Yikes. Is this your machine? If it's a cluster, is there documentation
that tells you how to compile and run MPI programs? With the current
setup, I have no way of telling if the MPI programs in your /usr/bin
correspond to the OpenMPI dev files or MPICH2 dev files located in
/usr/include/{openmpi/,mpich2/}.
If something is clarified via documentation, I would suggest referring to
that. Otherwise, I would suggest building your own MPI. You can use the
configure_openmpi included with Amber to build an MPI that will work with
Amber. I would probably suggest this route.
If you do that, you should put $AMBERHOME/bin at the beginning of your PATH
before running configure for Amber (but after building the MPI). So your
workflow should go something like this:
1) Download OpenMPI (
http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.3.tar.bz2)
2) Extract that tarball in $AMBERHOME/AmberTools/src
3) Run configure_openmpi (this will also build OpenMPI)
4) Put AMBERHOME/bin at the beginning of your path
5) Follow the AmberTools/Amber parallel build instructions, starting with
the configure step.
In Unix commands (assuming AMBERHOME is set):
cd $AMBERHOME/AmberTools/src/
wget
http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.3.tar.bz2
tar jxvf openmpi-1.4.3.tar.bz2
./configure_openmpi gnu
export PATH=$AMBERHOME/bin\:$PATH
./configure -mpi gnu
cd ../../src && make clean && make parallel
HTH,
Jason
On Thu, Jan 26, 2012 at 12:06 PM, Massimiliano Porrini
<M.Porrini.ed.ac.uk>wrote:
> Jason, I located them and I've got them but in "slightly" different paths:
>
> /usr/include/mpich2/mpi.h
> and
> /usr/lib/openmpi/include/mpi.h
>
> /usr/include/mpich2/mpif.h
> and
> /usr/lib/openmpi/include/mpif.h
>
>
> Il 26 gennaio 2012 14:46, Jason Swails <jason.swails.gmail.com> ha
> scritto:
> > Do you have the files /usr/include/mpi.h and /usr/include/mpif.h ?
> >
> > On Thu, Jan 26, 2012 at 8:27 AM, Massimiliano Porrini <
> M.Porrini.ed.ac.uk>wrote:
> >
> >> Here it is:
> >>
> >> max.nexus:~$ 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
>
> _______________________________________________
> 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
Received on Thu Jan 26 2012 - 10:30:02 PST
