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
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Received on Thu Jan 26 2012 - 07:00:03 PST
