Commit 003c20cf authored by Floreal Cabanettes's avatar Floreal Cabanettes
Browse files

Fix submit jobs cluster prepare

parent 8e62fecd
......@@ -356,22 +356,25 @@ class JobManager:
jt.outputPath = ":" + log_out
jt.errorPath = ":" + log_err
memory = self.config.cluster_memory
if self.query is None:
memory = self.config.cluster_memory_ava
if memory > 32:
name, order, contigs, reversed_c, abs_start, c_len = Index.load(self.idx_t, False)
if c_len <= 500000000:
memory = 32
if memory > self.tool.max_memory:
memory = self.tool.max_memory
if step == "start":
memory = self.config.cluster_memory
if self.query is None:
memory = self.config.cluster_memory_ava
if memory > 32:
name, order, contigs, reversed_c, abs_start, c_len = Index.load(self.idx_t, False)
if c_len <= 500000000:
memory = 32
if memory > self.tool.max_memory:
memory = self.tool.max_memory
else:
memory = 8000
native_specs = self.config.drmaa_native_specs
if batch_system_type == "slurm":
if native_specs == "###DEFAULT###":
native_specs = "--mem-per-cpu={0} --ntasks={1} --time={2}"
if step == "prepare":
jt.nativeSpecification = native_specs.format(8000, 1, "02:00:00")
jt.nativeSpecification = native_specs.format(memory, 1, "02:00:00")
elif step == "start":
jt.nativeSpecification = native_specs.format(memory // self.tool.threads_cluster * 1000,
self.tool.threads_cluster, "02:00:00")
......
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