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I'm trying to compile the following on 12.04 and I'm not sure how to approach it. There is no ./configure. I read online that I should use autogen.sh to generate the ./configure. Is this the right approach? I ran autogen and it's basically frozen in place and not doing anything.

There seems to be a kconfig file inside. But I'm not sure how that is different from configure..

https://github.com/torvalds/linux/tree/master/drivers/scsi/mpt3sas

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That directory is part of a full kernel source tree. The standard way to compile it is together with the rest of the kernel.

For some part of the tree it is possible to compile some module standalone --- but it s not a trivial task. You can look in this thread for a starting point.

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That is part of the kernel tree, and not a separate external module. It's to be built with the build of the kernel, depending on how the build is configured.

If you want to build that module for an older kernel, you need to build it in the context of the older kernel, as a module, and you may need to do quite some back-porting work on 12.04 as that tree is a clone of the current master tree, and not the kernel version that is available in 12.04.

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