> Date: Thu, 25 Apr 2013 22:57:55 +0200 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] Manual installation of new analysis tool > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <CAMNuMAT=tt7EJxdngFaVCK=4wko947kc_y7s_gsyrxg8nms...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy <[email protected]> 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. I added the pkg-config support with version 4.0.7 if I remember correctly. Without knowing further details, two things come to my mind: 0.) [Trivial] Make sure that pkg-config is actually installed. 1.) Try if $ pkg-config --libs libgmx returns some useful output like "-lgmx -lm". If not, you might need to set PKG_CONFIG_PATH to ${GMXLDLIB}/pkgconfig, but normally GMXRC does that for you automatically. 2.) Some functions in libgmx have been renamed/changed in the development from 4.0 to 4.5 to 4.6, so you might actually need to change the code, or use the same version as Dr.Luca Monticelli.
Cheers, Christoph > > 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 [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? 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