Merge pull request #396 from nicholasjnelson/ModelSetup

Reviewed Model Setup

doc/source/User_Guide/model_setup.rst

@@ -607,6 +607,7 @@ Classification of the Convective Regimes in Rotating Stars.” The Astrophysical
 
 
 ::
+   
    &problemsize_namelist
    n_r = 64
    n_theta = 192
@@ -706,107 +707,3 @@ Classification of the Convective Regimes in Rotating Stars.” The Astrophysical
    kappa_top = 4.d12
    /
 
-.. _surveys:
-
-Ensemble Mode
--------------
-
-Rayleigh can also be used to run multiple simulations under the umbrella
-of a single executable. This functionality is particularly useful for
-running parameter space studies, which often consist of mulitple,
-similarly-sized simulations, in one shot. Moreover, as some queuing
-systems favor large jobs over small jobs, an ensemble mode is useful for
-advancing multiple small simulations through the queue in a reasonable
-timeframe.
-
-Running Rayleigh in ensemble mode is relatively straightforward. To
-begin with, create a directory for each simulation as you normally
-would, and place an appropriately modified main_input into each
-directory. These directories should all reside within the same parent
-directory. Within that parent directory, you should place a copy of the
-Rayleigh executable (or a softlink). In addition, you should create a
-text file named **run_list** that contains the name of each simulation
-directory, one name per line. An ensemble job may then be executed by
-calling Rayleigh with **nruns** command line flag as:
-
-::
-
-   user@machinename ~/runs/ $ mpiexec -np Y ./rayleigh.opt -nruns X
-
-Here, Y is the total number of cores needed by all X simulations listed
-in run_list.
-
-**Example:** Suppose you wish to run three simulations at once from
-within a parent directory named *ensemble* and that the simulation
-directories are named run1, run2, and run3. When performing an *ls* from
-within *ensemble*, you should see 5 items.
-
-::
-
-   user@machinename ~/runs/ $ cd ensemble
-   user@machinename ~/runs/ensemble $ ls
-   rayleigh.opt          run1          run2          run3          run_list
-
-In this example, the contents of run_list should be the *local* names of
-your ensemble run-directories, namely run1, run2, and run3.
-
-::
-
-   user@machinename ~runs/ensemble $ more run_list
-   run1
-   run2
-   run3
-             <--  place an empty line here
-
-Note that some Fortran implementations will not read the last line in
-run_list unless it ends in a newline character. Avoid unexpected crashes
-by hitting "enter" following your final entry in run_list.
-
-Before running Rayleigh, make sure you know how many cores each
-simulation needs by examining the main_input files:
-
-::
-
-   user@machinename ~runs/ensemble $ head run1/main_input
-   &problemsize_namelist
-    n_r = 128
-    n_theta = 192
-    nprow = 16
-    npcol = 16
-   /
-
-   user@machinename ~runs/ensemble $ head run2/main_input
-   &problemsize_namelist
-    n_r = 128
-    n_theta = 384
-    nprow = 32
-    npcol = 16
-   /
-
-   user@machinename ~runs/ensemble $ head run3/main_input
-   &problemsize_namelist
-    n_r = 64
-    n_theta = 192
-    nprow = 16
-    npcol = 16
-   /
-
-In this example, we need a total of 1024 cores (256+512+256) to execute
-three simulations, and so the relevant call to Rayleigh would be:
-
-::
-
-   user@machinename ~/runs/ $ mpiexec -np 1024 ./rayleigh.opt -nruns 3
-
-**Closing Notes:** When running in ensemble mode, it is *strongly
-recommended* that you redirect standard output for each simulation to a
-text file (see §\ :ref:`io`). Otherwise, all simulations
-write to the same default (machine-dependent) log file, making it
-difficult to read. Moreover, some machines such as NASA Pleiades will
-terminate a run if the log file becomes too long. This is easy to do
-when multiple simulations are writing to the same file.
-
-Finally, The flags -nprow and -npcol **are ignored** when -nruns is
-specified. The row and column configuration for all simulations needs to
-be specified in their respective main_input files instead.
-

doc/source/User_Guide/run_at_scale.rst

@@ -33,4 +33,108 @@ Need text here.
 Sample Jobscripts
 -----------------
 
-Need text here.
+Need text here.
+
+.. _surveys:
+
+Ensemble Mode
+-------------
+
+Rayleigh can also be used to run multiple simulations under the umbrella
+of a single executable. This functionality is particularly useful for
+running parameter space studies, which often consist of mulitple,
+similarly-sized simulations, in one shot. Moreover, as some queuing
+systems favor large jobs over small jobs, an ensemble mode is useful for
+advancing multiple small simulations through the queue in a reasonable
+timeframe.
+
+Running Rayleigh in ensemble mode is relatively straightforward. To
+begin with, create a directory for each simulation as you normally
+would, and place an appropriately modified main_input into each
+directory. These directories should all reside within the same parent
+directory. Within that parent directory, you should place a copy of the
+Rayleigh executable (or a softlink). In addition, you should create a
+text file named **run_list** that contains the name of each simulation
+directory, one name per line. An ensemble job may then be executed by
+calling Rayleigh with **nruns** command line flag as:
+
+::
+
+   user@machinename ~/runs/ $ mpiexec -np Y ./rayleigh.opt -nruns X
+
+Here, Y is the total number of cores needed by all X simulations listed
+in run_list.
+
+**Example:** Suppose you wish to run three simulations at once from
+within a parent directory named *ensemble* and that the simulation
+directories are named run1, run2, and run3. When performing an *ls* from
+within *ensemble*, you should see 5 items.
+
+::
+
+   user@machinename ~/runs/ $ cd ensemble
+   user@machinename ~/runs/ensemble $ ls
+   rayleigh.opt          run1          run2          run3          run_list
+
+In this example, the contents of run_list should be the *local* names of
+your ensemble run-directories, namely run1, run2, and run3.
+
+::
+
+   user@machinename ~runs/ensemble $ more run_list
+   run1
+   run2
+   run3
+             <--  place an empty line here
+
+Note that some Fortran implementations will not read the last line in
+run_list unless it ends in a newline character. Avoid unexpected crashes
+by hitting "enter" following your final entry in run_list.
+
+Before running Rayleigh, make sure you know how many cores each
+simulation needs by examining the main_input files:
+
+::
+
+   user@machinename ~runs/ensemble $ head run1/main_input
+   &problemsize_namelist
+    n_r = 128
+    n_theta = 192
+    nprow = 16
+    npcol = 16
+   /
+
+   user@machinename ~runs/ensemble $ head run2/main_input
+   &problemsize_namelist
+    n_r = 128
+    n_theta = 384
+    nprow = 32
+    npcol = 16
+   /
+
+   user@machinename ~runs/ensemble $ head run3/main_input
+   &problemsize_namelist
+    n_r = 64
+    n_theta = 192
+    nprow = 16
+    npcol = 16
+   /
+
+In this example, we need a total of 1024 cores (256+512+256) to execute
+three simulations, and so the relevant call to Rayleigh would be:
+
+::
+
+   user@machinename ~/runs/ $ mpiexec -np 1024 ./rayleigh.opt -nruns 3
+
+**Closing Notes:** When running in ensemble mode, it is *strongly
+recommended* that you redirect standard output for each simulation to a
+text file (see §\ :ref:`io`). Otherwise, all simulations
+write to the same default (machine-dependent) log file, making it
+difficult to read. Moreover, some machines such as NASA Pleiades will
+terminate a run if the log file becomes too long. This is easy to do
+when multiple simulations are writing to the same file.
+
+Finally, The flags -nprow and -npcol **are ignored** when -nruns is
+specified. The row and column configuration for all simulations needs to
+be specified in their respective main_input files instead.