Multiple thread not working!

[xiekunwhy]

Hi,

I found that spaln -t option does'nt work (like following screenshot, -t20 using only 1 cpu).

Best,
Kun

[ogotoh]

Make sure that you 'Makefile' has the following lines and they are not commented out:

DEFLT = -DM_THREAD=1

CXX := $(CXX) $(CFLAGS) $(DEFLT)

Osamu,

[xiekunwhy]

yes, not commented out, but not work.

[ogotoh]

Please confirm two points.

1. The complier message looks like:
   g++ -O3 -march=native -DM_THREAD=1 -c blksrc.cc
   ...

2. The max number of threads that your system supports.

If possible, please try to run on other computer system that you can access.

Osamu,

[xiekunwhy]

By the way, the latest bioconda version of spaln always segmentation fault when running tsv to genome alignment. Ignore this problem if you are not the maintainer of bioconda version.

[ogotoh]

Dear Kun,

I don't know who maintains bioconda version. It is true that earlier versions of Spaln cause segmentation fault under some specific conditiosns. You may know the version number by running Spaln with -h option.

Osamu,