fixing merge

markcmiller86 · markcmiller86 · commit 5ab9bca41c50 · 2017-08-07T08:04:10.000-07:00
diff --git a/lessons/atpesc-instructions.md b/lessons/atpesc-instructions.md
@@ -1,7 +1,7 @@
 
-# Instructions for Numerical Package Hands-on
+# Instructions for Numerical Package Hands-on Setup (ATPESC 2017)
 
-ATPESC participants will work in groups of 2 for hands-on exercises.  Forming groups of 2 helps us to cut in half the number of IT issues that may arise during hands-on exercises.  Moreover, [pair programming](https://en.wikipedia.org/wiki/Pair_programming) (the practice of having two people work together on one machine, each taking turns between typing and commenting) results in real-time code review, which [research has shown](http://www.sciencedirect.com/science/article/pii/S0950584909000123) results in higher productivity. If you are not using an OSX or Linux laptop, it would be best to try to pair with someone who is.  
+Participants in [ATPESC 2017](https://extremecomputingtraining.anl.gov) will work in groups of 2 for hands-on exercises.  Forming groups of 2 helps us to cut in half the number of IT issues that may arise during hands-on exercises.  Moreover, [pair programming](https://en.wikipedia.org/wiki/Pair_programming) (the practice of having two people work together on one machine, each taking turns between typing and commenting) results in real-time code review, which [research has shown](http://www.sciencedirect.com/science/article/pii/S0950584909000123) results in higher productivity. If you are not using an OSX or Linux laptop, it would be best to try to pair with someone who is.  
 
 ## Basic Instructions
 
@@ -26,7 +26,7 @@ MPIEXEC=/soft/libraries/mpi/mvapich2/gcc/bin/mpiexec
 ```
 resoft
 ```
-  - **WARNING: Do not attempt next step until after 9:30 am, when our cooley reservation begins.**
+  - **WARNING: Do not attempt next step until after 9:30 am, when our Cooley reservation begins.  Please be sure to work in pairs for the node reservations so that we have sufficient nodes for each pair to use 2 compute nodes for the exercises throughout the day.**
   - Obtain 2 compute nodes in _interactive_ (`-I`) mode to run the hands on exercises by running the following `qsub` command...
 ```
 qsub -I -n 2 -t 720 -A ATPESC2017
diff --git a/lessons/iterativesolvers/lesson.md b/lessons/iterativesolvers/lesson.md
@@ -6,54 +6,57 @@
 ```
 Questions                 |Objectives                     |Key Points
 --------------------------|-------------------------------|-------------------------------------
-Does the preconditioner   | See that the preconditioner   |
- affect the convergence   |  can be crucial for           |
- rate?                    |  convergence                  |
-                         
+Does the preconditioner   | See that the preconditioner   | Through a single interface,
+affect the convergence    | can be crucial for            | PETSc supports runtime choices 
+rate of Krylov solvers?   | convergence.                  | of algorithms and options.
+                          |                               |
+How can I choose algs.    | Learn the basics of using     | Experimenting with
+and options at runtime    | PETSc solvers & understanding | algorithms is essential
+when using PETSc?         | output.                       | for good performance.
 ```
 
-Before running the examples you must switch to the bash shell by using 
+Before running the examples, you must switch to the bash shell by using
 
 ```
 bash
 ```
 
 ## Example 1: Structural Mechanics Beam Deflection:
 
-This code uses MFEM and [PETSc/TAO](https://www.mcs.anl.gov/petsc/) to demonstrates convergence of Krylov methods.
+This code uses MFEM and [PETSc/TAO](https://www.mcs.anl.gov/petsc/) to demonstrate the convergence of Krylov methods.
 
 The source code is included in [ex2p.c](./ex2p.c)
 
-Notes: Normally PETSc options can be passed in as command line arguments but MFEM turns off this capability, thus they must be passed either in a file or in the PETSC_OPTIONS environmental variable. See the file rc_ex2p for the PETSc options that are supplied to the application in these examples.
+Notes: Normally PETSc options can be passed as command line arguments. But because MFEM turns off this capability, PETSc options must be passed either in a file or in the PETSC_OPTIONS environmental variable. See the file rc_ex2p for the PETSc options that are supplied to the application in these examples.
 
 ### Run 1: Run with Jacobi preconditioner
 
 ```
-PETSC_OPTIONS="-pc_type jacobi -ksp_max_it 25" ./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh 
+PETSC_OPTIONS="-pc_type jacobi -ksp_max_it 25" ./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh
 ```
 
 The first column of the output is the residual norm. The next two are the maximum and minimum estimated eigenvalues of the operator and the final column is the condition number.
 
 #### Questions
 > **Is the iteration converging?**
 
-> **Read the output at the bottom from -ksp_view, what Krylov method and preconditioner is it using?**
+> **Read the output at the bottom from -ksp_view ... What Krylov method and preconditioner are being used?**
 
 ### Run 2: Run with the algebraic multigrid preconditioner
 
 ```
-./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh 
+./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh
 ```
 
 #### Questions
 > **Is the iteration now converging?**
 
-> **Read the output at the bottom from -ksp_view, what Krylov method and preconditioner is it using?**
+> **Read the output at the bottom from -ksp_view ... What Krylov method and preconditioner are being used?**
 
 ### Run 3: Run with the algebraic multigrid preconditioner but no conjugate gradient method
 
 ```
-PETSC_OPTIONS="-ksp_norm_type preconditioned -ksp_type richardson -ksp_max_it 25"  ./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh 
+PETSC_OPTIONS="-ksp_norm_type preconditioned -ksp_type richardson -ksp_max_it 25"  ./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh
 ```
 
 #### Questions
@@ -62,25 +65,27 @@ PETSC_OPTIONS="-ksp_norm_type preconditioned -ksp_type richardson -ksp_max_it 25
 ### Run 4: Run with the algebraic multigrid preconditioner but with GMRES and a restart of 10
 
 ```
-PETSC_OPTIONS="-ksp_norm_type preconditioned -ksp_type gmres -ksp_gmres_restart 10"  ./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh 
+PETSC_OPTIONS="-ksp_norm_type preconditioned -ksp_type gmres -ksp_gmres_restart 10"  ./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh
 ```
 
 Now run with a gmres restart of 30
 
 ```
-PETSC_OPTIONS="-ksp_norm_type preconditioned -ksp_type gmres -ksp_gmres_restart 30"  ./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh 
+PETSC_OPTIONS="-ksp_norm_type preconditioned -ksp_type gmres -ksp_gmres_restart 30"  ./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh
 ```
 
 Note the convergence is now very similar to that with CG.
 
-Now attempt to run this parallelly and obtain solver performance data
+Now attempt to run this in parallel and obtain solver performance data
 ```
 PETSC_OPTIONS="-log_view -ksp_norm_type preconditioned -ksp_type gmres -ksp_gmres_restart 30" ${MPIEXEC_OMPI} -n 4 ./ex2p -petscopts rc_ex2p --mesh /projects/ATPESC2017/NumericalPackages/handson/mfem/data/beam-tri.mesh
 ```
 
 ## Out-Brief
 
-We have used [PETSc](https://www.mcs.anl.gov/petsc/) to demonstrate Krylov methods and nonlinear solver methods.
+We have used [PETSc](https://www.mcs.anl.gov/petsc/) to demonstrate the use of preconditioned Krylov methods. Many examples are available for various aspects of PETSc functionality, including
+* [Krylov solver examples](http://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examples/tutorials)
+* [Nonlinear solver examples](http://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials)
 
 
 <!-- Insert space, horizontal line, and link to HandsOnLesson table -->
diff --git a/tools/atpesc2017_cooley_vnc_setup.sh b/tools/atpesc2017_cooley_vnc_setup.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 acct=ATPESC2017
-nnodes=1
+nnodes=2
 tl=720
 localos=`uname`
 linuxvnc=''
@@ -96,7 +96,7 @@ done
 ssh ${cooley_username}@cooley-nph "rm -f ~/.vnc/passwd; echo $pw | vncpasswd -f > ~/.vnc/passwd; chmod 600 ~/.vnc/passwd"
 
 #
-# Reserve 3 nodes for interactive use all day
+# Reserve 2 nodes for interactive use all day
 #
 ssh -t -t -f ${cooley_username}@cooley-nph "qsub -I -n $nnodes -t $tl -A $acct" > ./qsub-interactive.out 2>&1 &
 

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`#!/bin/sh`
`2`	`2`	`acct=ATPESC2017`
`3`		`-nnodes=1`
	`3`	`+nnodes=2`
`4`	`4`	`tl=720`
`5`	`5`	localos=`uname`
`6`	`6`	`linuxvnc=''`
`@@ -96,7 +96,7 @@ done`
`96`	`96`	`ssh ${cooley_username}@cooley-nph "rm -f ~/.vnc/passwd; echo $pw \| vncpasswd -f > ~/.vnc/passwd; chmod 600 ~/.vnc/passwd"`
`97`	`97`
`98`	`98`	`#`
`99`		`-# Reserve 3 nodes for interactive use all day`
	`99`	`+# Reserve 2 nodes for interactive use all day`
`100`	`100`	`#`
`101`	`101`	`ssh -t -t -f ${cooley_username}@cooley-nph "qsub -I -n $nnodes -t $tl -A $acct" > ./qsub-interactive.out 2>&1 &`
`102`	`102`