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 |
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Received on Mon Jul 25 2011 - 10:00:03 PDT
