Hello.
One of the researchers I support has requested a fresh build of Amber 11
with the GPU binaries enabled. (most recent version this site has a
license for). Digging out my archived source tarball, and a copy of
Amber Tools 1.5, I am attempting to apply all the bugfixes before
beginning to build. The bugfixes for Amber Tools apply cleanly, but the
big apply_bugfix script and bugfix.all.tar.gz will not. I've snipped
the successes out of the apply bugfix output. Should I ignore all the
patch errors, or do I have a bad set of sources/patches? I'm currently
building in the /scratch space on the machine since there's a non-gpu
enabled working copy in /usr/local/amber. AMBERHOME is properly set
before applying any patches. I have tried it applying the tools fix
before and after the main amber fixes. Doesn't change outcome.
Thank you for any help on this obsolete version.
[root.ursa amber]# tar xjf Amber11.tar.bz2
[root.ursa amber]# tar xjf AmberTools-1.5.tar.bz2
[root.ursa amber]# cd amber11/
[root.ursa amber11]# /scratch/amber/Amber11.apply_bugfix.x
/scratch/amber/Amber11.bugfix.all.tar.bz2
Applying all bugfixes in /scratch/amber/Amber11.bugfix.all.tar.bz2
Patching AMBER installation in /scratch/amber/amber11
Directory exists warnings can be safely ignored.
<snip no errors>
patching file AmberTools/src/configure
Hunk #1 FAILED at 19.
Hunk #2 FAILED at 369.
Hunk #3 FAILED at 495.
Hunk #4 FAILED at 629.
Hunk #5 FAILED at 642.
Hunk #6 FAILED at 654.
Hunk #7 FAILED at 986.
Hunk #8 FAILED at 1018.
Hunk #9 FAILED at 1055.
Hunk #10 FAILED at 1309.
Hunk #11 FAILED at 1343.
Hunk #12 FAILED at 1497.
Hunk #13 FAILED at 1551.
13 out of 13 hunks FAILED -- saving rejects to file
AmberTools/src/configure.rej
<snip no errors>
patching file AmberTools/src/configure
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file
AmberTools/src/configure.rej
<snip no errors>
Applied patches 1 to 16. Now applying bugfix.17
Applied patch 17. CUDA upgrade complete.
Applying patches after 17...
<snip no errors>
patching file src/pmemd/src/extra_pnts_nb14.fpp
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file
src/pmemd/src/extra_pnts_nb14.fpp.rej
patching file src/pmemd/src/gb_ene.fpp
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/gb_ene.fpp.rej
patching file src/pmemd/src/pairs_calc_novec.i
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/pairs_calc_novec.i.rej
patching file src/pmemd/src/pairs_calc_vec.i
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/pairs_calc_vec.i.rej
patching file src/sander/egb.f
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/sander/egb.f.rej
patching file src/sander/extra_pts.f
Reversed (or previously applied) patch detected! Skipping patch.
6 out of 6 hunks ignored -- saving rejects to file
src/sander/extra_pts.f.rej
The next patch would delete the file src/sander/ifdefs,
which does not exist! Skipping patch.
1 out of 1 hunk ignored
patching file src/sander/nonbond_list.f
Reversed (or previously applied) patch detected! Skipping patch.
3 out of 3 hunks ignored -- saving rejects to file
src/sander/nonbond_list.f.rej
patching file src/sander/short_ene.f
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/sander/short_ene.f.rej
patching file src/pmemd/src/cuda/gpu.cpp
Hunk #1 FAILED at 442.
Hunk #2 FAILED at 3035.
Hunk #3 FAILED at 3070.
Hunk #4 FAILED at 3861.
4 out of 4 hunks FAILED -- saving rejects to file
src/pmemd/src/cuda/gpu.cpp.rej
patching file src/pmemd/src/cuda/gputypes.h
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/cuda/gputypes.h.rej
patching file src/pmemd/src/cuda/kBNL.h
Hunk #1 FAILED at 42.
Hunk #2 FAILED at 63.
Hunk #3 FAILED at 122.
Hunk #4 FAILED at 381.
Hunk #5 FAILED at 456.
5 out of 5 hunks FAILED -- saving rejects to file
src/pmemd/src/cuda/kBNL.h.rej
patching file src/pmemd/src/cuda/gputypes.h
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/cuda/gputypes.h.rej
patching file src/pmemd/src/cuda/cuda_info.fpp
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/cuda/cuda_info.fpp.rej
patching file src/pmemd/src/cuda/gpu.cpp
Hunk #1 FAILED at 441.
Hunk #2 FAILED at 2511.
Hunk #3 FAILED at 3070.
Hunk #4 FAILED at 3765.
Hunk #5 FAILED at 3866.
Hunk #6 FAILED at 5447.
Hunk #7 FAILED at 5693.
Hunk #8 FAILED at 6849.
8 out of 8 hunks FAILED -- saving rejects to file
src/pmemd/src/cuda/gpu.cpp.rej
patching file src/pmemd/src/cuda/gputypes.h
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/cuda/gputypes.h.rej
patching file src/pmemd/src/cuda/kBNL.h
Reversed (or previously applied) patch detected! Skipping patch.
12 out of 12 hunks ignored -- saving rejects to file
src/pmemd/src/cuda/kBNL.h.rej
patching file src/pmemd/src/cuda/kNeighborList.cu
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file
src/pmemd/src/cuda/kNeighborList.cu.rej
patching file src/pmemd/src/cuda/gpu.cpp
Reversed (or previously applied) patch detected! Skipping patch.
18 out of 18 hunks ignored -- saving rejects to file
src/pmemd/src/cuda/gpu.cpp.rej
patching file src/pmemd/src/cuda/gputypes.cpp
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file
src/pmemd/src/cuda/gputypes.cpp.rej
patching file src/pmemd/src/cuda/gputypes.h
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file
src/pmemd/src/cuda/gputypes.h.rej
patching file src/pmemd/src/cuda/kCCF.h
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file
src/pmemd/src/cuda/kCCF.h.rej
patching file src/pmemd/src/cuda/kNeighborList.cu
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/cuda/kNeighborList.cu.rej
patching file src/pmemd/src/cuda/kShake.cu
Reversed (or previously applied) patch detected! Skipping patch.
3 out of 3 hunks ignored -- saving rejects to file
src/pmemd/src/cuda/kShake.cu.rej
patching file src/pmemd/src/master_setup.fpp
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/master_setup.fpp.rej
patching file src/pmemd/src/runfiles.fpp
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/pmemd/src/runfiles.fpp.rej
patching file src/pmemd/src/master_setup.fpp
patching file src/pmemd/src/runfiles.fpp
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!! !!!
!!! IMPORTANT IMPORTANT IMPORTANT IMPORTANT IMPORTANT !!!
!!! !!!
!!! BE SURE TO APPLY ALL BUG FIXES FOR AMBERTOOLS 1.5 !!!
!!! BEFORE ATTEMPTING TO BUILD PMEMD.CUDA. YOU MUST !!!
!!! HAVE AT LEAST UP TO BUGFIX.13 IN ORDER TO BUILD !!!
!!! THE UPDATED PMEMD.CUDA SUCCESSFULLY !!!
!!! !!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
[root.ursa amber11]#
--
Bob Healey
Systems Administrator
Biocomputation and Bioinformatics Constellation
and Molecularium
healer.rpi.edu
(518) 276-4407
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Received on Wed Jul 02 2014 - 08:30:03 PDT
