Hi there,
I would like to run gatk SNP call in TACC stampede2 machine (https://portal.tacc.utexas.edu/user-guides/stampede2) and they have the KNL node equipped with Intel Xeon Phi 7250. This CPU is kinda special because "Stampede2's KNL nodes have 68 cores, each with 4 hardware threads".
Right now, the command I used is:
java -Djava.io.tmpdir=/tmp -jar $TACC_GATK_DIR/GenomeAnalysisTK.jar -nct 136 -R assembly_selfref_v2.fa -T UnifiedGenotyper ......
Basically, TACC support people told me that I should use 136 threads because "In most cases it's best to specify no more than 64-68 MPI tasks or independent processes per node, and 1‑2 threads/core."
However, I feel this would be a waste of resources because, supposedly, one KNL node would have 272 (68 x 4) hardware threads.
Does gatk has special parameters I can use to make full use of such machine? some combination of -nct and -nt ?
Thanks very much in advance!
