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mourisl / centrifuger

Classifier for metagenomic sequences using FM-index with run-block compressed BWT.
MIT License
51 stars 4 forks source link

how to install using pthreads under Linux (ubuntu 24.04) #7

Closed koppk closed 6 months ago

koppk commented 6 months ago

Could you please explain how to install centrifuger using pthreads? Thanks

mourisl commented 6 months ago

I think pthreads comes with the LInux release. What is the error message you received when running "make" in Centrifuger folder?

koppk commented 6 months ago

Hi, thanks. No error message but plenty of warnings during make. Please, see attached file. make_stdout.txt

koppk commented 6 months ago

This did the trick:

  1. install the respective ubuntu 24.04 package: sudo apt-get install libpthread-stubs0-dev
  2. build within the centrifuger folder: make
  3. execute centrifuge and check numbers of threads used after identifying the process ID (PID) with: top ps hH p | wc -l
mourisl commented 6 months ago

Those warning messages should be fine. I did not get warnings on our server, but this is probably a gcc version thing. I saw those warnings on the github action. I will clean those up in the next release (or just change the gcc warning flags).