Rename references to master branch

applications/plexos-hpc-walkthrough/RunFiles/enhanced

@@ -42,7 +42,7 @@ module purge
 module load centos mono/$MONO_VERSION xpressmp/$XPRESSMP_VERSION plexos/$PLEXOS_VERSION
 
 # Get our data
-wget https://github.nrel.gov/tkaiser2/plexos/raw/master/week.tgz
+wget https://github.nrel.gov/tkaiser2/plexos/raw/code-examples/week.tgz
 tar -xzf week.tgz
 
 # What we have

applications/plexos-hpc-walkthrough/RunFiles/simple

@@ -27,7 +27,7 @@ module purge
 module load centos mono/$MONO_VERSION xpressmp/$XPRESSMP_VERSION plexos/$PLEXOS_VERSION
 
 # Get our data
-wget https://github.nrel.gov/tkaiser2/plexos/raw/master/week.tgz
+wget https://github.nrel.gov/tkaiser2/plexos/raw/code-examples/week.tgz
 tar -xzf week.tgz
 ls -lt
 

applications/plexos-quick-start/README.md

@@ -74,12 +74,12 @@ or just copy them from this page
 or
 
 ```bash
-wget https://github.nrel.gov/raw/tkaiser2/plexos/master/scripts/enhanced
+wget https://github.nrel.gov/raw/tkaiser2/plexos/code-examples/scripts/enhanced
 ```
 
 and
 ```bash
-wget https://github.nrel.gov/raw/tkaiser2/plexos/master/scripts/simple
+wget https://github.nrel.gov/raw/tkaiser2/plexos/code-examples/scripts/simple
 ```
 
 ## To run:
@@ -88,7 +88,7 @@ If you have never run Plexos on Eagle you will need to set up the license.
 There is a script to do that.  Download it and run it.
 
 ```bash
-wget https://github.nrel.gov/raw/tkaiser2/plexos/master/scripts/makelicense
+wget https://github.nrel.gov/raw/tkaiser2/plexos/code-examples/scripts/makelicense
 chmod 700 makelicense
 ./makelicense
 ```
@@ -146,7 +146,7 @@ module purge
 module load centos mono/$MONO_VERSION xpressmp/$XPRESSMP_VERSION plexos/$PLEXOS_VERSION
 
 # Get our data
-wget https://github.nrel.gov/tkaiser2/plexos/raw/master/week.tgz
+wget https://github.nrel.gov/tkaiser2/plexos/raw/code-examples/week.tgz
 tar -xzf week.tgz
 ls -lt
 
@@ -209,7 +209,7 @@ module purge
 module load centos mono/$MONO_VERSION xpressmp/$XPRESSMP_VERSION plexos/$PLEXOS_VERSION
 
 # Get our data
-wget https://github.nrel.gov/tkaiser2/plexos/raw/master/week.tgz
+wget https://github.nrel.gov/tkaiser2/plexos/raw/code-examples/week.tgz
 tar -xzf week.tgz
 
 # What we have

applications/spark/README.md

@@ -190,7 +190,7 @@ CPUs and are not bottle-necked by the storage.
 
 Here is an example of how to run `htop` on multiple nodes simulataneously with `tmux`.
 
-Download this script: https://raw.githubusercontent.com/johnko/ssh-multi/master/bin/ssh-multi
+Download this script: https://raw.githubusercontent.com/johnko/ssh-multi/code-examples/bin/ssh-multi
 
 Run it like this:
 ```

applications/vasp/Performance Study 2/README.md

@@ -1,4 +1,4 @@
-A study was performed to evaluate the performance on VASP on Swift and Eagle using [ESIF VASP Benchmarks](https://github.com/NREL/ESIFHPC3/tree/master/VASP) 1 and 2. Benchmark 1 is a system of 16 atoms (Cu<sub>4</sub>In<sub>4</sub>Se<sub>8</sub>), and Benchmark 2 is a system of 519 atoms (Ag<sub>504</sub>C<sub>4</sub>H<sub>10</sub>S<sub>1</sub>). 
+A study was performed to evaluate the performance on VASP on Swift and Eagle using [ESIF VASP Benchmarks](https://github.com/NREL/ESIFHPC3/tree/code-examples/VASP) 1 and 2. Benchmark 1 is a system of 16 atoms (Cu<sub>4</sub>In<sub>4</sub>Se<sub>8</sub>), and Benchmark 2 is a system of 519 atoms (Ag<sub>504</sub>C<sub>4</sub>H<sub>10</sub>S<sub>1</sub>). 
 
 On Swift, the default builds of VASP installed on the system as modules were used. The Intel MPI build was built with Intel compilers and the mkl math library, and it was accessed via the "vaspintel" module. The OpenMPI build was compiled with gnu using gcc and fortran compilers and used OpenMPI's math libraries, and was accessed via the "vasp" module. Both builds run VASP 6.1.1.
 
@@ -22,9 +22,9 @@ Running the OpenACC GPU build of VASP (vasp_gpu) on GPU nodes improves performan
 
    * Memory limitation: GPU nodes on Eagle cannot provide as much memory as CPU nodes for VASP jobs, and large VASP jobs may require more GPU nodes to provide enough memory for the calculation. For Benchmark 2, at least 2 full nodes were needed to provide enough memory to complete a calculation. Using more complicated parallelization schemes, the number of nodes necessary to provide enough memory scaled with the increase in number of problems handled simultaneousely. 
 
-![Eagle GPU Bench 2](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Eagle_GPU_2.png)
+![Eagle GPU Bench 2](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Eagle_GPU_2.png)
 
-![Eagle GPU Bench 1 4x4x2](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Eagle_GPU_1_4x4x2.png)
+![Eagle GPU Bench 1 4x4x2](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Eagle_GPU_1_4x4x2.png)
 
 ### MPI
 
@@ -33,7 +33,7 @@ Intel MPI is recommended over Open MPI. Using an Intel MPI build of VASP and run
 Find scripts for running the Intel MPI and Open MPI builds of VASP in [this section](#Scripts-for-Running-VASP-on-Eagle).
 
 ### --cpu-bind Flag
-The --cpu-bind flag changes how tasks are assigned to cores throughout the node. Setting --cpu-bind=cores or rank showed no improvement in the performance of VASP on 36 CPUs/node. When running on 18 CPUs/node, setting --cpu-bind=cores shows a small improvement in runtime (~5% decrease) using both Intel MPI and Open MPI. (See [cpu-bind analysis](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/cpu-bind%20data/cpu-bind_VASP.ipynb) for info on the effect of cpu-bind)
+The --cpu-bind flag changes how tasks are assigned to cores throughout the node. Setting --cpu-bind=cores or rank showed no improvement in the performance of VASP on 36 CPUs/node. When running on 18 CPUs/node, setting --cpu-bind=cores shows a small improvement in runtime (~5% decrease) using both Intel MPI and Open MPI. (See [cpu-bind analysis](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/cpu-bind%20data/cpu-bind_VASP.ipynb) for info on the effect of cpu-bind)
 
 cpu-bind can be set as a flag in an srun command, such as 
 ```
@@ -52,9 +52,9 @@ KPAR determines the number of groups across which to divide calculations at each
 Runtime does not scale well with the number of kpoints. Benchmark 1 uses a 10x10x5 kpoints grid (500 kpoints). When run with a 4x4x2 kpoints grid (16 kpoints), we should expect the runtime to scale by 16/500 (3.2%) since calculations are being performed at 16 points rather than 500. However, the average scaling factor between Benchmark 1 jobs on Eagle with 10x10x5 grids and 4x4x2 grids is 28% (ranging from ~20%-57%). 
 
 ### Scripts for Running VASP on Eagle
-  * [VASP on Eagle with Intel MPI](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/VASP%20scripts/Eagle_IntelMPI.slurm)
-  * [VASP on Eagle with Open MPI](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/VASP%20scripts/Eagle_OpenMPI.slurm)
-  * [VASP on Eagle on GPUs with OpenACC GPU build using Intel MPI](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/VASP%20scripts/Eagle_OpenACC_GPU.slurm)
+  * [VASP on Eagle with Intel MPI](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/VASP%20scripts/Eagle_IntelMPI.slurm)
+  * [VASP on Eagle with Open MPI](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/VASP%20scripts/Eagle_OpenMPI.slurm)
+  * [VASP on Eagle on GPUs with OpenACC GPU build using Intel MPI](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/VASP%20scripts/Eagle_OpenACC_GPU.slurm)
 
 ## Swift
 
@@ -70,11 +70,11 @@ The graphs below are meant to help users identify the number of CPUs/node that w
 
 Intel MPI, performance/core  |  Intel MPI, performance/node
 :-------------------------:|:-------------------------:
-![](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Swift_2_Intel_Cores.png) |  ![](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Swift_2_Intel_Nodes.png)
+![](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Swift_2_Intel_Cores.png) |  ![](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Swift_2_Intel_Nodes.png)
 
 Open MPI, performance/core  |  Open MPI, performance/node 
 :-------------------------:|:-------------------------:
-![](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Swift_2_Open_Cores.png)  |  ![](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Swift_2_Open_Nodes.png)
+![](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Swift_2_Open_Cores.png)  |  ![](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Swift_2_Open_Nodes.png)
 
 ### MPI
 
@@ -84,7 +84,7 @@ Find scripts for running the Intel MPI and Open MPI builds of VASP in [this sect
 
 ### --cpu-bind Flag
 
-The --cpu-bind flag changes how tasks are assigned to cores throughout the node. On Swift, it is recommended not to use cpu-bind. Running VASP on 64 CPUs/node and 128 CPUs/node, setting --cpu-bind=cores or rank showed no improvement in runtime. Running VASP on 32 CPUs/node, setting --cpu-bind=cores or rank increased runtime by up to 40%. (See [cpu-bind analysis](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/cpu-bind%20data/cpu-bind_VASP.ipynb) for info on the effect of cpu-bind)
+The --cpu-bind flag changes how tasks are assigned to cores throughout the node. On Swift, it is recommended not to use cpu-bind. Running VASP on 64 CPUs/node and 128 CPUs/node, setting --cpu-bind=cores or rank showed no improvement in runtime. Running VASP on 32 CPUs/node, setting --cpu-bind=cores or rank increased runtime by up to 40%. (See [cpu-bind analysis](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/cpu-bind%20data/cpu-bind_VASP.ipynb) for info on the effect of cpu-bind)
 
 ```
 srun --cpu-bind=cores vasp_std
@@ -102,17 +102,17 @@ KPAR determines the number of groups across which to divide calculations at each
 
 KPAR = 1  |  KPAR = 4
 :-------------------------:|:-------------------------:
-![](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Swift_1_K1_N4.png) |  ![](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Swift_1_K4_N4.png)
+![](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Swift_1_K1_N4.png) |  ![](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Swift_1_K4_N4.png)
 KPAR = 8   |  KPAR = 9
-![](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Swift_1_K8_N4.png) |  ![](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/Images/Swift_1_K9_N4.png)
+![](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Swift_1_K8_N4.png) |  ![](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/Images/Swift_1_K9_N4.png)
 
 
 ### K-Points Scaling 
 
 Runtime does not scale well with the number of kpoints. Benchmark 1 uses a 10x10x5 kpoints grid (500 kpoints). When run with a 4x4x2 kpoints grid (16 kpoints), we should expect the runtime to scale by 16/500 (3.2%) since calculations are being performed at 16 points rather than 500. However, the average scaling factor between Benchmark 1 jobs on Swift with 10x10x5 grids and 4x4x2 grids is 28% (ranging from ~19%-39%).
 
 ### Scripts for Running VASP on Swift
-  * [VASP on Swift with Intel MPI](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/VASP%20scripts/Swift_IntelMPI.slurm)
-  * [VASP on Swift with Open MPI](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/VASP%20scripts/Swift_OpenMPI.slurm)
-  * [VASP on Swift with Shared Nodes using Intel MPI](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/VASP%20scripts/Swift_IntelMPI_shared_nodes.slurm)
-  * [VASP on Swift with Shared Nodes using Open MPI](https://github.com/NREL/HPC/blob/master/applications/vasp/Performance%20Study%202/VASP%20scripts/Swift_OpenMPI_shared_nodes.slurm)
+  * [VASP on Swift with Intel MPI](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/VASP%20scripts/Swift_IntelMPI.slurm)
+  * [VASP on Swift with Open MPI](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/VASP%20scripts/Swift_OpenMPI.slurm)
+  * [VASP on Swift with Shared Nodes using Intel MPI](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/VASP%20scripts/Swift_IntelMPI_shared_nodes.slurm)
+  * [VASP on Swift with Shared Nodes using Open MPI](https://github.com/NREL/HPC/blob/code-examples/applications/vasp/Performance%20Study%202/VASP%20scripts/Swift_OpenMPI_shared_nodes.slurm)

applications/vasp/Performance Study 2/VASP Performance Analysis/VASP_Recommendations_Analysis.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# VASP Recommendations Analysis\n",
     "\n",
-    "In this study, the ESIF VASP Benchmarks (https://github.com/NREL/ESIFHPC3/tree/master/VASP) 1 and 2 were used. Benchmark 1 is a system of 16 atoms (Cu<sub>4</sub>In<sub>4</sub>Se<sub>8</sub>), and Benchmark 2 is a system of 519 atoms (Ag<sub>504</sub>C<sub>4</sub>H<sub>10</sub>S<sub>1</sub>). \n",
+    "In this study, the ESIF VASP Benchmarks (https://github.com/NREL/ESIFHPC3/tree/code-examples/VASP) 1 and 2 were used. Benchmark 1 is a system of 16 atoms (Cu<sub>4</sub>In<sub>4</sub>Se<sub>8</sub>), and Benchmark 2 is a system of 519 atoms (Ag<sub>504</sub>C<sub>4</sub>H<sub>10</sub>S<sub>1</sub>). \n",
     "\n",
     "On Swift, the default builds of VASP installed on the system as modules were used. The Intel MPI build was built with Intel compilers and the mkl math library, and it was accessed via the \"vaspintel\" module. The OpenMPI build was compiled with gnu using gcc and fortran compilers and used OpenMPI's math libraries, and was accessed via the \"vasp\" module. Both builds run VASP 6.1.1. \n",
     "\n",

applications/vasp/Performance Study 2/cpu-bind data/cpu-bind_VASP.ipynb

@@ -4,13 +4,13 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this study, the ESIF VASP Benchmark 2 (https://github.com/NREL/ESIFHPC3/tree/master/VASP/bench2) was used to study how the cpu-bind flag affects the way that tasks are assigned to cores throughout the node over the runtime of a VASP job on Swfit and Eagle. Benchmark 1 is a system of 16 atoms (Cu4In4Se8), and Benchmark 2 is a system of 519 atoms (Ag504C4H10S1).\n",
+    "In this study, the ESIF VASP Benchmark 2 (https://github.com/NREL/ESIFHPC3/tree/code-examples/VASP/bench2) was used to study how the cpu-bind flag affects the way that tasks are assigned to cores throughout the node over the runtime of a VASP job on Swfit and Eagle. Benchmark 1 is a system of 16 atoms (Cu4In4Se8), and Benchmark 2 is a system of 519 atoms (Ag504C4H10S1).\n",
     "\n",
     "On Swift, the default builds of VASP installed on the system as modules were used. The Intel MPI build was built with Intel compilers and the mkl math library, and it was accessed via the \"vaspintel\" module. The OpenMPI build was compiled with gnu using gcc and fortran compilers and used OpenMPI's math libraries, and was accessed via the \"vasp\" module. Both builds run VASP 6.1.1.\n",
     "\n",
     "On Eagle, the default build of VASP installed on the system is an Intel MPI version of VASP. The Intel MPI build was built with Intel compilers and the mkl math library, and it was accessed via the \"vasp\" module. It runs VASP 6.1.2. No Open MPI VASP build is accessible through the default modules on Eagle, but an Open MPI build can be accessed in an environment via \"source /nopt/nrel/apps/210830a/myenv.2108301742, ml vasp/6.1.1-l2mkbb2\". The OpenMPI build was compiled with gnu using gcc and fortran compilers and used OpenMPI's math libraries. It runs VASP 6.1.1.\n",
     "\n",
-    "The VASP repo (https://github.com/claralarson/HPC/tree/master/applications/vasp/VASP%20Recommendations) contains scripts that can be used to run the Intel MPI and Open MPI builds used in the study to perform calculations on Swift and Eagle.\n",
+    "The VASP repo (https://github.com/claralarson/HPC/tree/code-examples/applications/vasp/VASP%20Recommendations) contains scripts that can be used to run the Intel MPI and Open MPI builds used in the study to perform calculations on Swift and Eagle.\n",
     "\n",
     "The cpu-bind flag can be set in the srun command as follows:\n",
     "> srun --cpu-bind=cores vasp_std\n",