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

Mon Mar 31 21:12:45 CEST 2014

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.
-- 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!

On Mon, Mar 31, 2014 at 10:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/31/14, 11:49 AM, Ly Minh Nhat wrote:
>
>> Using cmake .. -DCMAKE_PREFIX_PATH=/usr/local/lib and cmake ..
>> -DCMAKE_PREFIX_PATH=/usr/local/include still not work.
>>
>>
> As they shouldn't.  As the option says, it's a prefix, i.e. it will look
> for lib/ and include/ within that directory.  So specifying /usr/local/lib
> as a prefix will go searching for /usr/local/lib/lib and
> /usr/local/lib/include, which clearly won't work!
>
>
>  ls for /usr/local/lib: libfftw3.a  libfftw3.la  pkgconfig  python2.7
>> python3.3
>>
>> ls for /usr/local/include: fftw3.f  fftw3.f03  fftw3.h  fftw3l.f03
>> fftw3q.f03
>>
>
> At least you've located where things are.  Since /usr/local is a standard
> location on most systems, I don't see why you need to specify any
> additional options, but -DCMAKE_PREFIX_PATH=/usr/local in theory should
> work.
>
> -Justin
>
>
>
>>
>>
>> On Mon, Mar 31, 2014 at 5:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 3/31/14, 6:33 AM, Ly Minh Nhat wrote:
>>>
>>>  I downloaded the fftw and gromacs tar file to the desktop, extract them
>>>> in
>>>> desktop. I install fftw by ./configure, make and make install, so I
>>>> (quite)
>>>> sure that the directory of fftw3 is Desktop/fftw3.3.4
>>>>
>>>>
>>>>  If you simply did ./configure, make, make install, then the default
>>> location for installing the libraries is in /usr/local/lib and
>>> /usr/local/include, not the source tree.  If you have lib/ and include/
>>> subdirectories within the source in ~/Desktop/fftw3.3.4, then you did
>>> install it there, but that requires explicitly setting that location with
>>> ./configure --prefix.
>>>
>>>
>>>   I also try Desktop/fftw3.3.4, /home/ooker/Desktop/fftw3.3.4 as your
>>>
>>>> suggestion, but it still doesn't work. And yes, I delete the build
>>>> folder
>>>> each time I try to install it.
>>>>
>>>>
>>> That indicates the libraries and headers are not, in fact, installed
>>> within ~/Desktop/fftw3.3.4.
>>>
>>>
>>> -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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
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>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>