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--- expanse [2021/08/20 09:07] – created edit
+++ expanse [2021/08/22 18:49] (current) – edit
@@ Line 4: / Line 4: @@
 \\
 Example files for equilibrium run (first-dyn.csh and first-dyn.scr) and production run (dyn.csh, dyn.scr, dyn-1.inp, and dyn-2.inp) could be found as follows:\\
-For **CPU** nodes @ /expanse/lustre/scratch/mkhsieh/temp_project/namd_run/cpu/ \\
+For **CPU** nodes @ /home/mkhsieh/script/namd_run/cpu/ \\
+OR download {{ :cpu.tgz |}} \\
 Note: \\
 Each standard compute node has ~256 GB of memory and 128 cores \\
@@ Line 10: / Line 11: @@
 \\
 Example of SBATCH lines
 <code>
 #SBATCH --job-name=your_job_name
 #SBATCH --account=**ask Dr. Klauda**
@@ Line 18: / Line 19: @@
 #SBATCH --cpus-per-task=1
 #SBATCH --mem=64G
+#SBATCH --time=48:00:00
 </code>
+Example of execution line \\
-For **GPU** nodes @ /expanse/lustre/scratch/mkhsieh/temp_project/namd_run/gpu \\
+<code>
+namd2 +p32 +setcpuaffinity dyn.inp >& dyn.out
+</code>
+For **GPU** nodes @ /home/mkhsieh/script/namd_run/gpu \\
+OR download {{ :gpu.tgz |}} \\
 Note: \\
 Each GPU node has 4 GPUs,  ~384GB of memory and 40 cores \\
 Default resource allocation for 1 GPU =  1 GPU, 1 CPU, and 1G of memory,  users will need to explicitly ask for additional resources in their job script. \\
 For max memory on a GPU node, users should request --mem = 374G; A GPU SU is equivalent to 1GPU, <10CPUs, and <96G of memory. \\
+\\
+Example of SBATCH lines \\
 <code>
 #SBATCH --job-name=your_job_name
@@ Line 36: / Line 44: @@
 #SBATCH --time=48:00:00
 </code>
+Example of execution line \\
+<code>
+mpirun --mca btl_openib_allow_ib true -np 1 --map-by ppr:1:node namd2 +ppn10 +setcpuaffinity +devices 0 dyn.inp >& dyn.out
+</code>