Every time we recompile our C# application we end up with EXEs with different MD5 signatures. We are recompiling on the same machine, minutes apart. Why doesn't the same source-code yield the same output? Is there a way to fix this?

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I guess you already have but... have you checked the manifest with IL DASM? – yeyeyerman Aug 26 '09 at 15:24
6 Answers
"So every assembly has:
- A Timestamp, in two locations
- A GUID that matched the PDB
- What appears to be a completely random GUID generated every compile.
- A counter indicating what the build of the assembly is - generated only in subsequent Visual Studio builds."
from:

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I think the key there might be "minutes apart". If there is a timestamp within the EXE, then that would alter the MD5 signature.

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I've never examined the EXE produced by the C# compiler, and I haven't touched C# in over a year. But it would explain everything nicely, and it makes sense. – Thomas Owens Aug 26 '09 at 15:19
I've had to dissect these cases before and it appears to just be DateTime-stamp type changes (it's a guess). If you put both assemblies under diff tools you'll see only a very small number of lines in the PE have changed; if you change even a small amount of code and compare assemblies you'll see drastically larger differences.
Here's a question I opened while researching tools to identify "real" differences from superficial ones:
Most likely you have several *'s in the version number of the assembly. This causes the assembly version number to be auto-incremented on build which will cause a visible difference in the outputted assembly. Hence a different MD5 checksum.
Try switching the version number to a constant assembly version and see if that fixes the issue.

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You could try running ildasm.exe (my path for this is C:\Program Files (x86)\Microsoft SDKs\Windows\v7.0A\bin
) on the two .exes.
Then dump out the raw view of the headers, and compare them with a diff tool. If there is still no difference, then it might be the PE headers which would need a more advanced tool to discover. Ildasm gives you the PE header size and other statistics on it though.

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There will be a built in version number that will change with every build.

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2Even if the assembly version is set statically to something like "1.0.0.0"? The only time a build-version should change is if you have it defined as "1.0.0.*" or manually change it, no? – STW Aug 26 '09 at 15:11