Fix some defaults

ablab · Sep 21, 2024 · 9573ebf · 9573ebf
1 parent fcf0c5c
commit 9573ebf
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Showing 2 changed files with 15 additions and 26 deletions.
diff --git a/src/projects/spades/pipeline/spades_pipeline/executors/executor_slurm.py b/src/projects/spades/pipeline/spades_pipeline/executors/executor_slurm.py
@@ -16,7 +16,7 @@
 class Executor(executors.ExecutorCluster):
     grid_engine = "SLURM"
     grid_engine_submit_command = "sbatch"
-    grid_engine_slurm_args = "--hint=compute_bound --mem-bind=verbose,none --exclusive --cpus-per-task {NCPUS} --open-mode=append --kill-on-invalid-dep=yes --mem {MEMORY_MB}M --partition={PARTITION} --account={ACCOUNT} --qos={QOS}"
+    grid_engine_slurm_args = "--hint=compute_bound --mem-bind=verbose,none --cpus-per-task {NCPUS} --open-mode=append --kill-on-invalid-dep=yes --mem {MEMORY_MB}M --time {TIME} {EXTRA}"
     grid_engine_output_option = "-o {OUT}"
     grid_engine_err_output_option = "-e {ERR}"
     grid_engine_job_name = "--job-name {JOB_NAME}"
@@ -30,20 +30,16 @@ def join(self, job_name):
         log_file = options_storage.args.output_dir + "/spades.log"
         cmd = self.grid_engine_submit_command.format(COMMAND="true", JOB_NAME="wait", OUT=log_file, ERR=log_file, NCPUS=1)
         cmd += " " + self.grid_engine_dependency_option.format(WAIT_TAG=job_name)
-        cmd += " " + self.grid_engine_credentials.format(PARTITION=options_storage.args.grid_partition,
-                                                         ACCOUNT=options_storage.args.grid_account,
-                                                         QOS=options_storage.args.grid_qos,
-                                                         QUEUE=options_storage.args.grid_queue)
+        cmd += " " + self.grid_engine_credentials.format(QUEUE=options_storage.args.grid_queue)
         cmd += " --wait"
         support.sys_call(cmd, log=self.log)
 
     def get_MPI_sh_preambula(self):
         memory_mb = int(options_storage.args.memory * 1024)
         preambula = "SLURM_ARGS=\"" + self.grid_engine_slurm_args.format(NCPUS=options_storage.args.threads,
                                                                          MEMORY_MB=memory_mb,
-                                                                         PARTITION=options_storage.args.grid_partition,
-                                                                         ACCOUNT=options_storage.args.grid_account,
-                                                                         QOS=options_storage.args.grid_qos,
+                                                                         TIME=options_storage.args.grid_time,
+                                                                         EXTRA=options_storage.args.grid_extra,
                                                                          QUEUE=options_storage.args.grid_queue) + "\"\n"
         preambula += "MPIRUN_ARGS=\"" + self.grid_engine_mpirun_args.format(NCPUS=options_storage.args.threads) + "\"\n"
         log_file = options_storage.args.output_dir + "/spades.log"
@@ -99,9 +95,8 @@ def get_command(self, command, prev_id, mpi):
         memory_mb = int(options_storage.args.memory * 1024)
         cmd += self.grid_engine_slurm_args.format(NCPUS=options_storage.args.threads,
                                                   MEMORY_MB=memory_mb,
-                                                  PARTITION=options_storage.args.grid_partition,
-                                                  ACCOUNT=options_storage.args.grid_account,
-                                                  QOS=options_storage.args.grid_qos,
+                                                  TIME=options_storage.args.grid_time,
+                                                  EXTRA=options.storage.args.grid_extra,
                                                   QUEUE=options_storage.args.grid_queue) + " "
         cmd += self.grid_engine_job_name.format(JOB_NAME=command.job_uuid) + " "
         cmd += self.grid_engine_err_output_option.format(ERR=log_file) + " "

diff --git a/src/projects/spades/pipeline/spades_pipeline/options_parser.py b/src/projects/spades/pipeline/spades_pipeline/options_parser.py
@@ -811,7 +811,7 @@ def add_cluster_args(pgroup_cluster):
     pgroup_cluster.add_argument("--grid-queue",
                                 metavar="<string>",
                                 dest="grid_queue",
-                                default="mpi-rh74",
+                                default="standard",
                                 help="submits the jobs to one of the specified queues",
                                 action="store")
     pgroup_cluster.add_argument("--grid-nnodes",
@@ -825,22 +825,16 @@ def add_cluster_args(pgroup_cluster):
                                 dest="grid_wait",
                                 help="wait for job finish",
                                 action="store_true")
-    pgroup_cluster.add_argument("--grid-qos",
-                                dest="grid_qos",
-                                default="lr_normal",
-                                help="quality of service for the jobs (for SLURM grid engine)",
+    pgroup_cluster.add_argument("--grid-extra",
+                                dest="grid_extra",
+                                default="",
+                                help="any extra commands",
                                 metavar="<string>",
                                 action="store")
-    pgroup_cluster.add_argument("--grid-partition",
-                                dest="grid_partition",
-                                default="lr3",
-                                help="partition for the resource allocation (for SLURM grid enging)",
-                                metavar="<string>",
-                                action="store")
-    pgroup_cluster.add_argument("--grid-account",
-                                dest="grid_account",
-                                default="ac_scsguest",
-                                help="charge resources used by this run to specified account (for SLURM grid engine)",
+    pgroup_cluster.add_argument("--grid-time",
+                                dest="grid_time",
+                                default="1:00:00",
+                                help="time limit",
                                 metavar="<string>",
                                 action="store")