From f162dabe86773378fb94980b6e3204293f7769e2 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Thu, 12 Sep 2024 18:12:42 -0400 Subject: [PATCH] remove GC thread settings since that likely wasn't correcting the problem --- workflow/rules/common.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 52fac0f..e6b7ad0 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -260,7 +260,7 @@ def get_stains(wildcards): # bigstitcher def get_fiji_launcher_cmd(wildcards, output, threads, resources): launcher_opts_find = "-Xincgc" - launcher_opts_replace = f"-XX:+UseG1GC -verbose:gc -XX:+PrintGCDateStamps -XX:ActiveProcessorCount={threads} -XX:ParallelGCThreads={int(threads/2)} -XX:ConcGCThreads={int(threads/4)}" + launcher_opts_replace = f"-XX:+UseG1GC -verbose:gc -XX:+PrintGCDateStamps -XX:ActiveProcessorCount={threads}" pipe_cmds = [] pipe_cmds.append("ImageJ-linux64 --dry-run --headless --console") pipe_cmds.append(f"sed 's/{launcher_opts_find}/{launcher_opts_replace}'/")