update slurm template and tunnel/mysql config

experimentation/.myconfig.dist

@@ -1,4 +1,5 @@
 host=<server>
+port=tunnel
 user=stree
 password=<password>
 database=stree_experiments

experimentation/.tunnel.dist

@@ -1,4 +1,5 @@
 ssh_address_or_host=(<host>, <port>)
 ssh_username=<user>
 ssh_private_key=<path_to>/id_rsa
-remote_bind_address=('127.0.0.1', 3306)
+remote_bind_address=('127.0.0.1', 3306)
+enabled=1

experimentation/Database.py

@@ -13,14 +13,13 @@ from .Utils import TextColor
 class MySQL:
     def __init__(self):
         self._server = None
-
-    def get_connection(self):
-        config_db = dict()
+        self._tunnel = False
+        self._config_db = dict()
         dir_path = os.path.dirname(os.path.realpath(__file__))
         with open(os.path.join(dir_path, ".myconfig")) as f:
             for line in f.read().splitlines():
                 key, value = line.split("=")
-                config_db[key] = value
+                self._config_db[key] = value
         config_tunnel = dict()
         with open(os.path.join(dir_path, ".tunnel")) as f:
             for line in f.read().splitlines():
@@ -32,11 +31,17 @@ class MySQL:
         config_tunnel["ssh_address_or_host"] = make_tuple(
             config_tunnel["ssh_address_or_host"]
         )
-        self._server = SSHTunnelForwarder(**config_tunnel)
-        self._server.daemon_forward_servers = True
-        self._server.start()
-        config_db["port"] = self._server.local_bind_port
-        self._database = mysql.connector.connect(**config_db)
+        self._tunnel = config_tunnel["enabled"] == "1"
+        if self._tunnel:
+            del config_tunnel["enabled"]
+            self._server = SSHTunnelForwarder(**config_tunnel)
+            self._server.daemon_forward_servers = True
+
+    def get_connection(self):
+        if self._tunnel:
+            self._server.start()
+            self._config_db["port"] = self._server.local_bind_port
+        self._database = mysql.connector.connect(**self._config_db)
         return self._database
 
     def find_best(self, dataset, classifier="any"):
@@ -60,7 +65,8 @@ class MySQL:
         return cursor.fetchone()
 
     def close(self):
-        self._server.close()
+        if self._tunnel:
+            self._server.close()
 
 
 class BD(ABC):

scripts/experiment.slurm

@@ -1,13 +1,11 @@
 #!/bin/bash
 
-#SBATCH --time=96:00:00   # walltime
+#SBATCH --partition=qdata
 #SBATCH --ntasks=4   # number of processor cores (i.e. tasks)
 #SBATCH --nodes=1   # number of nodes
-#SBATCH --mem-per-cpu=4096M   # memory per CPU core
 #SBATCH -J "<experiment>-<data>-<model>-<kernel>"   # job name
 #SBATCH --mail-user=ricardo.montanana@alu.uclm.es   # email address
-#SBATCH --mail-type=END
-#SBATCH --mail-type=FAIL
+#SBATCH --mail-type=END,FAIL
 
 # LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE
 cd <folder>

scripts/launchsome.sh

@@ -1,10 +1,11 @@
 #!/bin/bash
-if [ "$1" = "" -o "$2" = "" -o "$3" = "" -o "$4" = "" ] ; then
+if [ "$1" = "" -o "$2" = "" -o "$3" = "" -o "$4" = "" -o "$5" = "" ] ; then
 	echo "Hay que seleccionar:"
     echo " - el tipo de experimento {gridsearch, gridbest, cross}"
     echo " - el modelo {stree, adaBoost, bagging, odte}"
     echo " - el kernel {linear, poly, rbf, any}"
 	echo " - el archivo con nombres de datasets"
+	echo " - el tipo de plataforma {pbs, slurm}"
 	echo "opcionalmente al final: dry-run"
 	exit 1
 fi
@@ -20,16 +21,25 @@ if [[ ! "linearpolyrbfany"  == *$3* ]] ; then
 	echo "Hay que seleccionar el kernel {linear, poly, rbf, any}"
 	exit 1
 fi
+if [[ ! "pbsslurm"  == *$4* ]] ; then
+	echo "Hay que especificar la plataforma {pbs, slurm}"
+	exit 1
+fi
+if [ $4 = "pbs" ] ; then
+	launcher="qsub"
+else
+	launcher="sbatch"
+fi
 script_path="$(pwd)"
 cd $1/$2/$3
 counter=0
-lines="$(cat $script_path/$4|cut -d " " -f 2|tail -49)"
+lines="$(cat $script_path/$5|cut -d " " -f 2|tail -49)"
 for a in $lines; do
 	echo "launch experiment_$a.sh"
 	if [ "$5" = "dry-run" ] ; then
 		echo "not launched"
 	else
-		qsub experiment_$a.sh
+		$launcher experiment_$a.sh
 	fi
 	let counter++
 done