not be set manually. It is automatically filled in from `BUILD_USING_OTHER_LAPACK`. CMake does not search your build directory for dependencies (unless it is also on your LD_LIBRARY_PATH, CMAKE_PREFIX_PATH, etc.). So while placing them in the build directory may allow your executable to find them at runtime, CMake doesn't know about that.
Hope that helps.
-
Samuel Flores
- Posts: 189
- Joined: Mon Apr 30, 2007 1:06 pm
Re: Odd issue with Lapack
Hi Christopher,
Thanks, that got me further!
I was able to build the libraries without further errors. However I could not build the tests. I got what look like c++11 errors, appended below. But I believe I am setting the c++11 flags correctly.
In a probably unrelated issue, I also can't compile molmodel. I get this error:
-bash-4.1$ make
Scanning dependencies of target SimTKmolmodel
[ 4%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o
In file included from /home/flores/SimTK/include/SimTKcommon.h:40:0,
from /home/flores/svn/molmodel/src/About.cpp:37:
/home/flores/SimTK/include/SimTKcommon/basics.h:38:41: fatal error: SimTKcommon/internal/common.h: No such file or directory
#include "SimTKcommon/internal/common.h"
.. which seems odd because I am correctly setting
CMAKE_INSTALL_PREFIX /home/flores/SimTK
Any help and insight is much appreciated
Thanks
Sam
[ 7%] Linking CXX executable ../../TestSmallMatrix
CMakeFiles/TestSmallMatrix.dir/TestSmallMatrix.cpp.o: In function `_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag.isra.66':
TestSmallMatrix.cpp:(.text+0x153): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/TestSmallMatrix.dir/TestSmallMatrix.cpp.o: In function `SimTK::Exception::Base::setMessage(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x14): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x9e): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find_last_of(char const*, unsigned long, unsigned long) const'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x119): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x19d): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x234): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x2a1): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x2f3): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x353): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::swap(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
Thanks, that got me further!
I was able to build the libraries without further errors. However I could not build the tests. I got what look like c++11 errors, appended below. But I believe I am setting the c++11 flags correctly.
In a probably unrelated issue, I also can't compile molmodel. I get this error:
-bash-4.1$ make
Scanning dependencies of target SimTKmolmodel
[ 4%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o
In file included from /home/flores/SimTK/include/SimTKcommon.h:40:0,
from /home/flores/svn/molmodel/src/About.cpp:37:
/home/flores/SimTK/include/SimTKcommon/basics.h:38:41: fatal error: SimTKcommon/internal/common.h: No such file or directory
#include "SimTKcommon/internal/common.h"
.. which seems odd because I am correctly setting
CMAKE_INSTALL_PREFIX /home/flores/SimTK
Any help and insight is much appreciated
Thanks
Sam
[ 7%] Linking CXX executable ../../TestSmallMatrix
CMakeFiles/TestSmallMatrix.dir/TestSmallMatrix.cpp.o: In function `_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag.isra.66':
TestSmallMatrix.cpp:(.text+0x153): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/TestSmallMatrix.dir/TestSmallMatrix.cpp.o: In function `SimTK::Exception::Base::setMessage(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x14): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x9e): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find_last_of(char const*, unsigned long, unsigned long) const'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x119): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x19d): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x234): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x2a1): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x2f3): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
TestSmallMatrix.cpp:(.text._ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5SimTK9Exception4Base10setMessageERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x353): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::swap(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
-
Christopher Dembia
- Posts: 506
- Joined: Fri Oct 12, 2012 4:09 pm
Re: Odd issue with Lapack
I think it would be good to get the tests to compile and run before trying to use Simbody in Molmodel.
Are you setting C++11 flags yourself? You shouldn't; Simbody handles that for you. Which compiler are you using? If you set flags yourself, sometimes you might have to set the `-stdlib` flag as well (namely if you are using clang on Linux, I think you have to set `-stdlib=libc++`).
As for building molmodel, the way that downstream projects are supposed to find Simbody has changed. See the `cmake/SampleCMakeLists.txt` in the repo. When configuring molmodel in CMake, set the `CMAKE_PREFIX_PATH` variable to contain `/usr/local/SimTK/`.
Are you setting C++11 flags yourself? You shouldn't; Simbody handles that for you. Which compiler are you using? If you set flags yourself, sometimes you might have to set the `-stdlib` flag as well (namely if you are using clang on Linux, I think you have to set `-stdlib=libc++`).
As for building molmodel, the way that downstream projects are supposed to find Simbody has changed. See the `cmake/SampleCMakeLists.txt` in the repo. When configuring molmodel in CMake, set the `CMAKE_PREFIX_PATH` variable to contain `/usr/local/SimTK/`.
-
Samuel Flores
- Posts: 189
- Joined: Mon Apr 30, 2007 1:06 pm
Re: Odd issue with Lapack
Hi Christopher,
I tried it both ways.
CMAKE_CXX_FLAGS -std=c++11 -stdlib=libc++
gave me an error: g++: error: unrecognized command line option ‘-stdlib=libc++’
leaving it blank: CMAKE_CXX_FLAGS
again gave me what look like c++11 related errors:
[ 8%] Building CXX object SimTKcommon/tests/CMakeFiles/TestScalar.dir/TestScalar.cpp.o
[ 9%] Linking CXX executable ../../TestPrivateImplementation
CMakeFiles/TestPrivateImplementation.dir/TestPrivateImplementation.cpp.o: In function `_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag.isra.24':
TestPrivateImplementation.cpp:(.text+0x73): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/TestPrivateImplementation.dir/TestPrivateImplementation.cpp.o: In function `DerDerivedHandle::DerDerivedHandle()':
TestPrivateImplementation.cpp:(.text+0x3cf): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/TestPrivateImplementation.dir/TestPrivateImplementation.cpp.o: In function `Concrete::setString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
TestPrivateImplementation.cpp:(.text+0x1d8): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
I am using g++ . Not sure if I can access other compilers on this machine.
Any help is much appreciated
thanks
sam
I tried it both ways.
CMAKE_CXX_FLAGS -std=c++11 -stdlib=libc++
gave me an error: g++: error: unrecognized command line option ‘-stdlib=libc++’
leaving it blank: CMAKE_CXX_FLAGS
again gave me what look like c++11 related errors:
[ 8%] Building CXX object SimTKcommon/tests/CMakeFiles/TestScalar.dir/TestScalar.cpp.o
[ 9%] Linking CXX executable ../../TestPrivateImplementation
CMakeFiles/TestPrivateImplementation.dir/TestPrivateImplementation.cpp.o: In function `_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag.isra.24':
TestPrivateImplementation.cpp:(.text+0x73): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/TestPrivateImplementation.dir/TestPrivateImplementation.cpp.o: In function `DerDerivedHandle::DerDerivedHandle()':
TestPrivateImplementation.cpp:(.text+0x3cf): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/TestPrivateImplementation.dir/TestPrivateImplementation.cpp.o: In function `Concrete::setString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
TestPrivateImplementation.cpp:(.text+0x1d8): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
I am using g++ . Not sure if I can access other compilers on this machine.
Any help is much appreciated
thanks
sam
-
Samuel Flores
- Posts: 189
- Joined: Mon Apr 30, 2007 1:06 pm
Re: Odd issue with Lapack
Hi Christopher,
I append my CMakeCache.txt in case that is useful.
I tried setting #define _GLIBCXX_USE_CXX11_ABI 0 in the problem files and in the top level SimTK common files, but all that seemed to do is shift the problem around. Anyway I believe I ultimately have to compile to the c++11 standard.
I checked my blas, lapack, and atlas libraries and they were build with c++ 5.8 .. I can't say for sure that they are c++11 compliant though.
Sam
-bash-4.1$ pwd
/home/flores/github/simbody/build
-bash-4.1$ cat CMakeCache.txt
# This is the CMakeCache file.
# For build in directory: /home/flores/github/simbody/build
# It was generated by CMake: /home/flores/cmake-3.5.0-rc2-Linux-x86_64/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 GUIs 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=BLAS_Accelerate_LIBRARY-NOTFOUND
//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=/usr/lib64/atlas/libatlas.so.3.0
//Path to a library.
BLAS_blas_LIBRARY:FILEPATH=/usr/lib64/libblas.so.3.2.1
//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=/usr/lib64/atlas/libf77blas.so.3.0
//Path to a library.
BLAS_goto2_LIBRARY:FILEPATH=BLAS_goto2_LIBRARY-NOTFOUND
//Path to a library.
BLAS_mkl_gf_lp64_LIBRARY:FILEPATH=BLAS_mkl_gf_lp64_LIBRARY-NOTFOUND
//Path to a library.
BLAS_mkl_lapack_LIBRARY:FILEPATH=BLAS_mkl_lapack_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/flores/github/simbody/build
//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=ON
//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 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 libraries here, separated
// by semicolons (full paths or paths that are on the (DY)LD_LIBRARY_PATH
// (UNIX) or PATH (Windows)). See LAPACK_BEING_USED to see what's
// actually being used.
BUILD_USING_OTHER_LAPACK:STRING=/usr/lib64/atlas/liblapack.so.3.0
//Build library names, and assume dependency names, with version
// numbers?
BUILD_VERSIONED_LIBRARIES:BOOL=FALSE
//Control building of the visualizer component
BUILD_VISUALIZER:BOOL=OFF
//Path to a program.
BZRCOMMAND:FILEPATH=BZRCOMMAND-NOTFOUND
//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=/home/apps/gcc/5.3.0/bin/g++
//Flags used by the compiler during all build types.
CMAKE_CXX_FLAGS:STRING=
//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=/usr/bin/cc
//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= -L/home/apps/lib64 -L/home/apps/lib -L/opt/sqlite/lib
//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
//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
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DART_BUILD_ERROR_REPORT_LIMIT-ADVANCED:INTERNAL=1
//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: DOXYGEN_DOT_EXECUTABLE
DOXYGEN_DOT_EXECUTABLE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DOXYGEN_EXECUTABLE
DOXYGEN_EXECUTABLE-ADVANCED:INTERNAL=1
//Details about finding Doxygen
FIND_PACKAGE_MESSAGE_DETAILS_Doxygen:INTERNAL=[/home/apps/bin/doxygen][v1.8.5()]
//Details about finding OpenGL
FIND_PACKAGE_MESSAGE_DETAILS_OpenGL:INTERNAL=[/usr/lib64/libGL.so][/usr/include][v()]
//Details about finding Threads
FIND_PACKAGE_MESSAGE_DETAILS_Threads:INTERNAL=[TRUE][v()]
//ADVANCED property for variable: GITCOMMAND
GITCOMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: GLUT_INCLUDE_DIR
GLUT_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: GLUT_Xi_LIBRARY
GLUT_Xi_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: GLUT_Xmu_LIBRARY
GLUT_Xmu_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: GLUT_glut_LIBRARY
GLUT_glut_LIBRARY-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
//ADVANCED property for variable: LAPACK_Accelerate_LIBRARY
LAPACK_Accelerate_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: LAPACK_goto2_LIBRARY
LAPACK_goto2_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: LAPACK_lapack_LIBRARY
LAPACK_lapack_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: LAPACK_lapack_WORKS
LAPACK_lapack_WORKS-ADVANCED:INTERNAL=1
//Have function cheev_
LAPACK_lapack_WORKS:INTERNAL=
//ADVANCED property for variable: LAPACK_vecLib_LIBRARY
LAPACK_vecLib_LIBRARY-ADVANCED:INTERNAL=1
//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: OPENGL_INCLUDE_DIR
OPENGL_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: OPENGL_gl_LIBRARY
OPENGL_gl_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: OPENGL_glu_LIBRARY
OPENGL_glu_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: OPENGL_xmesa_INCLUDE_DIR
OPENGL_xmesa_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: P4COMMAND
P4COMMAND-ADVANCED:INTERNAL=1
//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: TESTING_PROCESSOR_COUNT
TESTING_PROCESSOR_COUNT-ADVANCED:INTERNAL=1
//CMAKE_INSTALL_PREFIX during last run
_GNUInstallDirs_LAST_CMAKE_INSTALL_PREFIX:INTERNAL=/usr/local
I append my CMakeCache.txt in case that is useful.
I tried setting #define _GLIBCXX_USE_CXX11_ABI 0 in the problem files and in the top level SimTK common files, but all that seemed to do is shift the problem around. Anyway I believe I ultimately have to compile to the c++11 standard.
I checked my blas, lapack, and atlas libraries and they were build with c++ 5.8 .. I can't say for sure that they are c++11 compliant though.
Sam
-bash-4.1$ pwd
/home/flores/github/simbody/build
-bash-4.1$ cat CMakeCache.txt
# This is the CMakeCache file.
# For build in directory: /home/flores/github/simbody/build
# It was generated by CMake: /home/flores/cmake-3.5.0-rc2-Linux-x86_64/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 GUIs 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=BLAS_Accelerate_LIBRARY-NOTFOUND
//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=/usr/lib64/atlas/libatlas.so.3.0
//Path to a library.
BLAS_blas_LIBRARY:FILEPATH=/usr/lib64/libblas.so.3.2.1
//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=/usr/lib64/atlas/libf77blas.so.3.0
//Path to a library.
BLAS_goto2_LIBRARY:FILEPATH=BLAS_goto2_LIBRARY-NOTFOUND
//Path to a library.
BLAS_mkl_gf_lp64_LIBRARY:FILEPATH=BLAS_mkl_gf_lp64_LIBRARY-NOTFOUND
//Path to a library.
BLAS_mkl_lapack_LIBRARY:FILEPATH=BLAS_mkl_lapack_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/flores/github/simbody/build
//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=ON
//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 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 libraries here, separated
// by semicolons (full paths or paths that are on the (DY)LD_LIBRARY_PATH
// (UNIX) or PATH (Windows)). See LAPACK_BEING_USED to see what's
// actually being used.
BUILD_USING_OTHER_LAPACK:STRING=/usr/lib64/atlas/liblapack.so.3.0
//Build library names, and assume dependency names, with version
// numbers?
BUILD_VERSIONED_LIBRARIES:BOOL=FALSE
//Control building of the visualizer component
BUILD_VISUALIZER:BOOL=OFF
//Path to a program.
BZRCOMMAND:FILEPATH=BZRCOMMAND-NOTFOUND
//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=/home/apps/gcc/5.3.0/bin/g++
//Flags used by the compiler during all build types.
CMAKE_CXX_FLAGS:STRING=
//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=/usr/bin/cc
//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= -L/home/apps/lib64 -L/home/apps/lib -L/opt/sqlite/lib
//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
//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, prepended onto install directories.
CMAKE_INSTALL_PREFIX:PATH=/usr/local
//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=-L/usr/lib64 -L/usr/lib64/atlas -L/home/apps/lib64 -L/home/apps/lib -L/opt/sqlite/lib
//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= -L/home/apps/lib64 -L/home/apps/lib -L/opt/sqlite/lib
//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
//Flags used by the linker during the creation of static libraries.
CMAKE_STATIC_LINKER_FLAGS:STRING=
//Flags used by the linker during debug builds.
CMAKE_STATIC_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//Path to a program.
CMAKE_STRIP:FILEPATH=/usr/bin/strip
//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=/home/apps/gcc/5.3.0/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 documentation generation tool (http://www.doxygen.org)
DOXYGEN_EXECUTABLE:FILEPATH=/home/apps/bin/doxygen
//Path to a program.
GITCOMMAND:FILEPATH=/usr/bin/git
//Path to a file.
GLUT_INCLUDE_DIR:PATH=GLUT_INCLUDE_DIR-NOTFOUND
//Path to a library.
GLUT_Xi_LIBRARY:FILEPATH=/usr/lib64/libXi.so
//Path to a library.
GLUT_Xmu_LIBRARY:FILEPATH=/usr/lib64/libXmu.so
//Path to a library.
GLUT_glut_LIBRARY:FILEPATH=GLUT_glut_LIBRARY-NOTFOUND
//Path to gunzip executable
GUNZIPCOMMAND:FILEPATH=/bin/gunzip
//Path to a program.
HGCOMMAND:FILEPATH=/opt/rocks/bin/hg
//Path to java command, used by the Dart server to create html.
JAVACOMMAND:FILEPATH=/usr/java/latest/bin/java
//Path to a library.
LAPACK_Accelerate_LIBRARY:FILEPATH=LAPACK_Accelerate_LIBRARY-NOTFOUND
//Basename of the actual Lapack library we're depending on; can't
// change here; see variable BUILD_USING_OTHER_LAPACK.
LAPACK_BEING_USED:STRING=/usr/lib64/atlas/liblapack.so.3.0
//Path to a library.
LAPACK_goto2_LIBRARY:FILEPATH=LAPACK_goto2_LIBRARY-NOTFOUND
//Path to a library.
LAPACK_lapack_LIBRARY:FILEPATH=/home/apps/lib/liblapack.a
//Path to a library.
LAPACK_vecLib_LIBRARY:FILEPATH=LAPACK_vecLib_LIBRARY-NOTFOUND
//Command to build the project
MAKECOMMAND:STRING=/home/flores/cmake-3.5.0-rc2-Linux-x86_64/bin/cmake --build . --config "${CTEST_CONFIGURATION_TYPE}" -- -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.
OPENGL_INCLUDE_DIR:PATH=/usr/include
//Path to a library.
OPENGL_gl_LIBRARY:FILEPATH=/usr/lib64/libGL.so
//Path to a library.
OPENGL_glu_LIBRARY:FILEPATH=/usr/lib64/libGLU.so
//Path to a file.
OPENGL_xmesa_INCLUDE_DIR:PATH=OPENGL_xmesa_INCLUDE_DIR-NOTFOUND
//Path to a program.
P4COMMAND:FILEPATH=P4COMMAND-NOTFOUND
//Path to scp command, used by CTest for submitting results to
// a Dart server
SCPCOMMAND:FILEPATH=/usr/bin/scp
//Soname version; appended to names of shared libs
//\n (can't be changed in GUI).
SIMBODY_SONAME_VERSION:STRING=3.6
//This is the version that will be built (can't be changed in GUI).
SIMBODY_VERSION:STRING=3.6
//Name of the computer/site where compile is being run
SITE:STRING=csb.bmc.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=/home/apps/subversion/1.9.3/bin/svn
//Base name of the library being built; can't be changed here;
// see BUILD_USING_NAMESPACE variable.
SimTKCOMMON_LIBRARY_NAME:STRING=SimTKcommon
//Base name of the library being built; can't be changed here;
// see BUILD_USING_NAMESPACE variable.
SimTKMATH_LIBRARY_NAME:STRING=SimTKmath
//Base name of the library being built; can't be changed here;
// see BUILD_USING_NAMESPACE variable.
SimTKSIMBODY_LIBRARY_NAME:STRING=SimTKsimbody
//Value Computed by CMake
SimTKcommon_BINARY_DIR:STATIC=/home/flores/github/simbody/build/SimTKcommon
//Dependencies for the target
SimTKcommon_LIB_DEPENDS:STATIC=general;/usr/lib64/atlas/liblapack.so.3.0;general;pthread;general;rt;general;dl;general;m;
//Value Computed by CMake
SimTKcommon_SOURCE_DIR:STATIC=/home/flores/github/simbody/SimTKcommon
//Value Computed by CMake
SimTKmath_BINARY_DIR:STATIC=/home/flores/github/simbody/build/SimTKmath
//Dependencies for the target
SimTKmath_LIB_DEPENDS:STATIC=general;SimTKcommon;general;/usr/lib64/atlas/liblapack.so.3.0;general;pthread;general;rt;general;dl;general;m;
//Value Computed by CMake
SimTKmath_SOURCE_DIR:STATIC=/home/flores/github/simbody/SimTKmath
//Value Computed by CMake
SimTKsimbody_BINARY_DIR:STATIC=/home/flores/github/simbody/build/Simbody
//Dependencies for the target
SimTKsimbody_LIB_DEPENDS:STATIC=general;SimTKmath;general;SimTKcommon;general;/usr/lib64/atlas/liblapack.so.3.0;general;pthread;general;rt;general;dl;general;m;
//Value Computed by CMake
SimTKsimbody_SOURCE_DIR:STATIC=/home/flores/github/simbody/Simbody
//Value Computed by CMake
Simbody_BINARY_DIR:STATIC=/home/flores/github/simbody/build
//Value Computed by CMake
Simbody_SOURCE_DIR:STATIC=/home/flores/github/simbody
//Number of CPUs to be used by the RUN_TESTS_PARALLEL target.
TESTING_PROCESSOR_COUNT:STRING=4
########################
# INTERNAL cache entries
########################
//ADVANCED property for variable: BLAS_Accelerate_LIBRARY
BLAS_Accelerate_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BLAS_WORKS
BLAS_WORKS-ADVANCED:INTERNAL=1
//Have function cheev_
BLAS_WORKS:INTERNAL=
//ADVANCED property for variable: BLAS_acml_LIBRARY
BLAS_acml_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BLAS_acml_mp_LIBRARY
BLAS_acml_mp_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BLAS_atlas_LIBRARY
BLAS_atlas_LIBRARY-ADVANCED:INTERNAL=1
//MODIFIED property for variable: BLAS_atlas_LIBRARY
BLAS_atlas_LIBRARY-MODIFIED:INTERNAL=ON
//ADVANCED property for variable: BLAS_blas_LIBRARY
BLAS_blas_LIBRARY-ADVANCED:INTERNAL=1
//MODIFIED property for variable: BLAS_blas_LIBRARY
BLAS_blas_LIBRARY-MODIFIED:INTERNAL=ON
//ADVANCED property for variable: BLAS_blas_WORKS
BLAS_blas_WORKS-ADVANCED:INTERNAL=1
//Have function sgemm_
BLAS_blas_WORKS:INTERNAL=1
//ADVANCED property for variable: BLAS_complib.sgimath_LIBRARY
BLAS_complib.sgimath_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BLAS_cxml_LIBRARY
BLAS_cxml_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BLAS_dxml_LIBRARY
BLAS_dxml_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BLAS_essl_LIBRARY
BLAS_essl_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BLAS_f77blas_LIBRARY
BLAS_f77blas_LIBRARY-ADVANCED:INTERNAL=1
//MODIFIED property for variable: BLAS_f77blas_LIBRARY
BLAS_f77blas_LIBRARY-MODIFIED:INTERNAL=ON
//ADVANCED property for variable: BLAS_f77blas_atlas_WORKS
BLAS_f77blas_atlas_WORKS-ADVANCED:INTERNAL=1
//Have function dgemm_
BLAS_f77blas_atlas_WORKS:INTERNAL=
//ADVANCED property for variable: BLAS_goto2_LIBRARY
BLAS_goto2_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: BLAS_mkl_gf_lp64_LIBRARY
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-
Christopher Dembia
- Posts: 506
- Joined: Fri Oct 12, 2012 4:09 pm
Re: Odd issue with Lapack
Hmm...I'm not sure what the issue is. I did not know about `_GLIBCXX_USE_CXX11_ABI`. Try a fresh build directory, or try building static libraries instead.
-
Samuel Flores
- Posts: 189
- Joined: Mon Apr 30, 2007 1:06 pm
Re: Odd issue with Lapack
Neither of these worked.
-
Christopher Dembia
- Posts: 506
- Joined: Fri Oct 12, 2012 4:09 pm
Re: Odd issue with Lapack
Try turning `BUILD_SHARED_LIBRARIES` off; do the static tests link properly?
-
Samuel Flores
- Posts: 189
- Joined: Mon Apr 30, 2007 1:06 pm
Re: Odd issue with Lapack
I should have mentioned this. Oddly, this variable is not used at all in Simbody's CMakeLists:
-bash-4.1$ grep BUILD_SHARED CMakeCache.txt
-bash-4.1$ grep BUILD_SHARED ../CMakeLists.txt
-bash-4.1$
I did manage to build on another server this time, and then move the files to the server of interest, but that does not always work. Since simbody is pretty important to me I like to be able to build on all my main machines.
Sam
-bash-4.1$ grep BUILD_SHARED CMakeCache.txt
-bash-4.1$ grep BUILD_SHARED ../CMakeLists.txt
-bash-4.1$
I did manage to build on another server this time, and then move the files to the server of interest, but that does not always work. Since simbody is pretty important to me I like to be able to build on all my main machines.
Sam