Hi all,
I have been trying to install Amber11 and AT1.5 on our GPU
workstation with one Kepler K20c and Ubuntu 13.04 OS .
The CUDA toolkit 5 and the Nvidia drivers were installed (not by me)
from the Ubuntu repositories (using the apt-get utility).
The issue is that I am experiencing problems with some bugfixes of Amber11,
specifically with bugfix.19, bugfix.20 and bugfix.22 .
This is what I get when I try to patch Amber11, both using the tarball
file (bugfix.all.tar.bz2) and the individual ones (19, 20 and 22,
as shown below):
patch -p0 -N < bugfix.19
patching file src/pmemd/src/cuda/gpu.cpp
Hunk #1 FAILED at 442.
Hunk #2 FAILED at 3033.
Hunk #3 FAILED at 3068.
Hunk #4 FAILED at 3859.
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 58.
Hunk #3 FAILED at 115.
Hunk #4 FAILED at 372.
Hunk #5 FAILED at 429.
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
patch -p0 -N < bugfix.20
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 3821.
Hunk #6 FAILED at 5372.
Hunk #7 FAILED at 5618.
Hunk #8 FAILED at 6774.
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
patch -p0 -N < bugfix.22
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
Hunk #1 FAILED at 269.
1 out of 1 hunk FAILED -- saving rejects to file
src/pmemd/src/runfiles.fpp.rej
>From what I read in amber mailing list archives I should do a "fresh"
installation
of Amebr11 and AT1.5, and this is what I have done twice,
but the above failures remain.
By the way, in one of my attempts, I did not care about these
"failure" messages and I continued installing. To bottom line:
I was able to build Amber11 and AT1.5 both in serial and parallel,
except the CUDA version of Amber11 (obviously..!).
In the mailing list archives, I also read that the best thing to do would
be upgrading
to Amber12, but I wonder if someone has the solution to these issues,
as for the moment I'd urgently need to install Amber11.
Does anybody have any suggestion on how to fix these CUDA
Amber11 patching failures?
Many thanks in advance,
Max
--
Dr Massimiliano Porrini
Institut Européen de Chimie et Biologie (IECB)
CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel : 33 (0)5 40 00 30 31
Fax : 33 (0)5 40 00 22 00
http://www.iecb.u-bordeaux.fr/
Emails: m.porrini.iecb.u-bordeaux.fr
M.Porrini.ed.ac.uk
maxp.iesl.forth.gr
mozz76.gmail.com
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Received on Thu Jul 25 2013 - 08:00:04 PDT
