Jason, I located them and I've got them but in "slightly" different paths:
/usr/include/mpich2/mpi.h
and
/usr/lib/openmpi/include/mpi.h
/usr/include/mpich2/mpif.h
and
/usr/lib/openmpi/include/mpif.h
Il 26 gennaio 2012 14:46, Jason Swails <jason.swails.gmail.com> ha scritto:
> Do you have the files /usr/include/mpi.h and /usr/include/mpif.h ?
>
> On Thu, Jan 26, 2012 at 8:27 AM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:
>
>> Here it is:
>>
>> max.nexus:~$ which mpif90
>> /usr/bin/mpif90
>>
>>
>> Il 26 gennaio 2012 13:21, Jason Swails <jason.swails.gmail.com> ha
>> scritto:
>> > You don't have to install the individual bug fixes 18 19 and 20 like
>> that. They are included in the bugfix.all.tar.bz2 file.
>> >
>> > What does "which mpif90" return?
>> >
>> > --
>> > Jason M. Swails
>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Candidate
>> > 352-392-4032
>> >
>> > On Jan 26, 2012, at 7:03 AM, Massimiliano Porrini <M.Porrini.ed.ac.uk>
>> wrote:
>> >
>> >> 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.comwhere
>> >>>> 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
>> >> <config.h>
>> >> _______________________________________________
>> >> 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 - 09:30:03 PST
