Hi Jason,
I enclosed the config.h file (taken from $AMBERHOME/src/ ).
And it seems that something went wrong because this file reports
only the line cited by you (although at the end it has "-I/usr/include"
instead of "-I/include"), as you can see:
PMEMD_CU_INCLUDES=-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon
-I/usr/include
However I am a bit confused now because I did apply all the bugfixes,
following the guidelines of your web page
http://jswails.wikidot.com
(and double checking with the manuals).
After having extracted the tarball source codes of AT1.5 and Amber11,
this is what I did step by step to apply the bugfixes:
cd $AMBERHOME
wget
http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all
patch -p0 -N < bugfix.all
cd $AMBERHOME
cd ../
wget
http://ambermd.org/bugfixes/11.0/apply_bugfix.x
wget
http://ambermd.org/bugfixes/11.0/bugfix.all.tar.bz2
chmod +x apply_bugfix.x
./apply_bugfix.x ./bugfix.all.tar.bz2
cd $AMBERHOME
wget
http://ambermd.org/bugfixes/11.0/bugfix.18
wget
http://ambermd.org/bugfixes/11.0/bugfix.19
wget
http://ambermd.org/bugfixes/11.0/bugfix.20
patch -p0 -N < bugfix.18
patch -p0 -N < bugfix.19
patch -p0 -N < bugfix.20
And then I proceeded and succeeded to install AT1.5 (serial and parallel),
Amber11 (serial and parallel) and pmemd.cuda, except pmemd.cuda.MPI .
Thanks again for your help.
Best,
Il 25 gennaio 2012 20:07, Jason Swails <jason.swails.gmail.com> ha scritto:
> Can you post your config.h file here? The C compiler for pmemd _should_ be
> mpicc, which should provide the proper include paths so that "mpi.h" should
> be found. Furthermore, the CUDA compilers should get the MPI include path
> as well, so you should see a line that looks like
>
> PMEMD_CU_INCLUDES=-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon
> -I/mpi/intel-12.1.0/mpich2-1.4.1p1/include
>
> in your config.h. The key component is the last one, which is
> "-I/path/to/mpi/include" so that the CUDA source files know about the MPI
> header file. If something went wrong, then it'll look like
>
> PMEMD_CU_INCLUDES=-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon
> -I/include
>
> which I think indicates that you have not applied the bug fixes (which you
> should definitely do).
>
> HTH,
> Jason
>
> On Wed, Jan 25, 2012 at 2:53 PM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:
>
>> Hi all,
>>
>> After having applied all the bugfixes for AT1.5 and Amber11, I've just
>> finished successfully
>> installing and testing AT1.5 (serial and parallel), Amber11 (serial
>> and parallel) and pmemd.cuda
>> (and it worked fine on all the 3 GPUs I have in my machine),
>> but when I try to install the parallel version of it (pmemd.cuda.MPI):
>>
>> cd $AMBERHOME/AmberTools/src/
>> make clean
>> ./configure -cuda -mpi gnu
>> cd ../../
>> ./AT15_Amber.py
>> cd src/
>> make clean
>> make cuda_parallel
>>
>> I get the following error (the last excerpt is reported):
>>
>>
>> ##############################################################################
>> *****
>> *****
>> *****
>> gputypes.h:1249: warning: ‘_gpuContext::pbImageSoluteAtomID’ will be
>> initialized after
>> gputypes.h:1217: warning: ‘GpuBuffer<unsigned int>*
>> _gpuContext::pbNLExclusionList’
>> gputypes.cpp:438: warning: when initialized here
>> gputypes.h:1229: warning: ‘_gpuContext::pbNLPosition’ will be initialized
>> after
>> gputypes.h:1219: warning: ‘GpuBuffer<uint2>*
>> _gpuContext::pbNLNonbondCellStartEnd’
>> gputypes.cpp:438: warning: when initialized here
>> gputypes.h:1269: warning: ‘_gpuContext::pbConstraintSolventConstraint’
>> will be initialized after
>> gputypes.h:1195: warning: ‘PMEDouble _gpuContext::ee_plasma’
>> gputypes.cpp:438: warning: when initialized here
>> /usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode
>> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA
>> -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C
>> -IB40C/KernelCommon -I/usr/include -c kForcesUpdate.cu
>> In file included from gpu.h:15,
>> from kForcesUpdate.cu:14:
>> gputypes.h:30:17: error: mpi.h: No such file or directory
>> make[3]: *** [kForcesUpdate.o] Error 1
>> make[3]: Leaving directory `/home/max/amber11/src/pmemd/src/cuda'
>> make[2]: *** [-L/usr/local/cuda/lib64] Error 2
>> make[2]: Leaving directory `/home/max/amber11/src/pmemd/src'
>> make[1]: *** [cuda_parallel] Error 2
>> make[1]: Leaving directory `/home/max/amber11/src/pmemd'
>> make: *** [cuda_parallel] Error 2
>>
>> ##############################################################################
>>
>>
>> Thanks as always for any prospective hints about this issue.
>>
>> Best,
>>
>> Il 21 gennaio 2012 15:28, Jason Swails <jason.swails.gmail.com> ha
>> scritto:
>> > If that is the same config.h file as before, then AT15_Amber11.py has
>> not been run (which also means that not all of the AmberTools bug fixes
>> have been applied.
>> >
>> > Either run that script or apply all of the bug fixes for both Amber 11
>> and AmberTools 1.5.
>> >
>> > You can see detailed instructions at http://jswails.wikidot.com where
>> there is a page dedicated to installing Amber 11 and AmberTools 1.5.
>> >
>> > HTH,
>> > Jason
>> >
>> > --
>> > Jason M. Swails
>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Candidate
>> > 352-392-4032
>> >
>> > On Jan 21, 2012, at 7:35 AM, Massimiliano Porrini <mozz76.gmail.com>
>> wrote:
>> >
>> >> Sorry, here is the config.h file.
>> >> Cheers,
>> >>
>> >>
>> >> Dr Massimiliano Porrini
>> >> Institute for Condensed Matter and Complex Systems
>> >> School of Physics & Astronomy
>> >> The University of Edinburgh
>> >> James Clerk Maxwell Building
>> >> The King's Buildings
>> >> Mayfield Road
>> >> Edinburgh EH9 3JZ
>> >>
>> >> Tel +44-(0)131-650-5229
>> >>
>> >> E-mails : M.Porrini.ed.ac.uk
>> >> mozz76.gmail.com
>> >> maxp.iesl.forth.gr
>> >>
>> >> Begin forwarded message:
>> >>
>> >>> From: max.complexity1.site
>> >>> Date: 21 January 2012 12:17:31 GMT
>> >>> To: mozz76.gmail.com
>> >>> Subject: Amber11 cuda config file
>> >>>
>> >>> Amber11 cuda config file created via ./config cuda gnu
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> Dr Massimiliano Porrini
>> Institute for Condensed Matter and Complex Systems
>> School of Physics & Astronomy
>> The University of Edinburgh
>> James Clerk Maxwell Building
>> The King's Buildings
>> Mayfield Road
>> Edinburgh EH9 3JZ
>>
>> Tel +44-(0)131-650-5229
>>
>> E-mails : M.Porrini.ed.ac.uk
>> mozz76.gmail.com
>> maxp.iesl.forth.gr
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Thu Jan 26 2012 - 04:30:02 PST
