Merge pull request #244 from cecilehannay/main

standardize the location of code and cases

notebooks/basics/cesm_workflow/case_build.ipynb

@@ -34,8 +34,8 @@
     "\n",
     "\n",
     "For the current tutorial on derecho, the paths are:\n",
-    "- `$SRCROOT`     = `/glade/work/$USER/code/my_cesm_code`\n",
-    "- `$CASEROOT`    = `/glade/work/$USER/cases/$CASE`\n",
+    "- `$SRCROOT`     = `/glade/u/home/$USER/code/my_cesm_code`\n",
+    "- `$CASEROOT`    = `/glade/u/home/$USER/cases/$CASE`\n",
     "-  `$EXEROOT`     =`/glade/derecho/scratch/$USER/$CASE/bld` \n",
     "- `$RUNDIR`      =`/glade/derecho/scratch/$USER/$CASE/run` "
    ]
@@ -63,7 +63,7 @@
     "\n",
     "You should still be in the `CASEROOT` directory after running `case.setup`\n",
     "```\n",
-    "cd /glade/work/$USER/cases/CASE\n",
+    "cd /glade/u/home/$USER/cases/CASE\n",
     "```\n",
     "    \n",
     "<br>\n",
@@ -93,7 +93,7 @@
     "<br>\n",
     "    \n",
     "```\n",
-    "Building case in directory /glade/work/$USER/cases/b1850.basics\n",
+    "Building case in directory /glade/u/home/$USER/cases/b1850.basics\n",
     "sharedlib_only is False\n",
     "model_only is False\n",
     "Generating component namelists as part of build\n",
@@ -121,7 +121,7 @@
     "Creating component namelists\n",
     "Calling /glade/u/home/$USER/my_cesm_code/components/cam//cime_config/buildnml\n",
     "...calling cam buildcpp to set build time options\n",
-    "CAM namelist copy: file1 /glade/work/$USER/cases/b1850.basics/Buildconf/camconf/atm_in file2 /glade/derecho/scratch/$USER/b1850.basics/run/atm_in\n",
+    "CAM namelist copy: file1 /glade/u/home/$USER/cases/b1850.basics/Buildconf/camconf/atm_in file2 /glade/derecho/scratch/$USER/b1850.basics/run/atm_in\n",
     "Calling /glade/u/home/$USER/my_cesm_code/components/clm//cime_config/buildnml\n",
     "Calling /glade/u/home/$USER/my_cesm_code/components/cice//cime_config/buildnml\n",
     "...buildnml calling cice buildcpp to set build time options\n",

notebooks/basics/cesm_workflow/case_setup.ipynb

@@ -30,8 +30,8 @@
     "\n",
     "\n",
     "For the current tutorial on derecho, the paths are:\n",
-    "- `$SRCROOT`     = `/glade/work/$USER/code/my_cesm_code`\n",
-    "- `$CASEROOT`    = `/glade/work/$USER/cases/$CASE`\n",
+    "- `$SRCROOT`     = `/glade/u/home/$USER/code/my_cesm_code`\n",
+    "- `$CASEROOT`    = `/glade/u/home/$USER/cases/$CASE`\n",
     "- `$EXEROOT`     =`/glade/derecho/scratch/$USER/$CASE/bld` \n",
     "- `$RUNDIR`      =`/glade/derecho/scratch/$USER/$CASE/run` "
    ]
@@ -65,7 +65,7 @@
     "\n",
     "<strong>Go to the `$CASEROOT` directory </strong>\n",
     "```\n",
-    "cd /glade/work/$USER/cases/CASE\n",
+    "cd /glade/u/home/$USER/cases/CASE\n",
     "```\n",
     "    \n",
     "<br>\n",
@@ -95,11 +95,11 @@
     "<br>\n",
     "    \n",
     "```\n",
-    "/glade/work/$USER/cases/b1850.basics/env_mach_specific.xml already exists, delete to replace\n",
+    "/glade/u/home/$USER/cases/b1850.basics/env_mach_specific.xml already exists, delete to replace\n",
     "job is case.run USER_REQUESTED_WALLTIME None USER_REQUESTED_QUEUE None WALLTIME_FORMAT %H:%M:%S\n",
     "Creating batch scripts\n",
-    "Writing case.run script from input template /glade/work/$USERrun\n",
-    "Writing case.st_archive script from input template /glade/work/$USER/code/my_cesm_code/cime/config/cesm/machines/template.st_archive\n",
+    "Writing case.run script from input template /glade/u/home/$USERrun\n",
+    "Writing case.st_archive script from input template /glade/u/home/$USER/code/my_cesm_code/cime/config/cesm/machines/template.st_archive\n",
     "Creating file case.st_archive\n",
     "Creating user_nl_xxx files for components and cpl\n",
     "If an old case build already exists, might want to run 'case.build --clean' before building\n",

notebooks/basics/cesm_workflow/case_submit.ipynb

@@ -35,8 +35,8 @@
     "*<p style=\"text-align: center;\"> Figure: Detailed view of the location of case.submit</p>*\n",
     "\n",
     "For the current tutorial on derecho, the paths are:\n",
-    "- `$SRCROOT`     = `/glade/work/$USER/code/my_cesm_code`\n",
-    "- `$CASEROOT`    = `/glade/work/$USER/cases/$CASE`\n",
+    "- `$SRCROOT`     = `/glade/u/home/$USER/code/my_cesm_code`\n",
+    "- `$CASEROOT`    = `/glade/u/home/$USER/cases/$CASE`\n",
     "- `$CIME_OUTPUT_ROOT` = `/glade/derecho/scratch/$USER`\n",
     "- `$EXEROOT`     =`/glade/derecho/scratch/$USER/$CASE/bld` \n",
     "- `$RUNDIR`      =`/glade/derecho/scratch/$USER/$CASE/run` "
@@ -65,7 +65,7 @@
     "\n",
     "You should still be in the `CASEROOT` directory after running `case.build`\n",
     "```\n",
-    "cd /glade/work/$USER/cases/CASE\n",
+    "cd /glade/u/home/$USER/cases/CASE\n",
     "```\n",
     "    \n",
     "<br>\n",
@@ -107,7 +107,7 @@
     "Copy rpointer /glade/campaign/cesm/cesmdata/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.drv\n",
     "Creating component namelists\n",
     "   Calling /glade/u/home/$USER/my_cesm_code/components/cam//cime_config/buildnml\n",
-    "CAM namelist copy: file1 /glade/work/$USER/cases/b1850.basics/Buildconf/camconf/atm_in file2 /glade/derecho/scratch/$USER/b1850.basics/run/atm_in \n",
+    "CAM namelist copy: file1 /glade/u/home/$USER/cases/b1850.basics/Buildconf/camconf/atm_in file2 /glade/derecho/scratch/$USER/b1850.basics/run/atm_in \n",
     "   Calling /glade/u/home/$USER/my_cesm_code/components/clm//cime_config/buildnml\n",
     "   Calling /glade/u/home/$USER/my_cesm_code/components/cice//cime_config/buildnml\n",
     "   Calling /glade/u/home/$USER/my_cesm_code/components/pop//cime_config/buildnml\n",

notebooks/basics/cesm_workflow/checking_jobs_and_status.ipynb

@@ -87,7 +87,7 @@
     "<strong>Status of the case recorded in the `$CASEROOT` CaseStatus file: </strong><br><br>\n",
     "\n",
     "```\n",
-    "cd /glade/work/$USER/cases/CASE\n",
+    "cd /glade/u/home/$USER/cases/CASE\n",
     "more CaseStatus\n",
     "```\n",
     "\n",

notebooks/basics/cesm_workflow/create_clone.ipynb

@@ -59,15 +59,15 @@
     "\n",
     "<strong>Go to the `cime/scripts` directory in the CESM code</strong>\n",
     "```\n",
-    "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n",
+    "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n",
     "```\n",
     "    \n",
     "<br>\n",
     "    \n",
     "<strong>Example of basic `./create_clone` syntax to create CASE2: </strong><br>    \n",
     "    \n",
     "```\n",
-    "./create_clone --clone /glade/work/$USER/cases/CASE1 --case /glade/work/$USER/cases/CASE2\n",
+    "./create_clone --clone /glade/u/home/$USER/cases/CASE1 --case /glade/u/home/$USER/cases/CASE2\n",
     "```\n",
     "    \n",
     "</div>\n"

notebooks/basics/cesm_workflow/create_newcase.ipynb

@@ -27,8 +27,8 @@
     "*<p style=\"text-align: center;\"> Figure: Detailed view of the location of create_newcase</p>*\n",
     "\n",
     "For the current tutorial on derecho, the paths are:\n",
-    "- `$SRCROOT`     = `/glade/work/$USER/code/my_cesm_code`\n",
-    "- `$CASEROOT`    = `/glade/work/$USER/cases/$CASE`\n",
+    "- `$SRCROOT`     = `/glade/u/home/$USER/code/my_cesm_code`\n",
+    "- `$CASEROOT`    = `/glade/u/home/$USER/cases/$CASE`\n",
     "<br>"
    ]
   },
@@ -58,15 +58,15 @@
     "\n",
     "<strong>Go to the `cime/scripts` directory in the CESM code</strong><br> \n",
     "```\n",
-    "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n",
+    "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n",
     "```\n",
     "    \n",
     "<br>\n",
     "    \n",
     "<strong>Example of basic `./create_newcase` syntax: </strong><br>    \n",
     "    \n",
     "```\n",
-    "./create_newcase --case /glade/work/$USER/cases/CASE --res RES --compset COMPSET\n",
+    "./create_newcase --case /glade/u/home/$USER/cases/CASE --res RES --compset COMPSET\n",
     "```\n",
     "    \n",
     "</div>\n",
@@ -89,7 +89,7 @@
     "    \n",
     "```\n",
     "Compset longname is 1850_CAM60_CLM50%BGC-CROP_CICE_POP2%ECO%ABIO-DIC_MOSART_CISM2%NOEVOLVE_WW3_BGC%BDRD\n",
-    "Compset specification file is /glade/work/$USER/code/cesm2.1.1/cime/../cime_config/config_compsets.xml\n",
+    "Compset specification file is /glade/u/home/$USER/code/cesm2.1.1/cime/../cime_config/config_compsets.xml\n",
     "Compset forcing is 1850\n",
     "Com forcing is Biogeochemistry intercomponent  with diagnostic CO2\n",
     "ATM component is CAM cam6 physics:\n",
@@ -100,7 +100,7 @@
     "GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):\n",
     "WAV component is Wave Watch\n",
     "ESP component is \n",
-    "Pes     specification file is /glade/work/$USER/code/cesm2.1.1/cime/../cime_config/config_pes.xml\n",
+    "Pes     specification file is /glade/u/home/$USER/code/cesm2.1.1/cime/../cime_config/config_pes.xml\n",
     "Compset specific settings: name is RUN_STARTDATE and value is 0001-01-01\n",
     "Compset specific settings: name is RUN_REFDATE and value is 0301-01-01\n",
     "Compset specific settings: name is RUN_TYPE and value is hybrid\n",
@@ -131,7 +131,7 @@
     "Batch_system_type is pbs\n",
     "job is case.run USER_REQUESTED_WALLTIME None USER_REQUESTED_QUEUE None WALLTIME_FORMAT %H:%M:%S\n",
     "job is case.st_archive USER_REQUESTED_WALLTIME None USER_REQUESTED_QUEUE None WALLTIME_FORMAT %H:%M:%S\n",
-    " Creating Case directory /glade/work/$USER/cases/b1850.basics\n",
+    " Creating Case directory /glade/u/home/$USER/cases/b1850.basics\n",
     "\n",
     "```\n",
     "\n",
@@ -179,15 +179,15 @@
    "id": "0ea36beb-fe98-4289-a15e-37c21ff2f4ad",
    "metadata": {},
    "source": [
-    "`--case` is the argument that specifies the **name** and **location** of the case being created. In the example above, the casename is `CASE` and the location of the case is `/glade/work/$USER/cases/`. Note that if a path preceding the casename is not specified, then the case is created as a subdirectory of the `$CIMEROOT/scripts` directory.\n"
+    "`--case` is the argument that specifies the **name** and **location** of the case being created. In the example above, the casename is `CASE` and the location of the case is `/glade/u/home/$USER/cases/`. Note that if a path preceding the casename is not specified, then the case is created as a subdirectory of the `$CIMEROOT/scripts` directory.\n"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "bb90ccd2-b4d4-4ab7-96ec-749a596f25ae",
    "metadata": {},
    "source": [
-    "- The path `/glade/work/$USER/cases/CASE` is your workspace `CASEROOT`, as described in the [workspaces section](https://ncar.github.io/CESM-Tutorial/notebooks/basics/cesm_workspaces.html#workspace-overview)."
+    "- The path `/glade/u/home/$USER/cases/CASE` is your workspace `CASEROOT`, as described in the [workspaces section](https://ncar.github.io/CESM-Tutorial/notebooks/basics/cesm_workspaces.html#workspace-overview)."
    ]
   },
   {
@@ -409,7 +409,7 @@
     "<strong>Cime Tool for listing configurations: </strong><br><br>\n",
     "\n",
     "```\n",
-    "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n",
+    "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n",
     "./query_config --compsets\n",
     "```\n",
     "</div>"

notebooks/basics/cesm_workflow/model_output.ipynb

@@ -28,8 +28,8 @@
     "\n",
     "\n",
     "For the current tutorial on derecho, the paths are:\n",
-    "- `$SRCROOT`     = `/glade/work/$USER/code/my_cesm_code`\n",
-    "- `$CASEROOT`    = `/glade/work/$USER/cases/$CASE`\n",
+    "- `$SRCROOT`     = `/glade/u/home/$USER/code/my_cesm_code`\n",
+    "- `$CASEROOT`    = `/glade/u/home/$USER/cases/$CASE`\n",
     "- `$EXEROOT`     =`/glade/derecho/scratch/$USER/$CASE/bld` \n",
     "- `$RUNDIR`      =`/glade/derecho/scratch/$USER/$CASE/run` \n",
     "- `$DOUT_S_ROOT` =`/glade/derecho/scratch/$USER/archive/$CASE` "

notebooks/basics/cesm_workspaces.ipynb

@@ -44,9 +44,9 @@
     "*<p style=\"text-align: center;\"> Figure: Overview of the CESM2 Workspace Directories </p>*\n",
     "\n",
     "For the current tutorial on derecho, the paths are:\n",
-    "- `$SRCROOT`     = `/glade/work/$USER/code/my_cesm_code`\n",
+    "- `$SRCROOT`     = `/glade/u/home/$USER/code/my_cesm_code`\n",
     "- `$DIN_LOC_ROOT` = `/glade/campaign/cesm/cesmdata/cseg/inputdata`\n",
-    "- `$CASEROOT`    = `/glade/work/$USER/cases/$CASE`\n",
+    "- `$CASEROOT`    = `/glade/u/home/$USER/cases/$CASE`\n",
     "- `$CIME_OUTPUT_ROOT` = `/glade/derecho/scratch/$USER`\n",
     "-  `$EXEROOT`     =`/glade/derecho/scratch/$USER/$CASE/bld` \n",
     "- `$RUNDIR`      =`/glade/derecho/scratch/$USER/$CASE/run` \n",
@@ -91,7 +91,7 @@
     "<div class=\"alert alert-info\">\n",
     "\n",
     "```\n",
-    "cd /glade/work/$USER\n",
+    "cd /glade/u/home/$USER\n",
     "mkdir code\n",
     "```\n",
     "   \n",
@@ -122,7 +122,7 @@
     "<div class=\"alert alert-info\">\n",
     "\n",
     "```\n",
-    "cd /glade/work/$USER\n",
+    "cd /glade/u/home/$USER\n",
     "mkdir cases\n",
     "```\n",
     "   \n",

notebooks/basics/code/cesm_code_explore.ipynb

@@ -32,7 +32,7 @@
     "*<p style=\"text-align: center;\"> Figure: Detailed view of the CESM2 Code Directory</p>*\n",
     "\n",
     "For the current tutorial on derecho, the paths are: \n",
-    "- `$SRCROOT = /glade/work/$USER/code/my_cesm_code`  "
+    "- `$SRCROOT = /glade/u/home/$USER/code/my_cesm_code`  "
    ]
   },
   {
@@ -55,15 +55,15 @@
     "<strong>Expected output:</strong><br>\n",
     "\n",
     "```\n",
-    "/glade/work/$USER/code/my_cesm_code\n",
+    "/glade/u/home/$USER/code/my_cesm_code\n",
     "```\n",
     "<br>\n",
     "\n",
     "     \n",
     "<strong>If you have not done anything since the last exercise then you will already be in the `$SRCROOT` location. If your output doesn't match the path above, then change the current directory to your Workspace Code directory: </strong><br>\n",
     "\n",
     "```\n",
-    "cd /glade/work/$USER/code/my_cesm_code\n",
+    "cd /glade/u/home/$USER/code/my_cesm_code\n",
     "```\n",
     "<br>\n",
     "    \n",
@@ -193,7 +193,7 @@
     "<strong>Change back to the Code Workspace Location: </strong><br>\n",
     "\n",
     "```\n",
-    "cd /glade/work/$USER/code/my_cesm_code\n",
+    "cd /glade/u/home/$USER/code/my_cesm_code\n",
     "```\n",
     "OR\n",
     "Alternatively, you can use the `cd ../..` to move up two levels in the directory hierarchy.\n",

notebooks/basics/code/git_download_cesm.ipynb

@@ -60,7 +60,7 @@
     "<div class=\"alert alert-info\">\n",
     "\n",
     "```\n",
-    "cd /glade/work/$USER\n",
+    "cd /glade/u/home/$USER\n",
     "mkdir code\n",
     "```\n",
     "   \n",
@@ -86,7 +86,7 @@
     "<strong>Change the current directory to the code workspace directory: </strong><br>\n",
     "\n",
     "```\n",
-    "cd /glade/work/$USER/code\n",
+    "cd /glade/u/home/$USER/code\n",
     "```\n",
     "<br>\n",
     "    \n",
@@ -227,7 +227,7 @@
     "<strong>Exercise: Run the `checkout_externals` command to download all the component models: </strong><br>\n",
     "\n",
     "```\n",
-    "cd /glade/work/$USER/code/my_cesm_code\n",
+    "cd /glade/u/home/$USER/code/my_cesm_code\n",
     "./manage_externals/checkout_externals\n",
     "```\n",
     "</br>\n",
@@ -251,15 +251,15 @@
     "\n",
     "    where `$USER` will be replaced by your user name\n",
     "```\n",
-    "Processing externals description file : Externals.cfg (/glade/work/$USER/code/my_cesm_code)\n",
+    "Processing externals description file : Externals.cfg (/glade/u/home/$USER/code/my_cesm_code)\n",
     "Checking local status of required & optional components: cam, cice, cime, cism, clm, mosart, pop, rtm, ww3, \n",
-    "Checking out externals: cime, cam, Processing externals description file : Externals_CAM.cfg (/glade/work/$USER/code/my_cesm_code/components/cam)\n",
+    "Checking out externals: cime, cam, Processing externals description file : Externals_CAM.cfg (/glade/u/home/$USER/code/my_cesm_code/components/cam)\n",
     "Checking out externals: chem_proc, carma, clubb, cosp2, \n",
-    "cice, cism, Processing externals description file : Externals_CISM.cfg (/glade/work/$USER/code/my_cesm_code/components/cism)\n",
+    "cice, cism, Processing externals description file : Externals_CISM.cfg (/glade/u/home/$USER/code/my_cesm_code/components/cism)\n",
     "Checking out externals: source_cism, \n",
-    "clm, Processing externals description file : Externals_CLM.cfg (/glade/work/$USER/code/my_cesm_code/components/clm)\n",
+    "clm, Processing externals description file : Externals_CLM.cfg (/glade/u/home/$USER/code/my_cesm_code/components/clm)\n",
     "Checking out externals: fates, ptclm, \n",
-    "mosart, pop, Processing externals description file : Externals_POP.cfg (/glade/work/$USER/code/my_cesm_code/components/pop)\n",
+    "mosart, pop, Processing externals description file : Externals_POP.cfg (/glade/u/home/$USER/code/my_cesm_code/components/pop)\n",
     "Checking out externals: cvmix, marbl, \n",
     "rtm, ww3, \n",
     "```\n",
@@ -273,7 +273,7 @@
    "id": "74d14003-78cc-48e6-bcbc-622f0150dfed",
    "metadata": {},
    "source": [
-    "- The path `/glade/work/$USER/code/my_cesm_code` is your workspace `$SRCROOT`, as described in the [workspaces section](https://ncar.github.io/CESM-Tutorial/notebooks/basics/cesm_workspaces.html#workspace-overview)."
+    "- The path `/glade/u/home/$USER/code/my_cesm_code` is your workspace `$SRCROOT`, as described in the [workspaces section](https://ncar.github.io/CESM-Tutorial/notebooks/basics/cesm_workspaces.html#workspace-overview)."
    ]
   },
   {
@@ -310,12 +310,12 @@
     "If you download CESM with the instructions above, the CESM code is located in:\n",
     "\n",
     "```\n",
-    "/glade/work/$USER/code/my_cesm_code\n",
+    "/glade/u/home/$USER/code/my_cesm_code\n",
     "```\n",
     "\n",
     "To navigate to that directory, use the UNIX command `cd`:\n",
     "```\n",
-    "cd /glade/work/$USER/code/my_cesm_code\n",
+    "cd /glade/u/home/$USER/code/my_cesm_code\n",
     "```\n",
     "\n",
     "If you are not familiar with UNIX commands, please review the [UNIX chapter](https://ncar.github.io/CESM-Tutorial/notebooks/resources/unix.html) of this documentation. \n",

notebooks/basics/exercises/extra.ipynb

@@ -32,7 +32,7 @@
     "<div class=\"alert alert-info\">\n",
     "    \n",
     "```\n",
-    "cd /glade/work/$USER/cases/b1850.basics/\n",
+    "cd /glade/u/home/$USER/cases/b1850.basics/\n",
     "```\n",
     "</div>"
    ]
@@ -118,7 +118,7 @@
     "<div class=\"alert alert-info\">\n",
     "    \n",
     "```\n",
-    "cd /glade/work/$USER/code/my_cesm_code/cime/scripts\n",
+    "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts\n",
     "```\n",
     "</div>"
    ]