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 22 gennaio 2012 09:56, Massimiliano Porrini <mozz76.gmail.com> ha scritto:
> I've just noticed that the two files are identical because $AMBERHOME/src/config.h
> is a symbolic link to $AMBERHOME/AmberTools/src/config.h .
>
> Besides I installed AT1.5 about 3/4 months ago and I followed the
> detailed procedure, applying all the bug fixes. Indeed I've used many
> AT commands without any troubles so far.
>
> By the way I'm going to re-install both AT1.5 and Amber11 with the help of your link.
>
> Many thanks for this.
> 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 21 Jan 2012, at 15:28, Jason Swails <jason.swails.gmail.com> wrote:
>
>> 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
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Received on Tue Jan 24 2012 - 04:00:03 PST
