Hello,
Those symbols are defined externally in the libPUPIL library and they
belongs to the libPUPILBlind library. It seams that your linking command
does not reach the proper library.
Have you already execute the stub tests in PUPIL before goes to
sander-PUPIL interface ?. This will allow you to check if the data
exchange through those libraries are running correctly.
Also, you can try both, add the $PUPIL_PATH/lib path to the
LD_LIBRARY_PATH environment variable, and add the full path to
libPUPIL.so and libPUPILBlind.so libraries keeping their order in the
Makefile, and recompile.
Regards,
Joan
En/na Aurum Bai ha escrit:
> Thanks very much
>
> When I use "./configure_amber ifort" and then "make sander.PUPIL" , there are some err happen again:
> "
> ack -lmkl -lguide -lpthread \
> -lrt -lm -lc -L/home/bai/workdir/pupil-v1_3_0/lib -lPUPIL -lPUPILBlind
> /home/bai/workdir/pupil-v1_3_0/lib/libPUPIL.so: undefined reference to `putdata_'
> /home/bai/workdir/pupil-v1_3_0/lib/libPUPIL.so: undefined reference to `putresiduetype_'
> /home/bai/workdir/pupil-v1_3_0/lib/libPUPIL.so: undefined reference to `putatomtype_'
> /home/bai/workdir/pupil-v1_3_0/lib/libPUPIL.so: undefined reference to `putcoordinates_'
> "
>
> What is wrong with it? Could you give me some suggest?
>
> --- On Mon, 6/7/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] The err of sander.PUPIL
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Monday, June 7, 2010, 2:19 PM
>
> Hello,
>
> sander.PUPIL I believe only works with a serial compilation (incompatible
> with MPI for amber10). At least this has been hard-coded into the
> makefile. You can get around this by going back to $AMBERHOME/src/ and
> re-running configure_amber to run in serial. Supposing you have ifort,
>
> cd $AMBERHOME/src/
> ./configure_amber ifort
>
> Then try and make sander.PUPIL. If you have gfortran, replace ifort with
> gfortran, etc.
>
> Good luck!
> Jason
>
> P.S. Also don't forget to make clean before you try to build sander.PUPIL
>
> On Mon, Jun 7, 2010 at 1:13 AM, Aurum Bai <javacfish.yahoo.com.cn> wrote:
>
>
>> Hello, everyone
>>
>> I follow the installation of PUPIL successfully. But when I compile the
>> source of sander.PUPIL, I get the err information as below:
>>
>> "mv libdivcon.a ../src/qmmm/
>> make[2]: Leaving directory `/home/bai/workdir/amber10/src/dcqtp/mod'
>> make[1]: Leaving directory `/home/bai/workdir/amber10/src/dcqtp'
>> ./checkserconf
>> Error: ../config_amber.h is not set up for serial compilation
>> make: *** [checkserconf] Error 1
>> "
>>
>> what is wrong with it? How do I solve it?
>>
>> Thanks
>>
>> javacfish
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>
>
--
Joan Torras-Costa
EUETII
Universitat Politècnica de Catalunya
Pça. Rei, 15
08700 - Igualada
SPAIN
Telf.: +34 93 803 5300
Fax : +34 93 803 1589
--
This mail was scanned by BitDefender
For more information please visit http://www.bitdefender.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 07 2010 - 12:00:03 PDT
