Description of problem:

I've yum updated to keep to the current Fedora 17, x86_65 release as of 25Sep2012.. The following test have occurred over many weeks. I can repeat some if you think things have changed.

It all started when I had a series of probably duplicate files, but I wanted to make sure so I used cmp to see and kept getting different answers; Sometimes equal sometimes different and at different locations. So with too many new things in play what could be wrong?

A) cmp is broken or can't handle large binary files [400MB to 3.1GB dtv recordings]

1) I wrote a java program to compare two files. It kept giving different answers too. So it doesn't seem to be cmp.

B) Could it be my brand new USB->SATA drive?

2) I copied one of the suspicions files to another drive and then duplicated it.  When comparing them over and over still got different answers.  It doesn't look like the drive.

C) Could it be ext4. I have never used ext4 except last month when installing Fedora17 for the first time and had a drive failure loosing almost everything. [Or was it a drive failure?]

3) Copied the files from #2 to an ext3 partition on drive from #2 and to a fat32 partition on the USB drive from #1.  Both compared differently on different attempts.  So it doesn't seem like it relates to the file system.

D) Could it be Fedora17 x86_64.  The first time I've used the 64 bit release.

4) I downloaded and created a live CD for Fedora17 i686.  When running that I got 3 'wrong' compares in 45 tests.  When running a x86_64 booted from a USB stick I got 15 wrong out of 45.  I got 53 failures out of 63 runs on the 'real' Fedora17 x86_64. All with the same files on the same USB->SATA drive w/ ext4. So that was somewhat inconclusive. 

E) Could it be Fedora17?

5) Though the home partition of my old Fedora7 installation was destroyed the boot and root partitions seemed intact so I made a new TempHome7 partition (ext3) and added three pairs of files and a test script.  Something went wrong during boot and the X server or video driver didn't come up but I logged on as root and ran the test getting only one failure out of 67 runs.  That one failure really bothers me.

F) It is interesting that I used cp on Fedora17 to make the test files and expected there to be some errors in the copy but cmp on Fedora7 said (mostly) they were equal.  Is there any difference between the way cp makes a copy and cmp tests for equal? like mapping a file into memory vs reading one block at a time? 

6) I may never know, but I did modify the java program to try both regular I/O and memory mapped files and ran numerous tests on those same 3 pairs of files on that same ext3 partition.

	Fedora17 Equal/Runs
	cmp:	10/135
	Mapped:	54/135
	I/O:	135/135

So far the java program's regular I/O has always said each pair [on that drive w/ ext3] are equal and cmp almost never does with the memory mapped java somewhere in the middle.  When using the original set of 13 files with both cmp and the new expanded java program, I get:

	cmp:	12/86
	Mapped:	24/86
	I/O:	54/86
	not eq:	5+5+5
	no file:10

Now it's harder to analyze the results as I now believe that at least two of those files are genuinely not equal and one is a different size and the pair of another has been deleted.  But there seems to still be a difference between the methods.

7) Downloaded a Fedora16 i686 live CD and after a lot of frustration built another bootable USB stick. No java on the stick.

		TempHome7		Original 13
	cmp:	93/95		cmp:	20/47
				no file:7

Not completely conclusive.  It sure started out good, but I kept running the tests and eventually it started to fail.  Eventually I had a system halt... it did say panic in the tiny tiny text but I don't really know what happened.

G) Could it be my 5 year old motherboard/CPU?

8) I ran one pass of the memtest from the Fedora17 x86_64 CD [Memtest86 v4.20] and it passed. But that's just mostly memory, right?

----

Ok, I know, too much data.  All I really know at the moment is that on Fedora17 x86_64 files that are probably equal almost never match w/ cmp and most of the time match with java I/O and about half of the time match with java memory mapped files.  It appears that cp can successfully copy a file that cmp won't match afterward.  I've had two partitions wiped out and several weird freezes and program failures since starting to use Fedora17.  It doesn't make sense to report any of these until I have confidence in my hardware and Fedora17's disk I/O.

Q1) So what do I try next? How can I help figure out what (if anything) is wrong?

Q2) Are there any CPU diagnostic test programs out there? disk I/O too?

Q3) I am using dialup so it takes about 2 1/2 days to download a CD-sized iso.  But if there's a Fedora version that I should try let me know.  

Q4) Any tools out there to attempt to resurrect my lost data [ext3 partition]? The live CD/USB systems just hang when I try and mount or dd copy or fsck the partition. 

Q5) I'm thinking of extracting the drive into a USB external case so perhaps the system won't hang when it gets confused.  Would that make a difference?

Version-Release number of selected component (if applicable):


How reproducible:
Very, given enough time.

Steps to Reproduce:
1. make a large file, perhaps dd from random around 1GB
2. cp it to another location
3. cmp the two, for more details see above
  
Actual results:
Sometimes equal, sometimes not equal, and at different locations

Expected results:
always equal

Additional info:
Pentium D x 2 3.4GHz extra L2 cache; 2GB DDR2 interleaved ram