On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy <venkat...@gmail.com> wrote:
> Dear all, > I have got an analysis tool for analyzing membrane density from Dr.Luca > monticelli. I have followed the installation instructions as given. > > 1) First thing is to load GROMACS > $ *source /usr/local/gromacs/bin/GMXRC* > 2) Enter the source directory of the program then make > $ cd g_mydensity > $ make > According to the instructions, it should create an executable > "*g_mydensity*" > but I am getting the following errors > > *cc `pkg-config --libs libgmx` g_mydensity.o matrix.o distances.o > Looks like his Makefile is relying on valid pkg-config registration. I've no idea for what GROMACS versions under what conditions pkg-config actually works, but I suggest you follow his instructions really precisely, and/or contact him to resolve any doubtful points. Mark > dist_mode.o grid_mode.o -o g_mydensity* > *g_mydensity.o: In function `gmx_log2':* > *g_mydensity.c:(.text+0xa8): undefined reference to `log'* > *g_mydensity.o: In function `gmx_invsqrt':* > *g_mydensity.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'* > *g_mydensity.c:(.text+0x101): undefined reference to > `gmx_invsqrt_fracttab'* > *g_mydensity.o: In function `matrix_convert':* > *g_mydensity.c:(.text+0x381): undefined reference to `cos'* > *g_mydensity.c:(.text+0x3ad): undefined reference to `sin'* > *g_mydensity.c:(.text+0x3da): undefined reference to `cos'* > *g_mydensity.c:(.text+0x403): undefined reference to `cos'* > *g_mydensity.c:(.text+0x416): undefined reference to `cos'* > *g_mydensity.c:(.text+0x429): undefined reference to `cos'* > *g_mydensity.c:(.text+0x447): undefined reference to `sin'* > *g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'* > *g_mydensity.o: In function `get_electrons':* > *g_mydensity.c:(.text+0x527): undefined reference to `ffopen'* > *g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'* > *g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'* > *g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'* > *g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0x68d): undefined reference to `gmx_fatal'* > *g_mydensity.c:(.text+0x6eb): undefined reference to `gmx_fatal'* > *g_mydensity.c:(.text+0x74f): undefined reference to `ffclose'* > *g_mydensity.o: In function `center_coords':* > *g_mydensity.c:(.text+0x88f): undefined reference to `calc_box_center'* > *g_mydensity.o: In function `calc_electron_density':* > *g_mydensity.c:(.text+0x945): undefined reference to `gmx_fatal'* > *g_mydensity.c:(.text+0x973): undefined reference to `read_first_x'* > *g_mydensity.c:(.text+0x9a0): undefined reference to `gmx_fatal'* > *g_mydensity.c:(.text+0xa38): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0xa81): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0xac1): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0xaf6): undefined reference to `gmx_rmpbc_init'* > *g_mydensity.c:(.text+0xb18): undefined reference to `set_pbc'* > *g_mydensity.c:(.text+0xb38): undefined reference to `gmx_rmpbc'* > *g_mydensity.c:(.text+0xe0b): undefined reference to `read_next_x'* > *g_mydensity.c:(.text+0xe1e): undefined reference to `gmx_rmpbc_done'* > *g_mydensity.c:(.text+0xe29): undefined reference to `close_trj'* > *g_mydensity.c:(.text+0xecc): undefined reference to `save_free'* > *g_mydensity.o: In function `calc_density':* > *g_mydensity.c:(.text+0xf32): undefined reference to `gmx_fatal'* > *g_mydensity.c:(.text+0xf60): undefined reference to `read_first_x'* > *g_mydensity.c:(.text+0xf8d): undefined reference to `gmx_fatal'* > *g_mydensity.c:(.text+0x101c): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0x1065): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0x10a5): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0x10da): undefined reference to `gmx_rmpbc_init'* > *g_mydensity.c:(.text+0x10fc): undefined reference to `set_pbc'* > *g_mydensity.c:(.text+0x111c): undefined reference to `gmx_rmpbc'* > *g_mydensity.c:(.text+0x143a): undefined reference to `read_next_x'* > *g_mydensity.c:(.text+0x144d): undefined reference to `gmx_rmpbc_done'* > *g_mydensity.c:(.text+0x146e): undefined reference to `close_trj'* > *g_mydensity.c:(.text+0x1511): undefined reference to `save_free'* > *g_mydensity.o: In function `plot_density':* > *g_mydensity.c:(.text+0x159c): undefined reference to `xvgropen'* > *g_mydensity.c:(.text+0x15bf): undefined reference to `xvgr_legend'* > *g_mydensity.c:(.text+0x16ea): undefined reference to `ffclose'* > *g_mydensity.o: In function `gmx_mydensity':* > *g_mydensity.c:(.text+0x18bd): undefined reference to `CopyRight'* > *g_mydensity.c:(.text+0x1923): undefined reference to `parse_common_args'* > *g_mydensity.c:(.text+0x19a0): undefined reference to `ftp2fn'* > *g_mydensity.c:(.text+0x19af): undefined reference to `read_top'* > *g_mydensity.c:(.text+0x1a84): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0x1ab4): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0x1ae4): undefined reference to `save_calloc'* > *g_mydensity.c:(.text+0x1b0b): undefined reference to `ftp2fn_null'* > *g_mydensity.c:(.text+0x1b39): undefined reference to `get_index'* > *g_mydensity.c:(.text+0x1b67): undefined reference to `ftp2fn'* > *g_mydensity.c:(.text+0x1be1): undefined reference to `ftp2fn'* > *g_mydensity.c:(.text+0x1c6a): undefined reference to `opt2fn_null'* > *g_mydensity.c:(.text+0x1caa): undefined reference to `opt2fn'* > *g_mydensity.c:(.text+0x1d04): undefined reference to `opt2bSet'* > *g_mydensity.c:(.text+0x1d36): undefined reference to `ftp2fn'* > *g_mydensity.c:(.text+0x1d63): undefined reference to `opt2fn'* > *g_mydensity.c:(.text+0x1e20): undefined reference to `ftp2fn'* > *g_mydensity.c:(.text+0x1edb): undefined reference to `opt2fn'* > *g_mydensity.c:(.text+0x1f39): undefined reference to `opt2fn'* > *g_mydensity.c:(.text+0x1f50): undefined reference to `do_view'* > *g_mydensity.c:(.text+0x1f5d): undefined reference to `thanx'* > *matrix.o: In function `realMatrix':* > *matrix.c:(.text+0x29): undefined reference to `save_malloc'* > *matrix.c:(.text+0x66): undefined reference to `save_malloc'* > *matrix.o: In function `deleteRealMat':* > *matrix.c:(.text+0xe4): undefined reference to `save_free'* > *matrix.c:(.text+0x113): undefined reference to `save_free'* > *matrix.o: In function `intMatrix':* > *matrix.c:(.text+0x142): undefined reference to `save_malloc'* > *matrix.c:(.text+0x17f): undefined reference to `save_malloc'* > *matrix.o: In function `deleteIntMat':* > *matrix.c:(.text+0x1fd): undefined reference to `save_free'* > *matrix.c:(.text+0x22c): undefined reference to `save_free'* > *distances.o: In function `gmx_log2':* > *distances.c:(.text+0xa8): undefined reference to `log'* > *distances.o: In function `gmx_invsqrt':* > *distances.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'* > *distances.c:(.text+0x101): undefined reference to `gmx_invsqrt_fracttab'* > *distances.o: In function `matrix_convert':* > *distances.c:(.text+0x332): undefined reference to `cos'* > *distances.c:(.text+0x35e): undefined reference to `sin'* > *distances.c:(.text+0x38b): undefined reference to `cos'* > *distances.c:(.text+0x3b4): undefined reference to `cos'* > *distances.c:(.text+0x3c7): undefined reference to `cos'* > *distances.c:(.text+0x3da): undefined reference to `cos'* > *distances.c:(.text+0x3f8): undefined reference to `sin'* > *distances.c:(.text+0x45e): undefined reference to `sqrt'* > *distances.o: In function `pbc_rvec_sub':* > *distances.c:(.text+0x4e8): undefined reference to `pbc_dx'* > *distances.o: In function `get_distance':* > *distances.c:(.text+0x550): undefined reference to `sqrtf'* > *distances.o: In function `center_of_mass':* > *distances.c:(.text+0x6b5): undefined reference to `save_calloc'* > *dist_mode.o: In function `gmx_log2':* > *dist_mode.c:(.text+0xa8): undefined reference to `log'* > *dist_mode.o: In function `gmx_invsqrt':* > *dist_mode.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'* > *dist_mode.c:(.text+0x101): undefined reference to `gmx_invsqrt_fracttab'* > *dist_mode.o: In function `norm':* > *dist_mode.c:(.text+0x1fc): undefined reference to `sqrt'* > *dist_mode.o: In function `matrix_convert':* > *dist_mode.c:(.text+0x2fa): undefined reference to `cos'* > *dist_mode.c:(.text+0x326): undefined reference to `sin'* > *dist_mode.c:(.text+0x353): undefined reference to `cos'* > *dist_mode.c:(.text+0x37c): undefined reference to `cos'* > *dist_mode.c:(.text+0x38f): undefined reference to `cos'* > *dist_mode.c:(.text+0x3a2): undefined reference to `cos'* > *dist_mode.c:(.text+0x3c0): undefined reference to `sin'* > *dist_mode.c:(.text+0x414): undefined reference to `sqrt'* > *dist_mode.o: In function `_min_distance':* > *dist_mode.c:(.text+0x505): undefined reference to `pbc_dx'* > *dist_mode.o: In function `build_dist':* > *dist_mode.c:(.text+0x5af): undefined reference to `save_calloc'* > *dist_mode.c:(.text+0x65c): undefined reference to `save_calloc'* > *dist_mode.c:(.text+0x6a3): undefined reference to `save_calloc'* > *dist_mode.c:(.text+0x710): undefined reference to `save_calloc'* > *dist_mode.c:(.text+0x73f): undefined reference to `save_calloc'* > *dist_mode.o:dist_mode.c:(.text+0x76e): more undefined references to > `save_calloc' follow* > *dist_mode.o: In function `build_dist':* > *dist_mode.c:(.text+0x7b2): undefined reference to `get_index'* > *dist_mode.c:(.text+0x839): undefined reference to `xvgropen'* > *dist_mode.c:(.text+0x865): undefined reference to `xvgr_legend'* > *dist_mode.o: In function `clean_dist':* > *dist_mode.c:(.text+0x8bd): undefined reference to `save_free'* > *dist_mode.c:(.text+0x8f1): undefined reference to `save_free'* > *dist_mode.c:(.text+0x917): undefined reference to `save_free'* > *dist_mode.c:(.text+0x948): undefined reference to `save_free'* > *grid_mode.o: In function `build_grids':* > *grid_mode.c:(.text+0x81): undefined reference to `save_calloc'* > *grid_mode.c:(.text+0x177): undefined reference to `gmx_fatal'* > *grid_mode.c:(.text+0x1a2): undefined reference to `save_calloc'* > *grid_mode.c:(.text+0x201): undefined reference to `ffopen'* > *grid_mode.o: In function `clean_grids':* > *grid_mode.c:(.text+0x2b8): undefined reference to `save_free'* > *grid_mode.c:(.text+0x2c6): undefined reference to `ffclose'* > *grid_mode.c:(.text+0x2e9): undefined reference to `save_free'* > *grid_mode.o: In function `grid_store':* > *grid_mode.c:(.text+0x41a): undefined reference to `put_atom_in_box'* > *collect2: ld returned 1 exit status* > *make: *** [g_mydensity] Error 1* > > Please help me in this regard. Thanks for your valuable time and concern. > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? 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