[CMake] cmake ld fails

[Michael Wild]

On 19. May, 2010, at 7:17 , Michael Hertling wrote:

> On 05/18/2010 11:13 PM, R. Bryn Fenwick wrote:
>> 
>> Hi,
>> 
>> I have received some code that works on one system, but is failing to  
>> work for me. Any suggestions how to debug this would be greatly  
>> appreciated.
>> 
>> I think that I am setting everything up correctly however it appears  
>> to need some hacks.
>> 
>> Scanning dependencies of target scimap
>> [  3%] Building CXX object src/CMakeFiles/scimap.dir/confstream.cpp.o
>> [  7%] Building CXX object src/CMakeFiles/scimap.dir/densematrix.cpp.o
>> [ 11%] Building CXX object src/CMakeFiles/scimap.dir/distance.cpp.o
>> [ 15%] Building CXX object src/CMakeFiles/scimap.dir/fibheap.cpp.o
>> [ 19%] Building CXX object src/CMakeFiles/scimap.dir/gzstream.cpp.o
>> [ 23%] Building CXX object src/CMakeFiles/scimap.dir/sparsematrix.cpp.o
>> [ 26%] Building CXX object src/CMakeFiles/scimap.dir/util.cpp.o
>> [ 30%] Building CXX object src/CMakeFiles/scimap.dir/VarMatrix.cpp.o
>> [ 34%] Building C object src/CMakeFiles/scimap.dir/RMPbheap.c.o
>> [ 38%] Building C object src/CMakeFiles/scimap.dir/RMPfbheap.c.o
>> [ 42%] Building C object src/CMakeFiles/scimap.dir/RMPkcenter.c.o
>> [ 46%] Building C object src/CMakeFiles/scimap.dir/RMPksplit.c.o
>> [ 50%] Building C object src/CMakeFiles/scimap.dir/RMPpermutation.c.o
>> [ 53%] Building C object src/CMakeFiles/scimap.dir/RMPprime.c.o
>> [ 57%] Building C object src/CMakeFiles/scimap.dir/RMPrandom.c.o
>> [ 61%] Building C object src/CMakeFiles/scimap.dir/RMPset.c.o
>> Linking CXX static library ../libscimap.a
>> [ 61%] Built target scimap
>> Scanning dependencies of target embedding
>> [ 65%] Building CXX object src/CMakeFiles/embedding.dir/embedding.cpp.o
>> Linking CXX executable ../embedding
>> ../libscimap.a(densematrix.cpp.o): In function  
>> `DenseMatrix::cost_matrix(SparseMatrix&)':
>> densematrix.cpp:(.text+0x1a50): undefined reference to `dgemm_'
>> ../libscimap.a(densematrix.cpp.o): In function  
>> `DenseMatrix::largest_eigenvectors(int&, DenseMatrix&, double*, int*)':
>> densematrix.cpp:(.text+0x3784): undefined reference to `dgemv_'
>> densematrix.cpp:(.text+0x3849): undefined reference to `dgemv_'
>> densematrix.cpp:(.text+0x3a6a): undefined reference to `dgemm_'
>> ../../../ARPACK/libparpack.a(pdseupd.o): In function `pdseupd_':
>> pdseupd.f:(.text+0x70c): undefined reference to `dcopy_'
>> 
>> many more similar errors follow including these for lapack itself...
>> 
>> /home/fenwick/opt/lapack-3.2.1/SRC/dlarfg.f:116: undefined reference  
>> to `dnrm2_'
>> /home/fenwick/opt/lapack-3.2.1/SRC/dlarfg.f:120: undefined reference  
>> to `dscal_'
>> /home/fenwick/opt/lapack-3.2.1/liblapack_LINUX.a(dlarft.o): In  
>> function `dlarft_':
>> /home/fenwick/opt/lapack-3.2.1/SRC/dlarft.f:157: undefined reference  
>> to `dgemv_'
>> /home/fenwick/opt/lapack-3.2.1/SRC/dlarft.f:169: undefined reference  
>> to `dgemv_'
>> /home/fenwick/opt/lapack-3.2.1/SRC/dlarft.f:176: undefined reference  
>> to `dtrmv_'
>> /home/fenwick/opt/lapack-3.2.1/SRC/dlarft.f:214: undefined reference  
>> to `dgemv_'
>> /home/fenwick/opt/lapack-3.2.1/SRC/dlarft.f:230: undefined reference  
>> to `dgemv_'
>> /home/fenwick/opt/lapack-3.2.1/SRC/dlarft.f:237: undefined reference  
>> to `dtrmv_'
>> /home/fenwick/opt/lapack-3.2.1/liblapack_LINUX.a(dorg2r.o): In  
>> function `dorg2r_':
>> /home/fenwick/opt/lapack-3.2.1/SRC/dorg2r.f:117: undefined reference  
>> to `dscal_'
>> /home/fenwick/opt/lapack-3.2.1/liblapack_LINUX.a(dorgl2.o): In  
>> function `dorgl2_':
>> /home/fenwick/opt/lapack-3.2.1/SRC/dorgl2.f:120: undefined reference  
>> to `dscal_'
>> 
>> 
>> 
>> I generate the makefiles with:
>> 
>> CC=/opt/mvapich2-1.2rc1/bin/mpicc CXX=/opt/mvapich2-1.2rc1/bin/mpicxx  
>> cmake -DCMAKE_BUILD_TYPE=Release ../.. -DCMAKE_EXE_LINKER_FLAGS='-L/ 
>> home/opt/lapack-3.2.1' -DMPIEXEC='/opt/mvapich2-1.2rc1/bin/mpiexec
>> ' -DCMAKE_MODULE_LINKER_FLAGS='-L/home/fenwick/opt/lapack-3.2.1'
>> 
>> I am trying to use lapack though in the CmakeLists file there is no  
>> mention of a fortran compiler
>> 
>> project(SCIMAP CXX C)
>> cmake_minimum_required(VERSION 2.6)
>> 
>> set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules")
>> set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR})
>> set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR})
>> 
>> find_package(ZLIB REQUIRED)
>> 
>> # Find MPI
>> set(MPI_COMPILER "/opt/mvapich2-1.2rc1/bin/mpicxx")
>> set(MPI_LIBRARY "/opt/mvapich2-1.2rc1/lib/libmpich.a")
>> set(MPI_INCLUDE_PATH "/opt/mvapich2-1.2rc1/include")
>> set(MPI_FLAGS "-DMPICH_IGNORE_CXX_SEEK")
>> find_package(MPI REQUIRED)
>> 
>> find_package(LAPACK REQUIRED)
>> #find_package(BLAS   REQUIRED)
>> find_package(ARPACK REQUIRED)
>> include_directories(${ZLIB_INCLUDE_DIR} ${MPI_INCLUDE_PATH})
>> add_definitions(${MPI_COMPILE_FLAGS})
>> set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} $ 
>> {MPI_LINK_FLAGS}")
>> set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} $ 
>> {MPI_LINK_FLAGS}")
>> 
>> add_subdirectory(src)
> 
> Obviously, the linker can't find all necessary symbols in the named
> libraries to link against, but most probably, the relevant stuff is
> set up in src/CMakeLists.txt, so please post this file, too.
> 
> Regards,
> 
> Michael

Also, setting CMAKE_XXX_LINKER_FLAGS won't do you any good, since FindBLAS and FindLAPACK will use full paths for the libraries they find. If you want to tell CMake where to find libraries, either use CMAKE_PREFIX_PATH or CMAKE_LIBRARY_PATH and CMAKE_INCLUDE_PATH as appropriate (read the doc for more info on the search order of libraries and headers).


Michael