[gmx-users] Please test the new Gromacs-4.5!
Florian Dommert
dommert at icp.uni-stuttgart.de
Thu Sep 2 14:09:17 CEST 2010
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On 09/02/2010 01:45 PM, Rossen Apostolov wrote:
> Hi Florian,
>
> What options did you give to cmake?
>
> You have to specify the library name in FFTW3_LIBRARIES, not the lib
> directory. E.g.
>
> $ cmake ../gromacs-4.5.1
> -DFFTW3F_LIBRARIES=/home/dommert/local/fftw3/lib/libfftw3f.so
>
Hi Rossen,
thanks for this very helpful information. Compilation works fine now.
However when I try to install with
make install
I get following error message:
CMake Error at share/cmake_install.cmake:40 (FILE):
file INSTALL cannot find
"/home/dommert/Downloads/gromacs-4.5.1/share/template/CMakeLists.txt.template".
Call Stack (most recent call first):
cmake_install.cmake:37 (INCLUDE)
/Flo
> Rossen
>
> On 9/2/10 1:21 PM, Florian Dommert wrote:
> On 09/02/2010 12:37 PM, Rossen Apostolov wrote:
>>>> Hi,
>>>>
>>>> Some CMake specific files were missing from the distributed tarball and
>>>> were breaking the build system. I've made a new release, 4.5.1, that
>>>> has a working CMake support. Nothing has changed for autoconf users.
>>>>
>>>> Rossen
>>>>
>>>> On 9/2/10 10:51 AM, Rossen Apostolov wrote:
>>>>> Dear users,
>>>>>
>>>>> Gromacs-4.5 is finally out and although all major and critical bugs
>>>>> have been cleared, we are aware that there are probably many small
>>>>> issues still left.
>>>>>
>>>>> We would like to ask all users to go ahead and *heavy* test run the
>>>>> code. For example,
>>>>>
>>>>> * compile on different platforms with different compilers
>>>>> * use different MPI and math libraries
>>>>> * use exclusively the CMake build system. Autoconf **will be
>>>>> removed** after this release!
>>>>> * try all new features
>>>>> o Amber and Charmm forcefields
>>>>> o simulated nucleic acids
>>>>> o implicit solvent simulations
>>>>> o Velocity-Verlet integrators, MTTK pressure control and
>>>>> Nose-Hoover chains
>>>>> o Free energy calculations and g_bar
>>>>> * errors/inconsistencies/typos in the documentation
>>>>>
>>>>> If you find any kind of reproducible problems, even minor ones, please
>>>>> file a *bugzilla report *! We will clear them out as soon as possible.
>>>>> If there is no report, we'll assume there is no bug :)
>>>>>
>>>>> This test run will be important for distribution package maintainers -
>>>>> let us know if you have issues specific to your systems.
>>>>>
>>>>> And one more thing - there is a deadline :) We'll try to fix all
>>>>> reports that are filed in *the next two weeks* (i.e by *Sept. 15*)!
>>>>> After that priority will be given to development work on major code
>>>>> restructuring towards 5.0.
>>>>>
>>>>> We're awaiting your reports!
> Hello,
>
> when I try to use CMake I get a bunch of warnings when generating the
> Makefile:
> WARNING: Target "md" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_luck" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_protonate" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_x2top" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "gmxcheck" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "gmxdump" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "gmxpreprocess" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "grompp" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "mdrun" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "pdb2gmx" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "tpbconv" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "do_dssp" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "editconf" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "eneconv" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_anadock" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_anaeig" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_analyze" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_angle" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_bar" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_bond" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_bundle" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_chi" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_cluster" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_clustsize" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_confrms" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_covar" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_current" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_density" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_densmap" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_dielectric" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_dih" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_dipoles" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_disre" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_dist" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_dyndom" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_enemat" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_energy" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_filter" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_gyrate" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_h2order" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_hbond" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_helix" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_helixorient" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_lie" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_mdmat" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_membed" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_mindist" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_morph" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_msd" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_nmeig" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_nmens" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_nmtraj" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_order" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_pme_error" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_polystat" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_potential" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_principal" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_rama" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_rdf" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_rms" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_rmsdist" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_rmsf" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_rotacf" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_rotmat" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_saltbr" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_sas" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_select" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_sgangle" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_sham" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_sigeps" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_sorient" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_spatial" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_spol" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_tcaf" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_traj" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_tune_pme" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_vanhove" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_velacc" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_wham" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "g_wheel" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "genbox" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "genconf" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "genion" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "genrestr" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "gmxana" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "make_edi" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "make_ndx" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "mk_angndx" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "trjcat" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "trjconv" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "trjorder" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
> WARNING: Target "xpm2ps" requests linking to directory
> "/home/dommert/local/fftw3/lib". Targets may link only to libraries.
> CMake is dropping the item.
>
> This finally results in an inability to link to FFTW3 correctly, giving
> me following errors:
>
> [ 61%] Built target gmx
> [ 70%] Built target md
> [ 74%] Built target gmxpreprocess
> [ 74%] Built target g_luck
> [ 74%] Built target g_protonate
> [ 74%] Built target g_x2top
> [ 75%] Built target gmxcheck
> [ 75%] Built target gmxdump
> Linking C executable grompp
> ../mdlib/libmd_mpi.a(fft5d.c.o): In function `fft5d_execute':
> fft5d.c:(.text+0xd2c): undefined reference to `fftwf_execute'
> ../mdlib/libmd_mpi.a(fft5d.c.o): In function `fft5d_plan_3d':
> fft5d.c:(.text+0x6e37): undefined reference to `fftwf_plan_guru_dft'
> fft5d.c:(.text+0x7207): undefined reference to `fftwf_plan_guru_dft_r2c'
> fft5d.c:(.text+0x723d): undefined reference to `fftwf_plan_guru_dft_c2r'
> ../mdlib/libmd_mpi.a(fft5d.c.o): In function `fft5d_execute':
> fft5d.c:(.text+0x1886): undefined reference to `fftwf_execute'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_destroy':
> gmx_fft_fftw3.c:(.text+0x16): undefined reference to `fftwf_destroy_plan'
> gmx_fft_fftw3.c:(.text+0x2b): undefined reference to `fftwf_destroy_plan'
> gmx_fft_fftw3.c:(.text+0x41): undefined reference to `fftwf_destroy_plan'
> gmx_fft_fftw3.c:(.text+0x57): undefined reference to `fftwf_destroy_plan'
> gmx_fft_fftw3.c:(.text+0x6d): undefined reference to `fftwf_destroy_plan'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x83):
> more undefined references to `fftwf_destroy_plan' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_3d_real':
> gmx_fft_fftw3.c:(.text+0x152): undefined reference to
> `fftwf_execute_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x17a): undefined reference to
> `fftwf_execute_dft_r2c'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_2d_real':
> gmx_fft_fftw3.c:(.text+0x212): undefined reference to
> `fftwf_execute_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x23a): undefined reference to
> `fftwf_execute_dft_r2c'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_1d_real':
> gmx_fft_fftw3.c:(.text+0x2d2): undefined reference to
> `fftwf_execute_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x2fa): undefined reference to
> `fftwf_execute_dft_r2c'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_3d':
> gmx_fft_fftw3.c:(.text+0x391): undefined reference to `fftwf_execute_dft'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_2d':
> gmx_fft_fftw3.c:(.text+0x421): undefined reference to `fftwf_execute_dft'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_1d':
> gmx_fft_fftw3.c:(.text+0x4b1): undefined reference to `fftwf_execute_dft'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function
> `gmx_fft_init_3d_real':
> gmx_fft_fftw3.c:(.text+0x511): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x555): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x56d): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x5a6): undefined reference to
> `fftwf_plan_dft_c2r_3d'
> gmx_fft_fftw3.c:(.text+0x5c6): undefined reference to
> `fftwf_plan_dft_r2c_3d'
> gmx_fft_fftw3.c:(.text+0x5e3): undefined reference to
> `fftwf_plan_dft_c2r_3d'
> gmx_fft_fftw3.c:(.text+0x600): undefined reference to
> `fftwf_plan_dft_r2c_3d'
> gmx_fft_fftw3.c:(.text+0x61d): undefined reference to
> `fftwf_plan_dft_c2r_3d'
> gmx_fft_fftw3.c:(.text+0x63a): undefined reference to
> `fftwf_plan_dft_r2c_3d'
> gmx_fft_fftw3.c:(.text+0x655): undefined reference to
> `fftwf_plan_dft_c2r_3d'
> gmx_fft_fftw3.c:(.text+0x670): undefined reference to
> `fftwf_plan_dft_r2c_3d'
> gmx_fft_fftw3.c:(.text+0x6e3): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x6ed): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x744): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x74c): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x7a4): undefined reference to `fftwf_free'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x7ae):
> more undefined references to `fftwf_free' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_init_3d':
> gmx_fft_fftw3.c:(.text+0x811): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x847): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x860): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x8a1): undefined reference to `fftwf_plan_dft_3d'
> gmx_fft_fftw3.c:(.text+0x8c8): undefined reference to `fftwf_plan_dft_3d'
> gmx_fft_fftw3.c:(.text+0x8eb): undefined reference to `fftwf_plan_dft_3d'
> gmx_fft_fftw3.c:(.text+0x90e): undefined reference to `fftwf_plan_dft_3d'
> gmx_fft_fftw3.c:(.text+0x931): undefined reference to `fftwf_plan_dft_3d'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x954):
> more undefined references to `fftwf_plan_dft_3d' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_init_3d':
> gmx_fft_fftw3.c:(.text+0xa03): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0xa0d): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0xa64): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0xa6c): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0xac4): undefined reference to `fftwf_free'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0xace):
> more undefined references to `fftwf_free' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function
> `gmx_fft_init_2d_real':
> gmx_fft_fftw3.c:(.text+0xb2b): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0xb6c): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0xb85): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0xbbc): undefined reference to
> `fftwf_plan_dft_c2r_2d'
> gmx_fft_fftw3.c:(.text+0xbdb): undefined reference to
> `fftwf_plan_dft_r2c_2d'
> gmx_fft_fftw3.c:(.text+0xbf5): undefined reference to
> `fftwf_plan_dft_c2r_2d'
> gmx_fft_fftw3.c:(.text+0xc0f): undefined reference to
> `fftwf_plan_dft_r2c_2d'
> gmx_fft_fftw3.c:(.text+0xc29): undefined reference to
> `fftwf_plan_dft_c2r_2d'
> gmx_fft_fftw3.c:(.text+0xc43): undefined reference to
> `fftwf_plan_dft_r2c_2d'
> gmx_fft_fftw3.c:(.text+0xc5b): undefined reference to
> `fftwf_plan_dft_c2r_2d'
> gmx_fft_fftw3.c:(.text+0xc73): undefined reference to
> `fftwf_plan_dft_r2c_2d'
> gmx_fft_fftw3.c:(.text+0xce3): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0xced): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0xd3c): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0xd44): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0xd9c): undefined reference to `fftwf_free'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0xda6):
> more undefined references to `fftwf_free' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_init_2d':
> gmx_fft_fftw3.c:(.text+0xe0b): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0xe3d): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0xe56): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0xe94): undefined reference to `fftwf_plan_dft_2d'
> gmx_fft_fftw3.c:(.text+0xeb8): undefined reference to `fftwf_plan_dft_2d'
> gmx_fft_fftw3.c:(.text+0xed8): undefined reference to `fftwf_plan_dft_2d'
> gmx_fft_fftw3.c:(.text+0xef8): undefined reference to `fftwf_plan_dft_2d'
> gmx_fft_fftw3.c:(.text+0xf18): undefined reference to `fftwf_plan_dft_2d'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0xf38):
> more undefined references to `fftwf_plan_dft_2d' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_init_2d':
> gmx_fft_fftw3.c:(.text+0xfe3): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0xfed): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x103c): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x1044): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x109c): undefined reference to `fftwf_free'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x10a6):
> more undefined references to `fftwf_free' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function
> `gmx_fft_init_many_1d_real':
> gmx_fft_fftw3.c:(.text+0x10fe): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x1136): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x116e): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x11ea): undefined reference to
> `fftwf_plan_many_dft_r2c'
> gmx_fft_fftw3.c:(.text+0x1247): undefined reference to
> `fftwf_plan_many_dft_r2c'
> gmx_fft_fftw3.c:(.text+0x12a3): undefined reference to
> `fftwf_plan_many_dft_r2c'
> gmx_fft_fftw3.c:(.text+0x12ff): undefined reference to
> `fftwf_plan_many_dft_r2c'
> gmx_fft_fftw3.c:(.text+0x1363): undefined reference to
> `fftwf_plan_many_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x13c5): undefined reference to
> `fftwf_plan_many_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x141f): undefined reference to
> `fftwf_plan_many_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x147c): undefined reference to
> `fftwf_plan_many_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x14ed): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x14f7): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x1524): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x152c): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x158a): undefined reference to `fftwf_free'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x1594):
> more undefined references to `fftwf_free' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function
> `gmx_fft_init_many_1d':
> gmx_fft_fftw3.c:(.text+0x15f5): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x1620): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x1648): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x16b8): undefined reference to
> `fftwf_plan_many_dft'
> gmx_fft_fftw3.c:(.text+0x170b): undefined reference to
> `fftwf_plan_many_dft'
> gmx_fft_fftw3.c:(.text+0x1759): undefined reference to
> `fftwf_plan_many_dft'
> gmx_fft_fftw3.c:(.text+0x17a7): undefined reference to
> `fftwf_plan_many_dft'
> gmx_fft_fftw3.c:(.text+0x17f8): undefined reference to
> `fftwf_plan_many_dft'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x1849):
> more undefined references to `fftwf_plan_many_dft' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function
> `gmx_fft_init_many_1d':
> gmx_fft_fftw3.c:(.text+0x1956): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x1960): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x19b4): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x19bc): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x1a1a): undefined reference to `fftwf_free'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x1a24):
> more undefined references to `fftwf_free' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_init_1d':
> gmx_fft_fftw3.c:(.text+0x1a82): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x1aa1): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x1ac0): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x1b2a): undefined reference to
> `fftwf_plan_many_dft'
> gmx_fft_fftw3.c:(.text+0x1b7f): undefined reference to
> `fftwf_plan_many_dft'
> gmx_fft_fftw3.c:(.text+0x1bcf): undefined reference to
> `fftwf_plan_many_dft'
> gmx_fft_fftw3.c:(.text+0x1c22): undefined reference to
> `fftwf_plan_many_dft'
> gmx_fft_fftw3.c:(.text+0x1c70): undefined reference to
> `fftwf_plan_many_dft'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x1cbb):
> more undefined references to `fftwf_plan_many_dft' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_init_1d':
> gmx_fft_fftw3.c:(.text+0x1dc6): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x1dce): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x1e1c): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x1e24): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x1e7a): undefined reference to `fftwf_free'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x1e82):
> more undefined references to `fftwf_free' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function
> `gmx_fft_init_1d_real':
> gmx_fft_fftw3.c:(.text+0x1ecb): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x1ef7): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x1f23): undefined reference to `fftwf_malloc'
> gmx_fft_fftw3.c:(.text+0x1fa1): undefined reference to
> `fftwf_plan_many_dft_r2c'
> gmx_fft_fftw3.c:(.text+0x1fff): undefined reference to
> `fftwf_plan_many_dft_r2c'
> gmx_fft_fftw3.c:(.text+0x205b): undefined reference to
> `fftwf_plan_many_dft_r2c'
> gmx_fft_fftw3.c:(.text+0x20ba): undefined reference to
> `fftwf_plan_many_dft_r2c'
> gmx_fft_fftw3.c:(.text+0x211b): undefined reference to
> `fftwf_plan_many_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x217d): undefined reference to
> `fftwf_plan_many_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x21d9): undefined reference to
> `fftwf_plan_many_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x2238): undefined reference to
> `fftwf_plan_many_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x229d): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x22a5): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x22d4): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x22dc): undefined reference to `fftwf_free'
> gmx_fft_fftw3.c:(.text+0x233a): undefined reference to `fftwf_free'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x2342):
> more undefined references to `fftwf_free' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_many_1d':
> gmx_fft_fftw3.c:(.text+0x23d1): undefined reference to
> `fftwf_execute_dft'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function
> `gmx_fft_many_1d_real':
> gmx_fft_fftw3.c:(.text+0x2462): undefined reference to
> `fftwf_execute_dft_c2r'
> gmx_fft_fftw3.c:(.text+0x248a): undefined reference to
> `fftwf_execute_dft_r2c'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function
> `gmx_many_fft_destroy':
> gmx_fft_fftw3.c:(.text+0x24b6): undefined reference to
> `fftwf_destroy_plan'
> gmx_fft_fftw3.c:(.text+0x24cb): undefined reference to
> `fftwf_destroy_plan'
> gmx_fft_fftw3.c:(.text+0x24e1): undefined reference to
> `fftwf_destroy_plan'
> gmx_fft_fftw3.c:(.text+0x24f7): undefined reference to
> `fftwf_destroy_plan'
> gmx_fft_fftw3.c:(.text+0x250d): undefined reference to
> `fftwf_destroy_plan'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o):gmx_fft_fftw3.c:(.text+0x2523):
> more undefined references to `fftwf_destroy_plan' follow
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function `gmx_fft_destroy':
> gmx_fft_fftw3.c:(.text+0xc0): undefined reference to `fftwf_free'
> ../mdlib/libmd_mpi.a(gmx_fft_fftw3.c.o): In function
> `gmx_many_fft_destroy':
> gmx_fft_fftw3.c:(.text+0x2560): undefined reference to `fftwf_free'
> collect2: ld returned 1 exit status
> make[2]: *** [src/kernel/grompp] Error 1
> make[1]: *** [src/kernel/CMakeFiles/grompp.dir/all] Error 2
> make: *** [all] Error 2
>
> I experience similar problems, when I try to compile gromacs with the
> --enable-shared flag.
>
> So I will try now shared FFTW3 libs and hope it works, but shouldn't it
> also work with static ones ?
>
> /Flo
>
>
> -- Florian Dommert
> Dipl.-Phys.
>
> Institute for Computational Physics
>
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> Phone: +49(0)711/685-6-3613
> Fax: +49-(0)711/685-6-3658
>
> EMail: dommert at icp.uni-stuttgart.de
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
- --
Florian Dommert
Dipl.-Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
Phone: +49(0)711/685-6-3613
Fax: +49-(0)711/685-6-3658
EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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