[CMake] cmake ld fails

[R. Bryn Fenwick]

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)