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

Venkat Reddy venkat4bt at gmail.com
Fri Apr 26 18:16:32 CEST 2013 

Dear Mark & Junghans,
I have got it. There is some problem in the Makefile. Thanks for your
suggestions and help


On Fri, Apr 26, 2013 at 11:12 AM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> Dear Mark & Junghans,
> Thanks for your valuable suggestions.
> I have gone through the README file. It says compatibility with 4.5.x
> version. I am using 4.5.5. So, I think its not a problem.
> @Junghans: I have installed pkg-config  in fact the $ pkg-config --libs
> libgmx returns
>    the expected output; -lgmx -lm
>
> Here I am sending you the README file as attachment. Please go through it.
> If needed, I am happy to provide the code also.
>
> Thanks a lot
>
>
> On Fri, Apr 26, 2013 at 4:21 AM, Christoph Junghans <junghans at votca.org>wrote:
>
>> > 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
>> >> --
>> >> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >
>> >
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>> --
>> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
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>>
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036

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