It's my machine (GPU workstation under my desk).
I will follow your instructions to build the "Amber MPI".
By the way, I wonder why I could install successfully the parallel version
of both AT1.5 and Amber11, if the issue is related to a general
MPI location.
Moreover, I read on
http://ambermd.org/gpus/ that MPICH2 is more efficient than OpenMP,
hence it is advised to use MPICH2 .
So, how about removing the OpenMP packages?
Something like:
apt-get remove openmp
Thanks again for your helps.
Best,
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
On 26 Jan 2012, at 18:20, Jason Swails <jason.swails.gmail.com> wrote:
> 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
_______________________________________________
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Received on Thu Jan 26 2012 - 11:30:02 PST
