Re: [gmx-users] Re: Manual installation of new analysis tool
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 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 wrote:
>
>> > Date: Thu, 25 Apr 2013 22:57:55 +0200
>> > From: Mark Abraham
>> > Subject: Re: [gmx-users] Manual installation of new analysis tool
>> > To: Discussion list for GROMACS users
>> > Message-ID:
>> > > 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
>> 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+0xb
Re: [gmx-users] Re: Manual installation of new analysis tool
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 wrote:
> > Date: Thu, 25 Apr 2013 22:57:55 +0200
> > From: Mark Abraham
> > Subject: Re: [gmx-users] Manual installation of new analysis tool
> > To: Discussion list for GROMACS users
> > Message-ID:
> > 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
> 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): unde
[gmx-users] Re: Manual installation of new analysis tool
> Date: Thu, 25 Apr 2013 22:57:55 +0200
> From: Mark Abraham
> Subject: Re: [gmx-users] Manual installation of new analysis tool
> To: Discussion list for GROMACS users
> Message-ID:
>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy 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:(
