integrating recent changes from fermi-test into fermi

(i'll use "fermi" for more disruptive changes to the pipeline model such
as updating the MSHRs and getting rid of the warp tracker, ripping out DWF, etc...)

[git-p4: depot-paths = "//depot/gpgpu_sim_research/fermi/distribution/": change = 7805]

1 files changed, 0 insertions, 99 deletions

diff --git a/benchmarks/CUDA/MUM/README b/benchmarks/CUDA/MUM/README
deleted file mode 100644
index b48d9ff..0000000
--- a/benchmarks/CUDA/MUM/README
+++ /dev/null
@@ -1,99 +0,0 @@
-MUMmerGPU 1.0
-August 7, 2007
-Michael Schatz, Cole Trapnel, Art Delcher, & Amitabh Varshney
--------------------------------------------------------------
-MUMmerGPU is a high-throughput DNA exact sequence alignment program that
-runs on nVidia G80-class GPUs. It aligns sequences in parallel on the video
-card to achieve a more than 3-fold speedup over the widely used serial CPU
-program MUMmer. It is supports many of the same options as MUMmer, and in
-many cases, can be used as a drop in replacement.
-
-MUMmerGPU uses the "Compute Unified Device Architecture" (CUDA) Software
-development kit to program the graphics cards. If you do not have a nVidia
-G80, you can still use MUMmerGPU using the G80 emulator available in CUDA.
-The emulated version with run much slower than the native version, and
-potentially slower than the CPU version of MUMmer.
-
-Table of Contents
------------------
-. Build & Usage Instructions
-. FAQ
-. Acknowledgements
-
-
-
-
-Build & Usage Instructions
-------------------
-1) Download and install the CUDA Toolkit 1.0 for your OS from: 
-   http://developer.nvidia.com/object/cuda.html
-
-2) Download and install the Linux display driver (100.14) from:
-   http://developer.nvidia.com/object/cuda.html
-
-3) Edit the CUDA_INSTALL_PATH in the src/Makefile to point to the top level
-   directory where you installed the CUDA Toolkit.
-
-4) Run 'make' in the src directory, which will compile the program to run on
-   the GPU as:
-   bin/linux32/release/mummergpu
-
-   If you do not have a G80, you can also run 'make emu=1' which will compile
-   the program to run on the CPU with an emulator as:
-   bin/linux32/emurelease/mummergpu
-
-5) Usage: mummergpu [options] reference.fa query.fa
-   reference.fa must be a single sequence in fasta format
-   query.fa is a multi-fasta file containing your sequences the more
-   sequences you provide, the faster MUMmerGPU will execute.
-   See mummergpu -h for an explanation of the options, many of the options are
-   the same as those available in MUMmer.
-   See: http://mummer.sourceforge.net/manual/#mummer for more information
-
-
-FAQs
-----
-Q: I have a G70 or other older nVidia graphics card. Can I run MUMmerGPU on it?
-
-A: No, MUMmerGPU requires a G80 or later video card. You can run MUMmerGPU
-with the G80 emulator, but the alignments will be computed much slower than
-if you had a G80.
-
-
-
-Q: How does MUMmerGPU handle the MUMmer uniqueness options: -mum, -mumcand,
--mumreference, and -maxmatch?  
-
-A: MUMmerGPU does not filter matches by uniques and always computes all
-maximal matches regardless of their uniqueness (-maxmatch). The filtering
-options provided by MUMmer (-mum, -mumcand, & -mumreference) are heuristics to
-speed up the alignment process. This is not necessary with the very efficient
-MUMmerGPU. If you want to filter your alignments to report only the most
-biologically significant, you should use 'delta-filter' instead, which uses a
-more sophisticated algorithm for finding the best set of alignments.
-
-See the MUMmer manual for more information: 
-http://mummer.sourceforge.net/manual/#filter
-
-
-Q: How does MUMmerGPU handle ambiguous bases?
-
-A: MUMmerGPU only supports DNA characters (ACGT). Non DNA characters in the
-reference are converted arbitrarily to a DNA character (A). Non-DNA characters
-in the query set are converted to 'x' to guarantee a mis-match.
-
-
-Q: How can I get help with MUMmerGPU?
-
-A: Subscribe and post to the mailing list at: 
-   http://sourceforge.net/mail/?group_id=201280
-
-
-
-
-Acknowledgements
-----------------
-This work was supported in part by National Institutes of Health grants
-R01-LM006845 and R01-LM007938, and National Science Foundation CISE RI grant
-CNS 04-03313.
-