[gmx-users] Re: Manual installation of new analysis tool

[Christoph Junghans]

> Date: Thu, 25 Apr 2013 22:57:55 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> Subject: Re: [gmx-users] Manual installation of new analysis tool
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <CAMNuMAT=tt7EJxdngFaVCK=4Wko947Kc_Y7S_GSyrXg8nMSSOQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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.
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
>> --
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>
>

--
Christoph Junghans
Web: http://www.compphys.de