It still doesn't work. Here is the output: ooker@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 <jalem...@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 <jalem...@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 >>> >>> jalem...@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-requ...@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 > > jalem...@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-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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