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

Ly Minh Nhat ganuongphap at gmail.com
Tue Apr 1 08:37:22 CEST 2014 

Well, I have solve the first error by installing g++. The fftw error still
occurs:

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 GNU 4.8.1
-- 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
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- 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
-- Performing Test CXXFLAGS_WARN
-- Performing Test CXXFLAGS_WARN - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_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
-- Performing Test XXFLAGS_SSE - Success
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!



On Tue, Apr 1, 2014 at 4:45 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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