fixed error in scaling for measurements

README.md

@@ -42,6 +42,19 @@ Using a kdtree with a sorted length list and length dependant search radius the
 
 ### Running remotely
 
-to get the data from the baptiste's grid run 
+to get the data from the baptiste's grid run
 
     scp -r leo@10.30.128.49:/home/leo/gitrepos/networksim-cntfet/data /home/leo/Desktop/
+
+### Running on heisenberg
+put the srun script into a seperate directory for the data runtime
+then edit the number of cores for the measure_perc.py to match the number of tasks in the SBATCH section
+then run:
+
+    sbatch srun.sh
+
+To check on the job, use:
+
+    squeue -o "%.18i %.9P %.8j %.8u %.2t %.8M %.5D %.4C %R"
+
+usage of `squeue` found [here](https://slurm.schedmd.com/squeue.html)

measure_perc.py

@@ -11,7 +11,7 @@ def checkdir(directoryname):
     pass
 
 
-def measure_fullnet(n,scaling=60, l='exp', save=False, v=True ,remote=False):
+def measure_fullnet(n,scaling, l='exp', save=False, v=True ,remote=False):
     start = timer()
     data=pd.DataFrame(columns = ['sticks', 'size', 'density', 'nclust', 'maxclust', 'ion', 'ioff','ioff_totaltop', 'ioff_partialtop', 'runtime', 'fname'])
     try:
@@ -94,11 +94,11 @@ def measure_number_series_compareL(remote=True):
     pool = Pool(os.cpu_count()-1)
     pool.map(n_vary_expL_remote, nexp)
     pool.map(n_vary_066L_remote, nconst)
-def measure_async(cores,start,step,number,save=False):
+def measure_async(cores,start,step,number,scaling,save=False):
     starttime = timer()
     nrange=[start+i*step for i in range(number)]
     pool=Pool(cores)
-    results=[pool.apply_async(measure_fullnet,args=(n,5,'exp',save)) for n in nrange]
+    results=[pool.apply_async(measure_fullnet,args=(n,scaling,'exp',save)) for n in nrange]
     output=[res.get() for res in results]
     endtime = timer()
     runtime=endtime - starttime
@@ -114,9 +114,10 @@ def measure_async(cores,start,step,number,save=False):
     parser.add_argument("--start",type=int)
     parser.add_argument("--step",type=int,default=0)
     parser.add_argument("--number",type=int)
+    parser.add_argument("--scaling",type=int,default=5)
     args = parser.parse_args()
     checkdir('data')
     if args.test:
         measure_async(2,500,0,10,save=True)
     else:
-        measure_async(args.cores, args.start, args.step, args.number, args.save)
+        measure_async(args.cores, args.start, args.step, args.number,args.scaling, args.save)

srun.sh

@@ -1,12 +1,9 @@
 #!/bin/bash
-
 #SBATCH -N 1      # nodes requested
-#SBATCH -n 2     # tasks requested
+#SBATCH -n 32     # tasks requested. default is one core per task
 #SBATCH -o outfile  # send stdout to outfile
 #SBATCH -e errfile  # send stderr to errfile
-#SBATCH -t 0:01:00  # time requested in hour:minute:second
+#SBATCH -t 10:00:00  # time requested in hour:minute:second
 #SBATCH --mem-per-cpu=1024
 #SBATCH --mail-user=$USER@localhost
-
-python3 ~/gitrepos/networksim-cntfet/measure_perc.py -t
-
+python3 ~/gitrepos/networksim-cntfet/measure_perc.py -s --cores 32 --start 36000 --step 0 --number 32 --scaling 60