[gmx-users] How to provide the FFTW3 install directory

[Justin Lemkul]

On 3/31/14, 3:12 PM, Ly Minh Nhat wrote:
> It still doesn't work. Here is the output:
>
> ooker at ooker-Aspire-4741:~/Desktop/gromacs-4.5.7/build$ cmake ..
> -DCMAKE_PREFIX_PATH=/usr/local
>
> -- The C compiler identification is GNU 4.8.1
> -- The CXX compiler identification is unknown
> -- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> CMake Error: your CXX compiler: "CMAKE_CXX_COMPILER-NOTFOUND" was not
> found.   Please set CMAKE_CXX_COMPILER to a valid compiler path or name.

Here's problem #1 to fix.

> -- Performing Test CFLAGS_WARN
> -- Performing Test CFLAGS_WARN - Success
> -- Performing Test CFLAGS_EXCESS_PREC
> -- Performing Test CFLAGS_EXCESS_PREC - Success
> -- Performing Test CFLAGS_COPT
> -- Performing Test CFLAGS_COPT - Success
> -- Performing Test CFLAGS_NOINLINE
> -- Performing Test CFLAGS_NOINLINE - Success
> -- Using default binary suffix: ""
> -- Using default library suffix: ""
> -- Looking for include file string.h
> -- Looking for include file string.h - found
> -- Looking for include file math.h
> -- Looking for include file math.h - found
> -- Looking for include file limits.h
> -- Looking for include file limits.h - found
> -- Looking for include file memory.h
> -- Looking for include file memory.h - found
> -- Looking for include file unistd.h
> -- Looking for include file unistd.h - found
> -- Looking for include file direct.h
> -- Looking for include file direct.h - not found
> -- Looking for include file pwd.h
> -- Looking for include file pwd.h - found
> -- Looking for include file stdint.h
> -- Looking for include file stdint.h - found
> -- Looking for include file stdlib.h
> -- Looking for include file stdlib.h - found
> -- Looking for include file pthread.h
> -- Looking for include file pthread.h - found
> -- Looking for include file dirent.h
> -- Looking for include file dirent.h - found
> -- Looking for include file inttypes.h
> -- Looking for include file inttypes.h - found
> -- Looking for include file regex.h
> -- Looking for include file regex.h - found
> -- Looking for include file sys/types.h
> -- Looking for include file sys/types.h - found
> -- Looking for include file sys/stat.h
> -- Looking for include file sys/stat.h - found
> -- Looking for include file sys/time.h
> -- Looking for include file sys/time.h - found
> -- Looking for include file rpc/rpc.h
> -- Looking for include file rpc/rpc.h - found
> -- Looking for include files rpc/rpc.h, rpc/xdr.h
> -- Looking for include files rpc/rpc.h, rpc/xdr.h - found
> -- Looking for include file xmmintrin.h
> -- Looking for include file xmmintrin.h - not found
> -- Looking for include file emmintrin.h
> -- Looking for include file emmintrin.h - not found
> -- Looking for include file pmmintrin.h
> -- Looking for include file pmmintrin.h - not found
> -- Looking for include file smmintrin.h
> -- Looking for include file smmintrin.h - not found
> -- Looking for include file io.h
> -- Looking for include file io.h - not found
> -- Looking for strcasecmp
> -- Looking for strcasecmp - found
> -- Looking for strdup
> -- Looking for strdup - found
> -- Looking for vprintf
> -- Looking for vprintf - found
> -- Looking for memcmp
> -- Looking for memcmp - found
> -- Looking for posix_memalign
> -- Looking for posix_memalign - found
> -- Looking for memalign
> -- Looking for memalign - found
> -- Looking for _aligned_malloc
> -- Looking for _aligned_malloc - not found
> -- Looking for gettimeofday
> -- Looking for gettimeofday - found
> -- Looking for isnan
> -- Looking for isnan - found
> -- Looking for _isnan
> -- Looking for _isnan - not found
> -- Looking for fsync
> -- Looking for fsync - found
> -- Looking for _fileno
> -- Looking for _fileno - not found
> -- Looking for fileno
> -- Looking for fileno - found
> -- Looking for _commit
> -- Looking for _commit - not found
> -- Looking for sqrt in m
> -- Looking for sqrt in m - found
> -- Looking for cbrt in m
> -- Looking for cbrt in m - found
> -- Looking for stddef.h
> -- Looking for stddef.h - found
> -- Check size of bool
> -- Check size of bool - failed
> -- Check size of int
> -- Check size of int - done
> -- Check size of long int
> -- Check size of long int - done
> -- Check size of long long int
> -- Check size of long long int - done
> -- Check size of off_t
> -- Check size of off_t - done
> -- Check size of void *
> -- Check size of void * - done
> -- Check size of uid_t
> -- Check size of uid_t - done
> -- Check size of gid_t
> -- Check size of gid_t - done
> -- Check size of size_t
> -- Check size of size_t - done
> -- Check size of off_t
> -- Check size of off_t - done
> -- Check if the system is big endian
> -- Searching 16 bit integer
> -- Check size of unsigned short
> -- Check size of unsigned short - done
> -- Using unsigned short
> -- Check if the system is big endian - little endian
> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.26")
> -- checking for module 'libxml-2.0'
> --   package 'libxml-2.0' not found
> -- Could NOT find LibXml2 (missing:  LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
> -- Looking for include file pthread.h
> -- Looking for include file pthread.h - found
> -- Looking for pthread_create
> -- Looking for pthread_create - not found
> -- Looking for pthread_create in pthreads
> -- Looking for pthread_create in pthreads - not found
> -- Looking for pthread_create in pthread
> -- Looking for pthread_create in pthread - found
> -- Found Threads: TRUE
> -- Performing Test PTHREAD_SETAFFINITY
> -- Performing Test PTHREAD_SETAFFINITY - Success
> -- Looking for include file sched.h
> -- Looking for include file sched.h - found
> -- Looking for sysconf
> -- Looking for sysconf - found
> -- Atomics found
> -- Setting build user & time
> -- Setting build user & time - OK
> -- Checking floating point format
> -- Checking floating point format - IEEE754 (LE byte, LE word)
> -- Checking for 64-bit off_t
> -- Checking for 64-bit off_t - present
> -- Checking for fseeko/ftello
> -- Checking for fseeko/ftello - present
> -- Checking for return type of signals
> -- Checking for return type of signals - void
> -- Checking for SIGUSR1
> -- Checking for SIGUSR1 - found
> -- Checking for inline keyword
> -- Checking for inline keyword - inline
> -- Checking for inline keyword
> -- Checking for inline keyword - inline
> -- Checking for pipe support
> -- Checking for isfinite
> -- Performing Test isfinite_compile_ok
> -- Performing Test isfinite_compile_ok - Success
> -- Checking for isfinite - yes
> -- Checking for _isfinite
> -- Performing Test _isfinite_compile_ok
> -- Performing Test _isfinite_compile_ok - Failed
> -- Checking for _isfinite - no
> -- Checking for _finite
> -- Performing Test _finite_compile_ok
> -- Performing Test _finite_compile_ok - Failed
> -- Checking for _finite - no
> -- Checking for GCC x86 inline asm
> -- Checking for GCC x86 inline asm - supported
> -- Checking for MSVC x86 inline asm
> -- Checking for MSVC x86 inline asm - not supported
> -- Checking for system XDR support
> -- Checking for system XDR support - present
> -- Performing Test XFLAGS_SSE
> -- Performing Test XFLAGS_SSE - Success
> -- Performing Test XXFLAGS_SSE
> CMake Error at /usr/share/cmake-2.8/Modules/CMakeCXXInformation.cmake:37
> (get_filename_component):
>    get_filename_component called with incorrect number of arguments
> Call Stack (most recent call first):
>    CMakeLists.txt:3 (PROJECT)
>
>
> CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
> CMake Error: Internal CMake error, TryCompile configure of cmake failed
> -- Performing Test XXFLAGS_SSE - Failed
> CMake Error at
> /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
> (message):
>    Could not find FFTW3F.  Provide the fftw3 install directory in the
>    FFTW3F_ROOT_DIR environment variable.  (missing: FFTW3F_LIBRARIES)
> Call Stack (most recent call first):
>    /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315
> (_FPHSA_FAILURE_MESSAGE)
>    cmake/FindFFTW3F.cmake:31 (find_package_handle_standard_args)
>    CMakeLists.txt:729 (find_package)
>
>
> -- Configuring incomplete, errors occurred!
>

You have a couple of upstream problems.  Whether or not those are related to 
FFTW ultimately not being found, I don't know.  Other things to do:

1. Use a newer version.  There have been numerous changes to the build machinery 
over the last few months.  In principle, 4.5.7 should build, but newer versions 
should be even more reliable.

2. Install FFTW in a completely obvious place by itself, i.e. /usr/local/fftw so 
you always know where it should be found and you can completely control how it 
is found using -DCMAKE_PREFIX_PATH.  FWIW, this is what I always do.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================