[gmx-users] Please test the new Gromacs-4.5!

[Florian Dommert]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

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
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