Hi,
that is why I would use a shared version of libgmx (libgmx.so),
all these 'undefined reference' below are coming from libraries libgmx
depends on, e.g. libm, libpthreads and libdl. So either you add libm
and libthreads to GROMACS_DEP_LIBRARIES (like the error message
suggests) or just recompile gromacs with --enable-shared when using
configure.
You could also build gromacs using build.sh, then it is shared by
default as it uses gromacs' cmake files.
Cheers,
Christoph
Am 12. Oktober 2011 12:24 schrieb Patrick Kiley <pjki...@gmail.com>:
> Hi Christoph,
>
> I think I have made more progress, but am still getting stuck. I deleted
> the whole directory and started over. This time I compiled VOTCA this way:
> ./build.sh --prefix ${prefix} -DGMX_DOUBLE=ON tools csg
>
> The result was that it found libgmx_d this time. However, it died with this
> error:
>
> -- checking for module 'libgmx_d'
> -- found libgmx_d, version 4.5.4
> -- Looking for GromacsVersion in /usr/local/gromacs/lib/libgmx_d.a;
> -- Looking for GromacsVersion in /usr/local/gromacs/lib/libgmx_d.a; - not
> found
> CMake Error at CMakeModules/FindGROMACS.cmake:81 (message):
> Could not find GromacsVersion in /usr/local/gromacs/lib/libgmx_d.a;, take
> look at the error message in
> /home/patrick/votca/src/csg/CMakeFiles/CMakeError.log to find out what was
> going wrong. If you don't have pkg-config installed you will most likely
> have to set GROMACS_LIBRARY and GROMACS_DEP_LIBRARY by hand which sets the
> gromacs lib and it's depencies (i.e.
> -DGROMACS_LIBRARY='/path/to/libgmx.so'
> -DGROMACS_DEP_LIBRARIES='/path/to/libblas.so;/path/to/libm.so') !
> Call Stack (most recent call first):
> src/libcsg/CMakeLists.txt:23 (find_package)
>
>
> Here is the contents of
> /home/patrick/votca/src/csg/CMakeFiles/CMakeError.log:
>
> Determining if the function GromacsVersion exists in the
> /usr/local/gromacs/lib/libgmx_d.a; failed with the following output:
> Change Dir: /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp
>
> Run Build Command:/usr/bin/make "cmTryCompileExec/fast"
> /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make
> CMakeFiles/cmTryCompileExec.dir/build
> make[1]: Entering directory
> `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp'
> /usr/local/bin/cmake -E cmake_progress_report
> /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1
> Building C object CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o
> /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o
> CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -c
> /usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c
> Linking C executable cmTryCompileExec
> /usr/local/bin/cmake -E cmake_link_script
> CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1
> /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion
> CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec
> -rdynamic /usr/local/gromacs/lib/libgmx_d.a
> /usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
> `tMPI_Thread_key_delete':
> pthreads.c:(.text+0x619): undefined reference to `pthread_key_delete'
> /usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
> `tMPI_Thread_key_create':
> pthreads.c:(.text+0x68e): undefined reference to `pthread_key_create'
> /usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
> `tMPI_Thread_join':
> pthreads.c:(.text+0x800): undefined reference to `pthread_join'
> /usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
> `tMPI_Thread_create':
> pthreads.c:(.text+0x87a): undefined reference to `pthread_create'
> /usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
> `tMPI_Thread_cancel':
> pthreads.c:(.text+0x174): undefined reference to `pthread_cancel'
> /usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
> `tMPI_Thread_setspecific':
> pthreads.c:(.text+0x1ff): undefined reference to `pthread_setspecific'
> /usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
> `tMPI_Thread_getspecific':
> pthreads.c:(.text+0x21c): undefined reference to `pthread_getspecific'
> /usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
> `tMPI_Thread_mutex_trylock':
> pthreads.c:(.text+0x925): undefined reference to `pthread_mutex_trylock'
> /usr/local/gromacs/lib/libgmx_d.a(pbc.c.o): In function `low_set_pbc':
> pbc.c:(.text+0x71a0): undefined reference to `sqrt'
> pbc.c:(.text+0x7763): undefined reference to `sqrt'
> pbc.c:(.text+0x7800): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `dopdihs':
> bondfree.c:(.text+0x780): undefined reference to `sincos'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `FENE_bonds':
> bondfree.c:(.text+0x2256): undefined reference to `log'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `morse_bonds':
> bondfree.c:(.text+0x2d83): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `low_angres':
> bondfree.c:(.text+0x58a2): undefined reference to `acos'
> bondfree.c:(.text+0x5973): undefined reference to `sincos'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `dih_angle':
> bondfree.c:(.text+0x6648): undefined reference to `atan2'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `rbdihs':
> bondfree.c:(.text+0x6c5d): undefined reference to `sincos'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `pdihs':
> bondfree.c:(.text+0x76d7): undefined reference to `sincos'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `cmap_dihs':
> bondfree.c:(.text+0x9ec6): undefined reference to `cos'
> bondfree.c:(.text+0xa12e): undefined reference to `sqrt'
> bondfree.c:(.text+0xa1b8): undefined reference to `asin'
> bondfree.c:(.text+0xa2bf): undefined reference to `cos'
> bondfree.c:(.text+0xa528): undefined reference to `sqrt'
> bondfree.c:(.text+0xa5b9): undefined reference to `asin'
> bondfree.c:(.text+0xa757): undefined reference to `acos'
> bondfree.c:(.text+0xa7aa): undefined reference to `acos'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `do_1_thole':
> bondfree.c:(.text+0xb0dc): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `thole_pol':
> bondfree.c:(.text+0xb3b3): undefined reference to `pow'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `tab_angles':
> bondfree.c:(.text+0xc61b): undefined reference to `acos'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function
> `quartic_angles':
> bondfree.c:(.text+0xd11c): undefined reference to `acos'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `urey_bradley':
> bondfree.c:(.text+0xdb95): undefined reference to `acos'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `angles':
> bondfree.c:(.text+0xeae9): undefined reference to `acos'
> /usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `bond_angle':
> bondfree.c:(.text+0xb97b): undefined reference to `acos'
> /usr/local/gromacs/lib/libgmx_d.a(orires.c.o): In function `orires':
> orires.c:(.text+0x9af): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(orires.c.o): In function `init_orires':
> orires.c:(.text+0x2190): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(orires.c.o): In function
> `calc_orires_dev':
> orires.c:(.text+0x3dcf): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(disre.c.o): In function `ta_disres':
> disre.c:(.text+0x366): undefined reference to `pow'
> disre.c:(.text+0x392): undefined reference to `pow'
> disre.c:(.text+0x676): undefined reference to `pow'
> disre.c:(.text+0x8ed): undefined reference to `pow'
> disre.c:(.text+0x91b): undefined reference to `pow'
> /usr/local/gromacs/lib/libgmx_d.a(disre.c.o):disre.c:(.text+0xa2e): more
> undefined references to `pow' follow
> /usr/local/gromacs/lib/libgmx_d.a(disre.c.o): In function `ta_disres':
> disre.c:(.text+0xc27): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(disre.c.o): In function `calc_disres_R_6':
> disre.c:(.text+0xfea): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(disre.c.o): In function `init_disres':
> disre.c:(.text+0x1533): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(nonbonded.c.o): In function
> `do_listed_vdw_q':
> nonbonded.c:(.text+0x397): undefined reference to `sqrt'
> nonbonded.c:(.text+0xd44): undefined reference to `sqrt'
> nonbonded.c:(.text+0xd98): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(nb_generic_cg.c.o): In function
> `gmx_nb_generic_cg_kernel':
> nb_generic_cg.c:(.text+0xf0b): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(nb_free_energy.c.o): In function
> `gmx_nb_free_energy_kernel':
> nb_free_energy.c:(.text+0x9bf): undefined reference to `pow'
> nb_free_energy.c:(.text+0xc18): undefined reference to `pow'
> nb_free_energy.c:(.text+0x14f5): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(nb_kernel320.c.o): In function
> `nb_kernel320nf':
> nb_kernel320.c:(.text+0x3c0): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(nb_kernel320.c.o): In function
> `nb_kernel320':
> nb_kernel320.c:(.text+0x9f3): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(maths.c.o): In function `fast_float_erfc':
> maths.c:(.text+0x133): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(maths.c.o): In function `fast_float_erf':
> maths.c:(.text+0x217): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(maths.c.o):maths.c:(.text+0x581): more
> undefined references to `exp' follow
> /usr/local/gromacs/lib/libgmx_d.a(maths.c.o): In function `cuberoot':
> maths.c:(.text+0xcac): undefined reference to `pow'
> maths.c:(.text+0xc8b): undefined reference to `pow'
> /usr/local/gromacs/lib/libgmx_d.a(do_fit.c.o): In function
> `calc_similar_ind':
> do_fit.c:(.text+0x4379): undefined reference to `sqrt'
> do_fit.c:(.text+0x4391): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(do_fit.c.o): In function `rhodev':
> do_fit.c:(.text+0x7187): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(do_fit.c.o): In function `rhodev_ind':
> do_fit.c:(.text+0x72aa): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(do_fit.c.o): In function `rmsdev':
> do_fit.c:(.text+0x77a1): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(do_fit.c.o):do_fit.c:(.text+0x79ce): more
> undefined references to `sqrt' follow
> /usr/local/gromacs/lib/libgmx_d.a(trxio.c.o): In function `prec2ndec':
> trxio.c:(.text+0x577): undefined reference to `log'
> /usr/local/gromacs/lib/libgmx_d.a(pdbio.c.o): In function `read_cryst1':
> pdbio.c:(.text+0x2018): undefined reference to `cos'
> pdbio.c:(.text+0x206c): undefined reference to `cos'
> pdbio.c:(.text+0x20b9): undefined reference to `sincos'
> pdbio.c:(.text+0x214c): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(pdbio.c.o): In function
> `gmx_write_pdb_box':
> pdbio.c:(.text+0x4511): undefined reference to `acos'
> pdbio.c:(.text+0x45b8): undefined reference to `acos'
> pdbio.c:(.text+0x4674): undefined reference to `acos'
> pdbio.c:(.text+0x46d8): undefined reference to `sqrt'
> pdbio.c:(.text+0x4718): undefined reference to `sqrt'
> pdbio.c:(.text+0x4758): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(nb_generic.c.o): In function
> `gmx_nb_generic_kernel':
> nb_generic.c:(.text+0xb25): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(nb_kernel120.c.o): In function
> `nb_kernel120nf':
> nb_kernel120.c:(.text+0x34d): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(nb_kernel120.c.o): In function
> `nb_kernel120':
> nb_kernel120.c:(.text+0x8c8): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(nb_kernel124.c.o): In function
> `nb_kernel124nf':
> nb_kernel124.c:(.text+0xc99): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(nb_kernel124.c.o): In function
> `nb_kernel124':
> nb_kernel124.c:(.text+0x21f9): undefined reference to `exp'
> /usr/local/gromacs/lib/libgmx_d.a(nb_kernel221.c.o):nb_kernel221.c:(.text+0x5cc):
> more undefined references to `exp' follow
> /usr/local/gromacs/lib/libgmx_d.a(vmdio.c.o): In function
> `read_next_vmd_frame':
> vmdio.c:(.text+0x3fd): undefined reference to `sincos'
> vmdio.c:(.text+0x457): undefined reference to `cos'
> vmdio.c:(.text+0x494): undefined reference to `cos'
> vmdio.c:(.text+0x4e7): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(gmx_random.c.o): In function
> `print_gaussian_table':
> gmx_random.c:(.text+0xb76): undefined reference to `exp'
> gmx_random.c:(.text+0xc02): undefined reference to `exp'
> gmx_random.c:(.text+0xc7a): undefined reference to `sqrt'
> gmx_random.c:(.text+0xcb6): undefined reference to `sqrt'
> gmx_random.c:(.text+0xcf2): undefined reference to `exp'
> gmx_random.c:(.text+0xd7a): undefined reference to `exp'
> gmx_random.c:(.text+0xdc2): undefined reference to `sqrt'
> gmx_random.c:(.text+0xe1c): undefined reference to `exp'
> gmx_random.c:(.text+0xebc): undefined reference to `exp'
> gmx_random.c:(.text+0xf5c): undefined reference to `exp'
> gmx_random.c:(.text+0xfe6): undefined reference to `sqrt'
> gmx_random.c:(.text+0x1020): undefined reference to `sqrt'
> gmx_random.c:(.text+0x1068): undefined reference to `sqrt'
> gmx_random.c:(.text+0x10b0): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(gmx_random.c.o): In function
> `gmx_rng_gaussian_real':
> gmx_random.c:(.text+0x1876): undefined reference to `log'
> gmx_random.c:(.text+0x18c8): undefined reference to `sqrt'
> /usr/local/gromacs/lib/libgmx_d.a(vmddlopen.c.o): In function `vmddlclose':
> vmddlopen.c:(.text+0x1): undefined reference to `dlclose'
> /usr/local/gromacs/lib/libgmx_d.a(vmddlopen.c.o): In function `vmddlsym':
> vmddlopen.c:(.text+0x11): undefined reference to `dlsym'
> /usr/local/gromacs/lib/libgmx_d.a(vmddlopen.c.o): In function `vmddlerror':
> vmddlopen.c:(.text+0x21): undefined reference to `dlerror'
> /usr/local/gromacs/lib/libgmx_d.a(vmddlopen.c.o): In function `vmddlopen':
> vmddlopen.c:(.text+0x36): undefined reference to `dlopen'
> collect2: ld returned 1 exit status
> make[1]: *** [cmTryCompileExec] Error 1
> make[1]: Leaving directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp'
> make: *** [cmTryCompileExec/fast] Error 2
>
>
>
>
>
> On Tue, Oct 11, 2011 at 5:28 PM, Patrick Kiley <pjki...@gmail.com> wrote:
>>
>> I didn't specify anything by hand in the case above.
>>
>> Since I am using double precision gmx, should I specify -DGMX_D_LIBRARY
>> rather than _DGMX_LIBRARY?
>>
>> patrick
>>
>> On Tue, Oct 11, 2011 at 5:17 PM, Christoph Junghans <jungh...@votca.org>
>> wrote:
>>>
>>> Am 11. Oktober 2011 18:08 schrieb Patrick Kiley <pjki...@gmail.com>:
>>> > Here is the contents of the entire file:
>>> ....
>>> >
>>> > Determining if the function GromacsVersion exists in the
>>> > /usr/local/gromacs/lib failed with the following output:
>>> That looks strange to me, did you specify GMX_LIBRARY by hand?
>>>
>>> For very odd systems you can specify all libs by hand, for examples see
>>> the build.sh line in <https://code.google.com/p/votca/wiki/compiling_AIX>
>>>
>>> Christoph
>>>
>>>
>>> > Change Dir: /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp
>>> >
>>> > Run Build Command:/usr/bin/make "cmTryCompileExec/fast"
>>> > /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make
>>> > CMakeFiles/cmTryCompileExec.dir/build
>>> > make[1]: Entering directory
>>> > `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp'
>>> > /usr/local/bin/cmake -E cmake_progress_report
>>> > /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1
>>> > Building C object
>>> > CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o
>>> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o
>>> > CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -c
>>> > /usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c
>>> > Linking C executable cmTryCompileExec
>>> > /usr/local/bin/cmake -E cmake_link_script
>>> > CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1
>>> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion
>>> > CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -o
>>> > cmTryCompileExec
>>> > -rdynamic
>>> > CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o: In function
>>> > `main':
>>> > CheckFunctionExists.c:(.text+0x15): undefined reference to
>>> > `GromacsVersion'
>>> > collect2: ld returned 1 exit status
>>> > make[1]: Leaving directory
>>> > `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp'
>>> > make[1]: *** [cmTryCompileExec] Error 1
>>> > make: *** [cmTryCompileExec/fast] Error 2
>>> >
>>> >
>>> >
>>> > On Tue, Oct 11, 2011 at 5:02 PM, Christoph Junghans
>>> > <jungh...@votca.org>
>>> > wrote:
>>> >>
>>> >> Am 11. Oktober 2011 17:40 schrieb Patrick Kiley <pjki...@gmail.com>:
>>> >> > Sorry! I should have realized that was what you were asking
>>> >> > $ pkg-config --libs libgmx_d produces:
>>> >> > -L/usr/local/gromacs/lib -lgmx_d
>>> >> That looks ok to me, but it doesn't fit with
>>> >> > -- package 'libgmx_d' not found
>>> >> From your email above.
>>> >>
>>> >> What kind of error does csg/CMakeFiles/CMakeError.log report at the
>>> >> end?
>>> >>
>>> >> Christoph
>>> >>
>>> >> >
>>> >> > Patrick
>>> >> >
>>> >> >
>>> >> > On Tue, Oct 11, 2011 at 4:24 PM, Christoph Junghans
>>> >> > <jungh...@votca.org>
>>> >> > wrote:
>>> >> >>
>>> >> >> Am 11. Oktober 2011 17:05 schrieb Patrick Kiley
>>> >> >> <pjki...@gmail.com>:
>>> >> >> > I have definitely sourced gromacs. So many times . . .
>>> >> >> >
>>> >> >> > Here is the output of "ls /usr/local/gromacs/lib/pkgconfig/":
>>> >> >> > libgmxana_d.pc libgmx_d.pc libgmxpreprocess_d.pc libmd_d.pc
>>> >> >> Ah ok, so what is the output of
>>> >> >> $ pkg-config --libs libgmx_d
>>> >> >> then?
>>> >> >>
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > On Tue, Oct 11, 2011 at 3:57 PM, Christoph Junghans
>>> >> >> > <jungh...@votca.org>
>>> >> >> > wrote:
>>> >> >> >>
>>> >> >> >> Am 11. Oktober 2011 16:50 schrieb Patrick Kiley
>>> >> >> >> <pjki...@gmail.com>:
>>> >> >> >> > Hi Christoph,
>>> >> >> >> >
>>> >> >> >> > Here is the output of $ pkg-config --libs libgmx:
>>> >> >> >> > Package libgmx was not found in the pkg-config search path.
>>> >> >> >> > Perhaps you should add the directory containing `libgmx.pc'
>>> >> >> >> > to the PKG_CONFIG_PATH environment variable
>>> >> >> >> > No package 'libgmx' found
>>> >> >> >> what does contain /usr/local/gromacs/lib/pkgconfig then?
>>> >> >> >> Have you sourced GMXRC?
>>> >> >> >>
>>> >> >> >> Cheers,
>>> >> >> >>
>>> >> >> >> Christoph
>>> >> >> >>
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> > On Tue, Oct 11, 2011 at 3:45 PM, Christoph Junghans
>>> >> >> >> > <jungh...@votca.org>
>>> >> >> >> > wrote:
>>> >> >> >> >>
>>> >> >> >> >> Am 11. Oktober 2011 16:24 schrieb Patrick Kiley
>>> >> >> >> >> <pjki...@gmail.com>:
>>> >> >> >> >> > Hi Christoph,
>>> >> >> >> >> >
>>> >> >> >> >> > I tried your suggestion, but it doesn't work. I get this
>>> >> >> >> >> > error:
>>> >> >> >> >> > "relocation
>>> >> >> >> >> > R_X86_64_32 against `.rodata' can not be used when making a
>>> >> >> >> >> > shared
>>> >> >> >> >> > object;
>>> >> >> >> >> > recompile with -fPIC".
>>> >> >> >> >> Hmm, that could be the fPIC bug of gcc, but this looks more
>>> >> >> >> >> like
>>> >> >> >> >> a
>>> >> >> >> >> mixture of 64 and 32 bit libraries.
>>> >> >> >> >> Are all dependence libraries (gsl, fftw, libgmx ...) are
>>> >> >> >> >> compiled
>>> >> >> >> >> in
>>> >> >> >> >> 64bit? e.g.
>>> >> >> >> >> $ file ~/votca/lib/libgmx.so.6
>>> >> >> >> >> libgmx.so.6: ELF 64-bit LSB shared object, x86-64....
>>> >> >> >> >>
>>> >> >> >> >> >
>>> >> >> >> >> > I tried a fresh install of the normal gromacs compiled as
>>> >> >> >> >> > static,
>>> >> >> >> >> > and
>>> >> >> >> >> > tried
>>> >> >> >> >> Well, I hope you have a good reason to go through the pain of
>>> >> >> >> >> compiling statically!
>>> >> >> >> >> Even the gromacs people now compile shared by default.
>>> >> >> >> >>
>>> >> >> >> >> In case you still want to do it, here is a thread with hints:
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >> <https://groups.google.com/group/votca/browse_thread/thread/c4a847aabfa5f643/054959940df46f>
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >> > recompiling votca against it and finally I get this error:
>>> >> >> >> >> > -- package 'libgmx_d' not found
>>> >> >> >> >> > -- Could NOT find GMX_D (missing: GMX_D_LIBRARY
>>> >> >> >> >> > GMX_D_INCLUDE_DIR)
>>> >> >> >> >> > CMake Warning at src/libcsg/CMakeLists.txt:41 (message):
>>> >> >> >> >> > gromacs-4.5 double precision not found failback to
>>> >> >> >> >> > single
>>> >> >> >> >> > precision
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> > -- checking for module 'libgmx'
>>> >> >> >> >> > -- package 'libgmx' not found
>>> >> >> >> >> > -- Could NOT find GMX (missing: GMX_LIBRARY
>>> >> >> >> >> > GMX_INCLUDE_DIR)
>>> >> >> >> >> > CMake Error at src/libcsg/CMakeLists.txt:44 (message):
>>> >> >> >> >> > gromacs-4.5 (single or double) not found, make sure you
>>> >> >> >> >> > have
>>> >> >> >> >> > installed
>>> >> >> >> >> > the
>>> >> >> >> >> > gromacs-4.5 and it's dev package. If the gromacs module
>>> >> >> >> >> > was
>>> >> >> >> >> > not
>>> >> >> >> >> > found
>>> >> >> >> >> > above, make sure you have sourced GMXRC or set
>>> >> >> >> >> > PKG_CONFIG_PATH
>>> >> >> >> >> > yourself.
>>> >> >> >> >> > gromacs support can be disable it with -DWITH_GMX=OFF.
>>> >> >> >> >> > If
>>> >> >> >> >> > you
>>> >> >> >> >> > have
>>> >> >> >> >> > gromacs-5.0 installed enable to build against it with
>>> >> >> >> >> > -DWITH_GMX_DEVEL=ON
>>> >> >> >> >> >
>>> >> >> >> >> >
>>> >> >> >> >> > -- Configuring incomplete, errors occurred!
>>> >> >> >> >> >
>>> >> >> >> >> > According to Valentina's link:
>>> >> >> >> >> > echo $PKG_CONFIG_PATH produces:
>>> >> >> >> >> > /usr/local/gromacs/lib/pkgconfig
>>> >> >> >> >> >
>>> >> >> >> >> > which I believe is correct.
>>> >> >> >> >> Can you post the output of
>>> >> >> >> >> $ pkg-config --libs libgmx
>>> >> >> >> >>
>>> >> >> >> >> Cheers,
>>> >> >> >> >>
>>> >> >> >> >> Christoph
>>> >> >> >> >>
>>> >> >> >> >> >
>>> >> >> >> >> > Any other ideas?
>>> >> >> >> >>
>>> >> >> >> >> >
>>> >> >> >> >> > Kind regards,
>>> >> >> >> >> > Patrick
>>> >> >> >> >> > On Tue, Oct 11, 2011 at 1:23 PM, Patrick Kiley
>>> >> >> >> >> > <pjki...@gmail.com>
>>> >> >> >> >> > wrote:
>>> >> >> >> >> >>
>>> >> >> >> >> >> Hi Valentina,
>>> >> >> >> >> >>
>>> >> >> >> >> >> Thanks for the link, but unfortunately, I get zero errors
>>> >> >> >> >> >> during
>>> >> >> >> >> >> compilation, so I think this case is a little different
>>> >> >> >> >> >> from
>>> >> >> >> >> >> yours,
>>> >> >> >> >> >> but
>>> >> >> >> >> >> someone please correct me if I am wrong.
>>> >> >> >> >> >>
>>> >> >> >> >> >> Patrick
>>> >> >> >> >> >>
>>> >> >> >> >> >> On Tue, Oct 11, 2011 at 1:12 PM, Valentina
>>> >> >> >> >> >> <valentina_erast...@yahoo.co.uk> wrote:
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> Oh, sorry, I read topol.tpr at the beginning.
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> I had a similar problem before. This may be useful?
>>> >> >> >> >> >>>
>>> >> >> >> >> >>>
>>> >> >> >> >> >>>
>>> >> >> >> >> >>>
>>> >> >> >> >> >>>
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> http://groups.google.com/group/votca/browse_thread/thread/d24203fb92647bb9
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> Valentina
>>> >> >> >> >> >>>
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> On Oct 11, 12:52 pm, Patrick Kiley <pjki...@gmail.com>
>>> >> >> >> >> >>> wrote:
>>> >> >> >> >> >>> > I seem to remember that there used to be a --conf-opts
>>> >> >> >> >> >>> > option
>>> >> >> >> >> >>> > for
>>> >> >> >> >> >>> > build.sh
>>> >> >> >> >> >>> > that enabled me to build static libs. Does this still
>>> >> >> >> >> >>> > exist?
>>> >> >> >> >> >>> > I
>>> >> >> >> >> >>> > just
>>> >> >> >> >> >>> > tried
>>> >> >> >> >> >>> > using it, but it doesn't seem to be recognized.
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > Patrick
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > On Tue, Oct 11, 2011 at 12:48 PM, Patrick Kiley
>>> >> >> >> >> >>> > <pjki...@gmail.com>
>>> >> >> >> >> >>> > wrote:
>>> >> >> >> >> >>> > > Dear all,
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > > Sorry, that was a mistake on my part. I am actually
>>> >> >> >> >> >>> > > using
>>> >> >> >> >> >>> > > the
>>> >> >> >> >> >>> > > .tpr
>>> >> >> >> >> >>> > > files.
>>> >> >> >> >> >>> > > The command was:
>>> >> >> >> >> >>> > > csg_boltzmann --top topol.tpr --cg
>>> >> >> >> >> >>> > > map5-gly-pro-pro.xml
>>> >> >> >> >> >>> > > --excl
>>> >> >> >> >> >>> > > --trj
>>> >> >> >> >> >>> > > traj.trr
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > > sorry for the confusion.
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > > Patrick
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > > On Tue, Oct 11, 2011 at 12:40 PM, Sebastian Fritsch <
>>> >> >> >> >> >>> > > frit...@mpip-mainz.mpg.de> wrote:
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> Hello Patrick,
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> you need to use the topol.tpr which is the binary
>>> >> >> >> >> >>> > >> form
>>> >> >> >> >> >>> > >> of
>>> >> >> >> >> >>> > >> the
>>> >> >> >> >> >>> > >> topol.top.
>>> >> >> >> >> >>> > >> To get the .tpr you have to run the gromacs
>>> >> >> >> >> >>> > >> preprocessor
>>> >> >> >> >> >>> > >> (grompp).
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> -Sebastian
>>> >> >> >> >> >>> > >> > Dear all,
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> > I have recently recompiled GROMACS on my machine,
>>> >> >> >> >> >>> > >> > and
>>> >> >> >> >> >>> > >> > therefore
>>> >> >> >> >> >>> > >> > have
>>> >> >> >> >> >>> > >> > needed to recompile VOTCA.
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> > Here is how I did it:
>>> >> >> >> >> >>> > >> > 1) source gromacs
>>> >> >> >> >> >>> > >> > 2) sudo ./build.sh -R -dcu --release 1.2.1
>>> >> >> >> >> >>> > >> > --prefix=/home/votca/
>>> >> >> >> >> >>> > >> > tools csg
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> > This finishes with no errors, so I thought
>>> >> >> >> >> >>> > >> > everything
>>> >> >> >> >> >>> > >> > should
>>> >> >> >> >> >>> > >> > be
>>> >> >> >> >> >>> > >> > OK.
>>> >> >> >> >> >>> > >> > However, when I run this command:
>>> >> >> >> >> >>> > >> > csg_boltzmann --top topol.top --cg map.xml --excl
>>> >> >> >> >> >>> > >> > --trj
>>> >> >> >> >> >>> > >> > traj.trr
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> > I get this error:
>>> >> >> >> >> >>> > >> > an error occurred:
>>> >> >> >> >> >>> > >> > input format not supported: topol.top
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> > To me this means I have somehow compiled without
>>> >> >> >> >> >>> > >> > GMX
>>> >> >> >> >> >>> > >> > support,
>>> >> >> >> >> >>> > >> > but
>>> >> >> >> >> >>> > >> > how
>>> >> >> >> >> >>> > >> > could this be and how can I fix it? One other
>>> >> >> >> >> >>> > >> > thing,
>>> >> >> >> >> >>> > >> > I
>>> >> >> >> >> >>> > >> > have
>>> >> >> >> >> >>> > >> > compiled
>>> >> >> >> >> >>> > >> > gromacs with static libs, so maybe I need to tell
>>> >> >> >> >> >>> > >> > the
>>> >> >> >> >> >>> > >> > build
>>> >> >> >> >> >>> > >> > script
>>> >> >> >> >> >>> > >> > this explicitly?
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> > Thanks for any help you can give,
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> > Patrick Kiley
>>> >> >> >> >> >>> >
>>> >> >> >> >> >>> > >> --
>>> >> >> >> >> >>> > >> You received this message because you are subscribed
>>> >> >> >> >> >>> > >> to
>>> >> >> >> >> >>> > >> the
>>> >> >> >> >> >>> > >> Google
>>> >> >> >> >> >>> > >> Groups
>>> >> >> >> >> >>> > >> "votca" group.
>>> >> >> >> >> >>> > >> To post to this group, send email to
>>> >> >> >> >> >>> > >> votca@googlegroups.com.
>>> >> >> >> >> >>> > >> To unsubscribe from this group, send email to
>>> >> >> >> >> >>> > >> votca+unsubscr...@googlegroups.com.
>>> >> >> >> >> >>> > >> For more options, visit this group at
>>> >> >> >> >> >>> > >>http://groups.google.com/group/votca?hl=en.
>>> >> >> >> >> >>>
>>> >> >> >> >> >>> --
>>> >> >> >> >> >>> You received this message because you are subscribed to
>>> >> >> >> >> >>> the
>>> >> >> >> >> >>> Google
>>> >> >> >> >> >>> Groups
>>> >> >> >> >> >>> "votca" group.
>>> >> >> >> >> >>> To post to this group, send email to
>>> >> >> >> >> >>> votca@googlegroups.com.
>>> >> >> >> >> >>> To unsubscribe from this group, send email to
>>> >> >> >> >> >>> votca+unsubscr...@googlegroups.com.
>>> >> >> >> >> >>> For more options, visit this group at
>>> >> >> >> >> >>> http://groups.google.com/group/votca?hl=en.
>>> >> >> >> >> >>>
>>> >> >> >> >> >>
>>> >> >> >> >> >
>>> >> >> >> >> > --
>>> >> >> >> >> > You received this message because you are subscribed to the
>>> >> >> >> >> > Google
>>> >> >> >> >> > Groups
>>> >> >> >> >> > "votca" group.
>>> >> >> >> >> > To post to this group, send email to
>>> >> >> >> >> > votca@googlegroups.com.
>>> >> >> >> >> > To unsubscribe from this group, send email to
>>> >> >> >> >> > votca+unsubscr...@googlegroups.com.
>>> >> >> >> >> > For more options, visit this group at
>>> >> >> >> >> > http://groups.google.com/group/votca?hl=en.
>>> >> >> >> >> >
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >> --
>>> >> >> >> >> Christoph Junghans
>>> >> >> >> >> Votca Core Developer
>>> >> >> >> >>
>>> >> >> >> >> Web: http://www.votca.org
>>> >> >> >> >>
>>> >> >> >> >> --
>>> >> >> >> >> You received this message because you are subscribed to the
>>> >> >> >> >> Google
>>> >> >> >> >> Groups
>>> >> >> >> >> "votca" group.
>>> >> >> >> >> To post to this group, send email to votca@googlegroups.com.
>>> >> >> >> >> To unsubscribe from this group, send email to
>>> >> >> >> >> votca+unsubscr...@googlegroups.com.
>>> >> >> >> >> For more options, visit this group at
>>> >> >> >> >> http://groups.google.com/group/votca?hl=en.
>>> >> >> >> >>
>>> >> >> >> >
>>> >> >> >> > --
>>> >> >> >> > You received this message because you are subscribed to the
>>> >> >> >> > Google
>>> >> >> >> > Groups
>>> >> >> >> > "votca" group.
>>> >> >> >> > To post to this group, send email to votca@googlegroups.com.
>>> >> >> >> > To unsubscribe from this group, send email to
>>> >> >> >> > votca+unsubscr...@googlegroups.com.
>>> >> >> >> > For more options, visit this group at
>>> >> >> >> > http://groups.google.com/group/votca?hl=en.
>>> >> >> >> >
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> --
>>> >> >> >> Christoph Junghans
>>> >> >> >> Votca Core Developer
>>> >> >> >>
>>> >> >> >> Web: http://www.votca.org
>>> >> >> >>
>>> >> >> >> --
>>> >> >> >> You received this message because you are subscribed to the
>>> >> >> >> Google
>>> >> >> >> Groups
>>> >> >> >> "votca" group.
>>> >> >> >> To post to this group, send email to votca@googlegroups.com.
>>> >> >> >> To unsubscribe from this group, send email to
>>> >> >> >> votca+unsubscr...@googlegroups.com.
>>> >> >> >> For more options, visit this group at
>>> >> >> >> http://groups.google.com/group/votca?hl=en.
>>> >> >> >>
>>> >> >> >
>>> >> >> > --
>>> >> >> > You received this message because you are subscribed to the
>>> >> >> > Google
>>> >> >> > Groups
>>> >> >> > "votca" group.
>>> >> >> > To post to this group, send email to votca@googlegroups.com.
>>> >> >> > To unsubscribe from this group, send email to
>>> >> >> > votca+unsubscr...@googlegroups.com.
>>> >> >> > For more options, visit this group at
>>> >> >> > http://groups.google.com/group/votca?hl=en.
>>> >> >> >
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> --
>>> >> >> Christoph Junghans
>>> >> >> Votca Core Developer
>>> >> >>
>>> >> >> Web: http://www.votca.org
>>> >> >>
>>> >> >> --
>>> >> >> You received this message because you are subscribed to the Google
>>> >> >> Groups
>>> >> >> "votca" group.
>>> >> >> To post to this group, send email to votca@googlegroups.com.
>>> >> >> To unsubscribe from this group, send email to
>>> >> >> votca+unsubscr...@googlegroups.com.
>>> >> >> For more options, visit this group at
>>> >> >> http://groups.google.com/group/votca?hl=en.
>>> >> >>
>>> >> >
>>> >> > --
>>> >> > You received this message because you are subscribed to the Google
>>> >> > Groups
>>> >> > "votca" group.
>>> >> > To post to this group, send email to votca@googlegroups.com.
>>> >> > To unsubscribe from this group, send email to
>>> >> > votca+unsubscr...@googlegroups.com.
>>> >> > For more options, visit this group at
>>> >> > http://groups.google.com/group/votca?hl=en.
>>> >> >
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> Christoph Junghans
>>> >> Votca Core Developer
>>> >>
>>> >> Web: http://www.votca.org
>>> >>
>>> >> --
>>> >> You received this message because you are subscribed to the Google
>>> >> Groups
>>> >> "votca" group.
>>> >> To post to this group, send email to votca@googlegroups.com.
>>> >> To unsubscribe from this group, send email to
>>> >> votca+unsubscr...@googlegroups.com.
>>> >> For more options, visit this group at
>>> >> http://groups.google.com/group/votca?hl=en.
>>> >>
>>> >
>>> > --
>>> > You received this message because you are subscribed to the Google
>>> > Groups
>>> > "votca" group.
>>> > To post to this group, send email to votca@googlegroups.com.
>>> > To unsubscribe from this group, send email to
>>> > votca+unsubscr...@googlegroups.com.
>>> > For more options, visit this group at
>>> > http://groups.google.com/group/votca?hl=en.
>>> >
>>>
>>>
>>>
>>> --
>>> Christoph Junghans
>>> Votca Core Developer
>>>
>>> Web: http://www.votca.org
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups
>>> "votca" group.
>>> To post to this group, send email to votca@googlegroups.com.
>>> To unsubscribe from this group, send email to
>>> votca+unsubscr...@googlegroups.com.
>>> For more options, visit this group at
>>> http://groups.google.com/group/votca?hl=en.
>>>
>>
>
> --
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> votca+unsubscr...@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/votca?hl=en.
>
--
Christoph Junghans
Votca Core Developer
Web: http://www.votca.org
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