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ogotoh / spaln

Genome mapping and spliced alignment of cDNA or amino acid sequences
GNU General Public License v2.0
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Multiple thread not working! #76

Open xiekunwhy opened 3 weeks ago

xiekunwhy commented 3 weeks ago

Hi,

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

Best, Kun

ogotoh commented 2 weeks ago

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 commented 2 weeks ago

yes, not commented out, but not work. image

ogotoh commented 2 weeks ago

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 commented 2 weeks ago

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 commented 2 weeks ago

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,