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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Jul 25, 2011, at 7:18 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote: > Hi Ross. I want to thank you for the patience and for all the help > here. It may sound stupid but it seems that having an empty directory > for extraction is crucial after all. Everything turned out ok. All the > tests that were supposed to work worked and pmemd.cuda is working > nicely now. Benchmark for the GTX460 running FactorIX NPT benchmark is > 2.9 ns/day. > Thank you again. > > Fabrício > > 2011/7/25 Ross Walker <ross.rosswalker.co.uk>: >> Hi Fabricio, >> >> See all those files ending in ".rej" those are 'rejects' from the patch >> command which means that patch did not work correctly, either because the >> directory was not properly clean to begin with or you initial AMBER tar >> files are not the distributed ones but have been modified in some way. I >> would suggest doing the following... >> >> Delete your current AMBER directory (make sure AMBERHOME is set properly >> before doing this). - rm -rf $AMBERHOME >> >> Then get yourself copies of the original distributed tar files: >> Amber11.tar.bz2 and AmberTools-1.5.tar.bz2 >> >> Place these in the directory where you want the amber11 directory to be then >> do the following: >> >> 1) tar xvjf Amber11.tar.bz2 >> 2) tar xvjf AmberTools-1.5.tar.bz2 >> 3) export AMBERHOME=/path_to/amber11 >> 4) cd $AMBERHOME >> 5) wget http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all >> 6) patch -p0 < bugfix.all >> 7) rm -f bugfix.all >> 8) wget http://ambermd.org/bugfixes/11.0/bugfix.all >> 9) wget http://ambermd.org/bugfixes/11.0/apply_bugfix.x >> 10) ./apply_bugfix.x bugfix.all >> 11) cd $AMBERHOME/AmberTools/src/ >> 12) ./configure gnu >> 13) make >> 14) cd ../../ >> 15) ./AT15_Amber11.py >> 16) cd src >> 17) make serial >> >> At this point you have the serial (non-GPU) versions of AMBERTools and AMBER >> built. Best to test them at this point. >> >> 18) cd $AMBERHOME/AmberTools/test/ >> 19) make test >> >> Check the test logs to see if everything worked. >> >> 20) cd $AMBERHOME/test >> 21) make test >> >> Again check the test logs to see if everything worked. >> >> Now we can build the serial GPU code. >> >> 22) cd $AMBERHOME/src/ >> 23) make clean >> 24) cd $AMBERHOME/AmberTools/src/ >> 25) make clean >> 26) ./configure -cuda gnu >> 27) cd ../../ >> 28) ./AT15_Amber11.py >> 29) cd src >> 30) make cuda >> >> Hopefully this time it should build correctly. >> >> 31) cd ../test >> 32) make test.cuda >> >> All should be good... Fingers crossed... >> >> All the best >> Ross >> >>> -----Original Message----- >>> From: Fabrício Bracht [mailto:bracht.iq.ufrj.br] >>> Sent: Monday, July 25, 2011 10:11 AM >>> To: AMBER Mailing List >>> Subject: Re: [AMBER] Error compiling amber cuda >>> >>> Ok, I need a little help understanding what came out of md5sum. >>> This is my output. Is everything ok? >>> >>> zotac.zotac-desktop:~/Downloads/amber11/src/pmemd/src/cuda$ md5sum * >>> md5sum: B40C: Is a directory >>> 3339895f6f2599358465b9e17b5cf5c2 cuda_info.f90 >>> f4ed79de194d836246009d5c29051574 cuda_info.fpp >>> adf389d4e9d599b76cea06c6ad062ed0 cuda_info.fpp.orig >>> 2c646f72e82d589de51dd39a023ee239 cuda_info.fpp.rej >>> e40d46e32e05d4f40fd13c86dd1609d8 cuda_info.o >>> a9e4f660fcb5347b1273a8e3f76d3e74 gpu.cpp >>> 43c2c868c7b0ad16801b3a86edcd4482 gpu.cpp.orig >>> c690340fa3bbd86846acf6e9538369e9 gpu.cpp.rej >>> 307e64e078aa5f1f22bd78fd224c9f4b gpu.h >>> fd46d1afeb0e795ab91fc2529cd5b843 gpu.h.orig >>> 729c08b3c841bd87b1042f3d6c12374a gpu.h.rej >>> aa99a62e100dcf2e2bd7ad1136a24028 gpu.o >>> 9e6a4f93e46046cda29369feb0dd32e8 gputypes.cpp >>> feff7fe8bed8c11c1537c52729eab6ce gputypes.cpp.orig >>> 6d47d774d5b83ca3879391535be0165c gputypes.cpp.rej >>> 46f8ccf2bbee063ff35a73945b16a3a2 gputypes.h >>> cc12bdff2667c3798295ba22109eb499 gputypes.h.orig >>> 77b512c4d2565f61c95219f1ad08e37e gputypes.h.rej >>> 4c8e7585e957b3c70bceb8d71ef610b3 gputypes.o >>> 90ba8d068522a00074707a529469f5ea kCalculateGBBornRadii.cu >>> e5f918f895e61717963ade0d0fe22d51 kCalculateGBBornRadii.cu.rej >>> 97fbbcfb8a3833509d94072ecab05643 kCalculateGBNonbondEnergy1.cu >>> 97fbbcfb8a3833509d94072ecab05643 kCalculateGBNonbondEnergy1.cu.orig >>> dc47b131d709410fd317abd5f0216216 kCalculateGBNonbondEnergy1.cu.rej >>> 79fb7a5bba2a19ba351a7dd5996d31fc kCalculateGBNonbondEnergy2.cu >>> 67a458e51a76162edbcc907e7135500c kCalculateLocalForces.cu >>> f4299550e2e5a5e8354530484a640c73 kCalculateLocalForces.cu.rej >>> ce308f4fbe9468d5505beb0099d58e76 kCalculatePMENonbondEnergy.cu >>> 1d2918a17c9e540b334509fc93dc6dd1 kCalculatePMENonbondEnergy.cu.rej >>> 9b240d418e391a71b590e6dc3bc3b0ff kCCF.h >>> a38daf306f4183fbdc470dc81bb47ffb kCCF.h.rej >>> 5561a56bc236291cb87b4770453d67a4 kCLF.h >>> 7edeb669099330c6c73e9cd6e8443655 kCLF.h.rej >>> 86f220029e3a943a186ebcfd16e2dcd9 kCPNE.h >>> 86f220029e3a943a186ebcfd16e2dcd9 kCPNE.h.orig >>> d1e3a9216969c774fe7563e08fad0004 kCPNE.h.rej >>> 9905ed2e705bccf1ae705279d85d0e57 kForcesUpdate.cu >>> ccdeed1ab8011de006284ee519540f91 kForcesUpdate.cu.rej >>> edf2d74af7a4d401ccecc7bfa6d036c3 kNeighborList.cu >>> 44e96ce3db6e02ddfad4f76fe007dcb9 kNeighborList.cu.orig >>> 5ebd4b78db7c46991755e9e3e9d6c84e kNeighborList.cu.rej >>> bbf74d0dbd475e889fb20834119760ac kNTPKernels.h >>> 49f952b429618228fca8e23f44223c58 kPGGW.h >>> 0058536fbe45ceb7a79bc61df95adcea kPGGW.h.orig >>> fb86d5ad6feb20e5248f30a45cfc117f kPGGW.h.rej >>> 4aea91b87cbb3cf62b9fddafe607ab48 kPGS.h >>> 6c962b5a27e6bc6c4c53b7f685889343 kPGS.h.orig >>> 4db97cadd5b928a64a6fb6afb49cefd6 kPGS.h.rej >>> 9c5951cdf94402d2c0396b74498f72f5 kPMEInterpolation.cu >>> 56a2f1359d2662d12eacba3bfacc25f9 kPMEInterpolation.cu.orig >>> c487ee79fdefce8f8fee548ddbe8c70f kPMEInterpolation.cu.rej >>> 46f01611524128ea428c069ef58bd421 kPSSE.h >>> fd131be311aad3755f60aa3b51e89d29 kRandom.h >>> eefe9bd32e04ba2bbe2eb5611a6464bd kShake.cu >>> 2e606f90bc3ca2956eadc4ffad32e885 kShake.cu.rej >>> 4c6af869eda3380dd09c7b582c0fe0bd kU.h >>> 6947e1fae477c0bb9c637062a0ddbfd8 Makefile >>> e5a6173273e6812669c21abcd1530226 Makefile.advanced >>> e3eeff469aa56c8fea91f4911a3e0fa2 Makefile.advanced.rej >>> 9c8878e1723ae40a877e9a98352f1b54 Makefile.orig >>> 8c21b83dee0f294efd4f710134588a5f Makefile.rej >>> >>> Thank you >>> Fabrício >>> >>> 2011/7/25 Ross Walker <ross.rosswalker.co.uk>: >>>> Hi Fabricio, >>>> >>>> To be honest I have absolutely no idea what is causing the problem >>> you are >>>> seeing and I think it is going to take a considerable amount of >>> debugging >>>> etc to work out what is going wrong. I have not seen this problem >>> before and >>>> I do not think anybody else has either. Thus the options are: >>>> >>>> 1) The patch is not being applied properly. Either you are not >>> applying BOTH >>>> the AmberTools and AMBER 11 patches correctly or something is going >>> wrong >>>> during the patch procedure. To debug this we will need to know >>> exactly which >>>> command lines you used and exactly what the output was in each case >>> from the >>>> point of untarring the AMBER tar files into a clean directory to >>> applying >>>> all the patches. >>>> >>>> 2) Your compiler combination is in some way broken. Your NVCC looks >>> good so >>>> maybe something is strange with your C / Fortran compiler >>> combination. >>>> Although the error is coming from NVCC and not gcc which is strange. >>> You >>>> could try the intel compilers though and see if that helps although I >>> still >>>> suspect 1 is the issue here. >>>> >>>> Perhaps you could run an md5sum on each of the files in the >>>> $AMBERHOME/src/pmemd/src/cuda directory. Attached is what I get for >>> AMBER 11 >>>> + all the latest patches. >>>> >>>> foo.linux-jh9j:~/amber11_as_of_jul_22/src/pmemd/src/cuda> md5sum * >>>> md5sum: B40C: Is a directory >>>> f4ed79de194d836246009d5c29051574 cuda_info.fpp >>>> a9e4f660fcb5347b1273a8e3f76d3e74 gpu.cpp >>>> 307e64e078aa5f1f22bd78fd224c9f4b gpu.h >>>> 9e6a4f93e46046cda29369feb0dd32e8 gputypes.cpp >>>> 46f8ccf2bbee063ff35a73945b16a3a2 gputypes.h >>>> 90ba8d068522a00074707a529469f5ea kCalculateGBBornRadii.cu >>>> 97fbbcfb8a3833509d94072ecab05643 kCalculateGBNonbondEnergy1.cu >>>> 79fb7a5bba2a19ba351a7dd5996d31fc kCalculateGBNonbondEnergy2.cu >>>> 67a458e51a76162edbcc907e7135500c kCalculateLocalForces.cu >>>> ce308f4fbe9468d5505beb0099d58e76 kCalculatePMENonbondEnergy.cu >>>> 9b240d418e391a71b590e6dc3bc3b0ff kCCF.h >>>> 5561a56bc236291cb87b4770453d67a4 kCLF.h >>>> 86f220029e3a943a186ebcfd16e2dcd9 kCPNE.h >>>> 9905ed2e705bccf1ae705279d85d0e57 kForcesUpdate.cu >>>> edf2d74af7a4d401ccecc7bfa6d036c3 kNeighborList.cu >>>> fd65d023597024a68565c5a0e5ffd86c kNTPKernels.h >>>> 49f952b429618228fca8e23f44223c58 kPGGW.h >>>> 4aea91b87cbb3cf62b9fddafe607ab48 kPGS.h >>>> 9c5951cdf94402d2c0396b74498f72f5 kPMEInterpolation.cu >>>> 46f01611524128ea428c069ef58bd421 kPSSE.h >>>> ada7d510598c88ed4adb8d32a9dbf73d kRandom.h >>>> eefe9bd32e04ba2bbe2eb5611a6464bd kShake.cu >>>> b07e184d2840ffae27d8af5415fae04a kU.h >>>> 6947e1fae477c0bb9c637062a0ddbfd8 Makefile >>>> e5a6173273e6812669c21abcd1530226 Makefile.advanced >>>> >>>> Check you get EXACTLY the same for all your files. This will >>> determine if >>>> the patch is being applied correctly. >>>> >>>> All the best >>>> Ross >>>> >>>> /\ >>>> \/ >>>> |\oss Walker >>>> >>>> --------------------------------------------------------- >>>> | Assistant Research Professor | >>>> | San Diego Supercomputer Center | >>>> | Adjunct Assistant Professor | >>>> | Dept. of Chemistry and Biochemistry | >>>> | University of California San Diego | >>>> | NVIDIA Fellow | >>>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ | >>>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk | >>>> --------------------------------------------------------- >>>> >>>> Note: Electronic Mail is not secure, has no guarantee of delivery, >>> may not >>>> be read every day, and should not be used for urgent or sensitive >>> issues. >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> >> _______________________________________________ >> 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Jul 25 2011 - 18:30:04 PDT