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-- 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/amberReceived on Thu Jan 26 2012 - 05:30:04 PST