[gmx-users] Manual installation of new analysis tool

[Mark Abraham]

On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy <venkat4bt at 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
> --
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