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
>> >
>>
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Received on Mon Jul 25 2011 - 16:30:02 PDT
