From 10c2eba82a0ecadbec22e2f293e64794284322c4 Mon Sep 17 00:00:00 2001
From: suzm10 <suzanmanasreh@gmail.com>
Date: Wed, 19 Jun 2024 18:04:07 -0400
Subject: [PATCH] why is ompi manually installed

---
 .github/workflows/ice.yml |  2 +-
 CMakeLists.txt            | 30 ------------------------------
 README.md                 |  2 ++
 install/readme.md         |  2 +-
 4 files changed, 4 insertions(+), 32 deletions(-)

diff --git a/.github/workflows/ice.yml b/.github/workflows/ice.yml
index 1292b7f..d42633a 100644
--- a/.github/workflows/ice.yml
+++ b/.github/workflows/ice.yml
@@ -1,7 +1,7 @@
 name: 'Test on ICE'
 
 on:
-    # push:
+    push:
     pull_request:
     workflow_dispatch:
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 90570c4..a3907ee 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -149,33 +149,3 @@ foreach (casedir ${dirlist})
         add_dependencies(${casedir} ${file_target})
     endforeach()
 endforeach()
-
-# # make binary dir inside /build for case files
-# set(CASE_BINARY_DIR "${CMAKE_CURRENT_BINARY_DIR}/case")
-# file(MAKE_DIRECTORY ${CASE_BINARY_DIR})
-
-# add_subdirectory(examples/case case)
-# add_subdirectory(examples/case_sickles case_sickles)
-# # Find all Fortran files in the examples/case directory
-# file(GLOB case_F90s "${CMAKE_CURRENT_SOURCE_DIR}/examples/case/*.F90")
-# cmake_print_variables(case_F90s)
-
-# # Create a custom target with the name of the current directory
-# add_custom_target(case)
-
-# # Loop through each Fortran file
-# foreach(F90_filepath ${case_F90s})
-#     # Get the file name without extension
-#     get_filename_component(file_target ${F90_filepath} NAME_WE)
-#     add_executable(${file_target} ${F90_filepath})
-#     cmake_print_variables(file_target)
-
-#     set_target_properties(${file_target} PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CASE_BINARY_DIR})
-
-#     # Set include directories and link libraries
-#     target_include_directories(${file_target} PRIVATE ${PETSC_INCLUDE_DIRS})
-#     target_link_libraries(${file_target} PRIVATE common ${PETSC_LINK_LIBRARIES})
-
-#     # Add dependency to the custom target
-#     add_dependencies(case ${file_target})
-# endforeach()
diff --git a/README.md b/README.md
index aa0b4c2..494c59f 100644
--- a/README.md
+++ b/README.md
@@ -56,6 +56,8 @@ srun -n 1 ./initcond
 srun ./tube
 ```
 
+This will generate output files in `build/case/D`. To keep output files in `examples/case/D`, you can `cd examples/case` and `srun ../../build/case/initcond` and same for tube.
+
 On other supercomputing clusters, it should be easy to replace the module loads with the modules available on your system and make sure modules are setting appropriate environment variables via the `module show` command. If one of these isn't available, you can follow the manual build instructions [available here](https://github.com/comp-physics/RBC3D/blob/master/install/readme.md).
 
 ### Papers that use RBC3D
diff --git a/install/readme.md b/install/readme.md
index 6a0837d..bc8edad 100644
--- a/install/readme.md
+++ b/install/readme.md
@@ -184,5 +184,5 @@ Note that on Phoenix, `srun` only works if you [salloc](https://gatech.service-n
 
 ## Data and visualization
 
-After running `srun ./tube` or the equivalent, you should see `x000*.dat`, `wall000*.dat`, and restart files.
+After running `srun ./tube` or the equivalent, you should see `x000*.dat`, `wall000*.dat`, and restart files in the `D` folder.
 You can load the `.dat` files into Paraview to visualize them.