add hpcc

#std2.log#

@@ -0,0 +1,7 @@
+Sat Apr 11 22:19:25 PDT 2020
+folder: /rhome/wzeng002/working/github/belief-propagation
+hostname:
+i21
+/var/spool/slurmd/job976836/slurm_script: line 31: ./my_bp4.out: No such file or directory
+done sbatch
+Sat Apr 11 22:19:25 PDT 2020

gnuplot/result/my-bp4-iter-9-fb-5-data-500-schedule-3-hpcc.gnudat

@@ -0,0 +1,14 @@
+#header
+sizes: 13, 9, 5, 
+ p, P_c converge rate, zero error vectors, weight one error, weight 2 error
+0.199526	0.002400	50.000000	0.000000	0.000000	0.199526	0.043200	50.000000	0.000000	0.000000	0.199526	0.300800	50.000000	0.000000	0.000000	
+0.158489	0.002000	50.000000	0.000000	0.000000	0.158489	0.048800	50.000000	0.000000	0.000000	0.158489	0.377200	50.000000	0.000000	0.000000	
+0.125893	0.007200	50.000000	0.000000	0.000000	0.125893	0.094400	50.000000	0.000000	0.000000	0.125893	0.443200	50.000000	0.000000	0.000000	
+0.100000	0.017200	50.000000	0.000000	0.000000	0.100000	0.138400	50.000000	0.000000	0.000000	0.100000	0.518800	50.000000	0.000000	0.000000	
+0.079433	0.062400	50.000000	0.000000	0.000000	0.079433	0.228800	50.000000	0.000000	0.000000	0.079433	0.601600	50.000000	0.000000	0.000000	
+0.063096	0.123200	50.000000	0.000000	0.000000	0.063096	0.350800	50.000000	0.000000	0.000000	0.063096	0.700207	50.520000	0.000000	0.000000	
+0.050119	0.221200	50.000000	0.000000	0.000000	0.050119	0.478800	50.000000	0.000000	0.000000	0.050119	0.777438	55.360000	0.000000	0.000000	
+0.039811	0.360800	50.000000	0.000000	0.000000	0.039811	0.618800	50.000000	0.000000	0.000000	0.039811	0.841092	70.040000	0.000000	0.000000	
+0.031623	0.494000	50.000000	0.000000	0.000000	0.031623	0.723698	51.440000	0.000000	0.000000	0.031623	0.879500	84.680000	0.000000	0.000000	
+0.025119	0.630400	50.000000	0.000000	0.000000	0.025119	0.793450	55.120000	0.000000	0.000000	0.025119	0.920584	141.200000	0.000000	0.000000	
+0.019953	0.732921	51.440000	0.000000	0.000000	0.019953	0.855217	79.520000	0.000000	0.000000	0.019953	0.944091	220.600000	0.000000	0.000000	

my_bp4.c

@@ -28,12 +28,12 @@ int main(int argc, char **argv){
   //parser.get(filename_G,"filename_G");
 
   vector<future<int>> pool;
-  int cores=16;
+  int cores=32;
   vector<future<int>>::size_type pool_size = cores+2; //max number of threads, 15 with decreasing size for best performace
   std::chrono::milliseconds span (100);
   std::chrono::milliseconds final_thread_time (10000);//10 secs before prelimilary result print
   string filename_data;
-  filename_data="gnuplot/result/my-bp4-iter-9-fb-5-data-500-schedule-3.gnudat";
+  filename_data="gnuplot/result/my-bp4-iter-9-fb-5-data-500-schedule-3-hpcc.gnudat";
   int feedback=5;
   //  int cycles = 1000000;//70 sec for 2,000,000
   double time_out=200;//time out in seconds for each data points (p and size)
@@ -55,7 +55,8 @@ int main(int argc, char **argv){
   //split tasks into smaller chunks
   int chunk_num_data_points=10;//number of data points in each chunk
   int chunk_size=num_data_points/chunk_num_data_points;
-  double chunk_time_out = 20.0;//time_out/chunk_size;
+  //timeout should be 5 times longer in hpcc
+  double chunk_time_out = 100.0;//time_out/chunk_size;
   int chunk_cycles=chunk_num_data_points*1000;//1000 for prob 1/1000
 
   mat chunk_data(data_rows*chunk_size,5*5);

sbatch.sh

@@ -0,0 +1,36 @@
+#!/bin/bash -l
+
+#SBATCH --nodes=2
+#SBATCH --ntasks=2
+#SBATCH --cpus-per-task=32
+#SBATCH --mem-per-cpu=1G
+#SBATCH --time=0-00:30:00     # 1 day and 15 minutes
+#SBATCH --output=n1t2c32.log
+#SBATCH [email protected]
+#SBATCH --mail-type=ALL,TIME_LIMIT_80,TIME_LIMIT_90
+#SBATCH --job-name="n1t2c32"
+#SBATCH -p intel # This is the default partition, you can use any of the following; intel, batch, highmem, gpu
+
+
+# Print current date
+date
+
+# Load samtools
+module load itpp
+
+# Change directory to where you submitted the job from, so that relative paths resolve properly
+echo folder: $SLURM_SUBMIT_DIR
+cd $SLURM_SUBMIT_DIR
+
+
+# Print name of node
+echo hostname:
+hostname
+
+# . run_random_concatenation.sh $1
+./my_bp4.out &
+./my_bp4.out &
+wait
+
+echo done sbatch
+date

sbatch.sh~

@@ -0,0 +1,35 @@
+#!/bin/bash -l
+
+#SBATCH --nodes=2
+#SBATCH --ntasks=2
+#SBATCH --cpus-per-task=32
+#SBATCH --mem-per-cpu=1G
+#SBATCH --time=0-00:30:00     # 1 day and 15 minutes
+#SBATCH --output=n1t2c32.log
+#SBATCH [email protected]
+#SBATCH --mail-type=ALL,TIME_LIMIT_80,TIME_LIMIT_90
+#SBATCH --job-name="n1t2c32"
+#SBATCH -p intel # This is the default partition, you can use any of the following; intel, batch, highmem, gpu
+
+
+# Print current date
+date
+
+# Load samtools
+module load itpp
+
+# Change directory to where you submitted the job from, so that relative paths resolve properly
+echo folder: $SLURM_SUBMIT_DIR
+cd $SLURM_SUBMIT_DIR
+
+
+# Print name of node
+echo hostname:
+hostname
+
+# . run_random_concatenation.sh $1
+./my_bp4.out &
+./my_bp4.out &
+
+echo done sbatch
+date

status.sh

@@ -0,0 +1,14 @@
+date
+squeue -u $USER --start
+#slurm_limits
+group_cpus
+jobID=976834
+jobID=976851
+jobID=976860
+jobID=976865
+jobID=976879
+jobID=976895
+jobID=976899
+scontrol show job $jobID
+#sacct -u $USER -l >>temp.log
+#sacct -u $USER -S 2018-01-01 -E 2018-08-30 -l | less -S # Type 'q' to quit

status.sh~

@@ -0,0 +1,14 @@
+date
+squeue -u $USER --start
+#slurm_limits
+group_cpus
+jobID=976834
+jobID=976851
+jobID=976860
+jobID=976865
+jobID=976879
+jobID=976895
+jobID=976897
+scontrol show job $jobID
+#sacct -u $USER -l >>temp.log
+#sacct -u $USER -S 2018-01-01 -E 2018-08-30 -l | less -S # Type 'q' to quit