From 33747c6ebc08368dc7de27fbba2c6672a7eb6f16 Mon Sep 17 00:00:00 2001
From: ChunjiangZhu <chunjiang.zhu@uconn.edu>
Date: Mon, 20 Jul 2020 11:40:30 -0400
Subject: [PATCH] add XSEDE HPC example

---
 README.md | 50 ++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 48 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 9f37a72..5e410e2 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# Welcome to Molecular Similarity Search Benchmark (MssBenchmark)!
+	# Welcome to Molecular Similarity Search Benchmark (MssBenchmark)!
 
 A molecular similarity search benchmark.
 
@@ -162,7 +162,7 @@ Command Examples:
 
     python plot.py --dataset=chembl-1024-jaccard -Y -x=range --rq --radius=0.4 -o=results/chembl-1024-jaccard-0_4
 
-# Executions under an HPC environment
+# Executions under an HPC environment (Example: UConn HPC)
 
 1. Load anaconda module
 
@@ -186,8 +186,10 @@ An example "run.sh":
 
     #!/bin/bash
     
+	#SBATCH --partition=HaswellPriority
     #SBATCH --ntasks=1
     #SBATCH --exclude=cn[65-69,71-136,325-343,345-353,355-358,360-364,369-398,400-401],gpu[07-10]
+	#SBATCH --exclusive
       
     
     module load anaconda/5.1.0
@@ -202,6 +204,49 @@ An example "run.sh":
     
       
     
+    python run.py --dataset=chembl-1024-jaccard --algorithm='Hnsw(Nmslib)' --count=100 --sif-dir="./singularity"  
+
+
+# Executions under an HPC environment (Example: XSEDE Comet HPC)
+
+1. Please download and install miniconda [1] [2] in your HOME directory on Comet
+
+    [1] https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
+	[2] https://docs.conda.io/en/latest/miniconda.html
+
+2. Create anaconda environment, and then install dependent libraries
+
+    conda create -c rdkit -n ann_env rdkit python=3.7.7
+	
+	source activate ann_env
+	
+    pip install -r singularity-install/requirements.txt
+	
+	source deactivate ann_env
+
+3. Run your algorithm scripts by SLURM shell
+
+    sbatch run.sh
+
+An example "run.sh":
+
+    #!/bin/bash
+    
+	#SBATCH --partition=compute
+	#SBATCH --no-requeue
+    #SBATCH --ntasks=1
+	#SBATCH --exclusive
+    #SBATCH -t 48:00:00
+      
+    
+    source activate ann_env
+    
+    module purge
+    
+    module load singularity/3.5
+    
+      
+    
     python run.py --dataset=chembl-1024-jaccard --algorithm='Hnsw(Nmslib)' --count=100 --sif-dir="./singularity"  
 
 
@@ -214,6 +259,7 @@ An example "plot.sh":
 
     #!/bin/bash
     
+	#SBATCH --partition=HaswellPriority
     #SBATCH --ntasks=1
     #SBATCH --exclude=cn[65-69,71-136,325-343,345-353,355-358,360-364,369-398,400-401],gpu[07-10]