fix linking with -lcudart, should also include -lrt

[boegel]

@pescobar: this should fix the problem of building gzip with a goolfc toolchain

@ajdecon: does this make sense to you, i.e. is -lrt requires when linking with -lcudart, even for non-CUDA apps like gzip?

[boegel]

confirmed on my end that this fixes the problem

I would like to hear from @ajdecon why this is required though...

[ajdecon]

My impression was that this shouldn't be required, but my information might be wrong. Following up internally at NVIDIA to make sure I understand this. :)

[boegel]

@ajdecon: any updates?
Also note that it's (apparently) important that -lrt is listed before -lcudart, so it seems like libcudart is redefining some symbols and thus throwing off builds?

For future reference: these are the error message you run into when building gzip with a goolfc toolchain, without using -lrt before -lcudart:

gcc -std=gnu11   -O2 -march=native -Wl,--as-needed ... lib/libgzip.a  -lm -lcudart -lpthread
lib/libgzip.a(gettime.o): In function `gettime':
gettime.c:(.text+0xe): undefined reference to `clock_gettime'
collect2: error: ld returned 1 exit status

[ajdecon]

Still waiting on feedback from another engineer at NVIDIA. Sorry for the delays, we're all a little crazy right now due to our conference GTC next week. :)

I do suggest you check to see if a CUDA app such as Gromacs still builds correctly with this fix in place. If there are symbol conflicts between libcudart and librt, then I'd be concerned that this fix for non-CUDA builds might break CUDA apps.

[boegel]

I've tested a GROMACS build with the goolfc toolchain, adding -lrt before -lcudart doesn't break anything, so I'm merging this in.

Thanks @ajdecon for the responses!