[gmx-developers] Error occurs when compiling gromacs using vtcc

[Mark Abraham]

Hi,

That issue likely relates to the (wrapper) compiler not handling some
aspect of OpenMP correctly (from the "pomp" string). Likely the solution is
outside GROMACS space.

Mark


On Fri, Aug 1, 2014 at 7:56 AM, Theodore Si <sjyzhxw at gmail.com> wrote:

> I edited that file, and some other files, all the same problem(I wonder
> why just 3 or 4 files have that problem). I can compile now.
> Howerver, a new problem has arisen:
>
> ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to `pomp_rd_table'
> ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to `POMP_MAX_ID'
> collect2: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>
> make: *** [all] Error 2
>
>
> 于2014年8月1日 18:16:36,Theodore Si写到:
>
>  I tried to merge them to one line, it worked.
>> But there are many multi-line comments, it is impossible to change
>> them one by one.
>>
>>
>> 于2014年8月1日 17:38:28,Erik Lindahl写到:
>>
>>> Try adding a backslash at the end of line 24.
>>>
>>> Cheers,
>>>
>>> Erik
>>>
>>> On 01 Aug 2014, at 11:09, Theodore Si <sjyzhxw at gmail.com
>>> <mailto:sjyzhxw at gmail.com>> wrote:
>>>
>>>  Hi all,
>>>>
>>>> Does anyone know the instrumentation tool Vampir Trace? I am using
>>>> it, and I want to instrument the gromacs code.
>>>> So my cmake options are:
>>>>
>>>> cmake .. -DCMAKE_BUILD_OWN_FFTW=ON -DCMAKE_C_COMPILER=vtcc
>>>> -DCMAKE_CXX_COMPILER=vtcxx -DGMX_MPI=on
>>>> -DCMAKE_INSTALL_PREFIX=/home/theo/gmx
>>>> -CUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5
>>>>
>>>> Vampir Trace includes some binaries, like vtcc and vtcxx above. They
>>>> behave like compiler but are actually compiler wrapper.
>>>> For example, you can write main.c and vtcc main.c -o main, and the
>>>> binary main will be built and you can run it like a normal binary
>>>> file, but during the run, some files will be generated and can be
>>>> analysed latter.
>>>>
>>>> However, error occurs:
>>>>
>>>> [  2%] Building C object
>>>> src/gromacs/CMakeFiles/libgromacs.dir/__/external/
>>>> tng_io/src/compression/tng_compress.c.o
>>>>
>>>> /home/theo/gromacs-5.0/src/external/tng_io/src/
>>>> compression/tng_compress.c:25:
>>>>
>>>> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘speed’
>>>> /home/theo/gromacs-5.0/src/external/tng_io/src/
>>>> compression/tng_compress.c:
>>>>
>>>> In function ‘quantize’:
>>>> /home/theo/gromacs-5.0/src/external/tng_io/src/
>>>> compression/tng_compress.c:80:
>>>>
>>>> warning: implicit declaration of function ‘verify_input_data’
>>>> At top level:
>>>> cc1: warning: unrecognized command line option
>>>> "-Wno-maybe-uninitialized"
>>>> make[2]: ***
>>>> [src/gromacs/CMakeFiles/libgromacs.dir/__/external/
>>>> tng_io/src/compression/tng_compress.c.o]
>>>>
>>>> Error 1
>>>> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>>>> make: *** [all] Error 2
>>>>
>>>> When I open the tng_compress.c, I find that line 25 is just a comment.
>>>>
>>>> 24 #define SPEED_DEFAULT 2 /* Default to relatively fast compression.
>>>> For very      good compression it makes sense to
>>>> 25                            choose speed=4 or speed=5 */
>>>> 26
>>>>
>>>> Could you tell me what's going on?
>>>>
>>>> I'd appreciate you kind help.
>>>> --
>>>> Gromacs Developers mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>>>> before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>>>> or send a mail to gmx-developers-request at gromacs.org
>>>> <mailto:gmx-developers-request at gromacs.org>.
>>>>
>>>
>>>
>>>
>>>  --
> Gromacs Developers mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-developers_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20140801/cce0ca13/attachment.html>