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.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
>> <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
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Received on Thu Jan 26 2012 - 05:30:05 PST
