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I am trying to use OpenACC to accelerate the Samtools package by inserting pragmas at the applicable for loops. 

linux86-64/19.4/bin/pgcc -acc autopar -ta=tesla config.h stats.c

I get the following error message:

stats.c:
PGC-F-0206-Can't find include file config.h (stats.c: 41)
PGC/x86-64 Linux 19.4-0: compilation aborted

I checked and the config.h file is in the same directory as the stats.c file. So I'm not sure how to resolve this error so that I can GPU accelerate samtools.

I've also tried to install samtools after adding the pragmas to the stats.c program but I am not seeing a difference in acceleration. I also check if GPU is being utilized during the run, for instance when I use samtools sort and no GPUs appear to be used.

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  • I've fixed the formatting on your question. Please make a note of how I did this so you can do it yourself in the future. Commented Jun 7, 2019 at 23:33
  • You never compile .h files, they are only #included. It seems like your problem is figuring out how to use C, not how to use OpenACC. I'd suggest trying to reformulate your question around that or searching on include/compile terms without worrying about OpenAcc. Commented Jun 7, 2019 at 23:35
  • Possible duplicate of How do header and source files in C work? Commented Jun 7, 2019 at 23:36
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