diff --git a/notebooks/basics/cesm_workflow/case_build.ipynb b/notebooks/basics/cesm_workflow/case_build.ipynb index d733d9f6e..c94ff71a0 100644 --- a/notebooks/basics/cesm_workflow/case_build.ipynb +++ b/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", "
\n", @@ -93,7 +93,7 @@ "
\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/$USER/my_cesm_code/components/cice//cime_config/buildnml\n", "...buildnml calling cice buildcpp to set build time options\n", diff --git a/notebooks/basics/cesm_workflow/case_setup.ipynb b/notebooks/basics/cesm_workflow/case_setup.ipynb index 937f9b1a1..a1b30af93 100644 --- a/notebooks/basics/cesm_workflow/case_setup.ipynb +++ b/notebooks/basics/cesm_workflow/case_setup.ipynb @@ -30,8 +30,8 @@ "\n", "\n", "For the current tutorial on derecho, the paths are:\n", - "- `$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/$CASE/run` " ] @@ -65,7 +65,7 @@ "\n", "Go to the `$CASEROOT` directory \n", "```\n", - "cd /glade/work/$USER/cases/CASE\n", + "cd /glade/u/home/$USER/cases/CASE\n", "```\n", " \n", "
\n", @@ -95,11 +95,11 @@ "
\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", diff --git a/notebooks/basics/cesm_workflow/case_submit.ipynb b/notebooks/basics/cesm_workflow/case_submit.ipynb index b7b98320c..d3870ce8a 100644 --- a/notebooks/basics/cesm_workflow/case_submit.ipynb +++ b/notebooks/basics/cesm_workflow/case_submit.ipynb @@ -35,8 +35,8 @@ "*

Figure: Detailed view of the location of case.submit

*\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", "
\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", diff --git a/notebooks/basics/cesm_workflow/checking_jobs_and_status.ipynb b/notebooks/basics/cesm_workflow/checking_jobs_and_status.ipynb index fe99cc33c..eea2bb839 100644 --- a/notebooks/basics/cesm_workflow/checking_jobs_and_status.ipynb +++ b/notebooks/basics/cesm_workflow/checking_jobs_and_status.ipynb @@ -87,7 +87,7 @@ "Status of the case recorded in the `$CASEROOT` CaseStatus file:

\n", "\n", "```\n", - "cd /glade/work/$USER/cases/CASE\n", + "cd /glade/u/home/$USER/cases/CASE\n", "more CaseStatus\n", "```\n", "\n", diff --git a/notebooks/basics/cesm_workflow/create_clone.ipynb b/notebooks/basics/cesm_workflow/create_clone.ipynb index 49133f88a..6b1254fd9 100644 --- a/notebooks/basics/cesm_workflow/create_clone.ipynb +++ b/notebooks/basics/cesm_workflow/create_clone.ipynb @@ -59,7 +59,7 @@ "\n", "Go to the `cime/scripts` directory in the CESM code\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", "
\n", @@ -67,7 +67,7 @@ "Example of basic `./create_clone` syntax to create CASE2:
\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", "\n" diff --git a/notebooks/basics/cesm_workflow/create_newcase.ipynb b/notebooks/basics/cesm_workflow/create_newcase.ipynb index 6c263ed0e..99069c31e 100644 --- a/notebooks/basics/cesm_workflow/create_newcase.ipynb +++ b/notebooks/basics/cesm_workflow/create_newcase.ipynb @@ -27,8 +27,8 @@ "*

Figure: Detailed view of the location of create_newcase

*\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", "
" ] }, @@ -58,7 +58,7 @@ "\n", "Go to the `cime/scripts` directory in the CESM code
\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", "
\n", @@ -66,7 +66,7 @@ "Example of basic `./create_newcase` syntax:
\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", "\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", @@ -179,7 +179,7 @@ "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" ] }, { @@ -187,7 +187,7 @@ "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 @@ "Cime Tool for listing configurations:

\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", "" diff --git a/notebooks/basics/cesm_workflow/model_output.ipynb b/notebooks/basics/cesm_workflow/model_output.ipynb index feebad7b9..218f6b861 100644 --- a/notebooks/basics/cesm_workflow/model_output.ipynb +++ b/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` " diff --git a/notebooks/basics/cesm_workspaces.ipynb b/notebooks/basics/cesm_workspaces.ipynb index 2c00a02dc..d287b1c6f 100644 --- a/notebooks/basics/cesm_workspaces.ipynb +++ b/notebooks/basics/cesm_workspaces.ipynb @@ -44,9 +44,9 @@ "*

Figure: Overview of the CESM2 Workspace Directories

*\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/$CASE/run` \n", @@ -91,7 +91,7 @@ "
\n", "\n", "```\n", - "cd /glade/work/$USER\n", + "cd /glade/u/home/$USER\n", "mkdir code\n", "```\n", " \n", @@ -122,7 +122,7 @@ "
\n", "\n", "```\n", - "cd /glade/work/$USER\n", + "cd /glade/u/home/$USER\n", "mkdir cases\n", "```\n", " \n", diff --git a/notebooks/basics/code/cesm_code_explore.ipynb b/notebooks/basics/code/cesm_code_explore.ipynb index fe18a4f87..3ddbe7a7c 100644 --- a/notebooks/basics/code/cesm_code_explore.ipynb +++ b/notebooks/basics/code/cesm_code_explore.ipynb @@ -32,7 +32,7 @@ "*

Figure: Detailed view of the CESM2 Code Directory

*\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` " ] }, { @@ -55,7 +55,7 @@ "Expected output:
\n", "\n", "```\n", - "/glade/work/$USER/code/my_cesm_code\n", + "/glade/u/home/$USER/code/my_cesm_code\n", "```\n", "
\n", "\n", @@ -63,7 +63,7 @@ "If you have not done anything since the last exercise then you will already be in the `$SRCROOT` location. If your output doesn't match the path above, then change the current directory to your Workspace Code directory:
\n", "\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code\n", + "cd /glade/u/home/$USER/code/my_cesm_code\n", "```\n", "
\n", " \n", @@ -193,7 +193,7 @@ "Change back to the Code Workspace Location:
\n", "\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code\n", + "cd /glade/u/home/$USER/code/my_cesm_code\n", "```\n", "OR\n", "Alternatively, you can use the `cd ../..` to move up two levels in the directory hierarchy.\n", diff --git a/notebooks/basics/code/git_download_cesm.ipynb b/notebooks/basics/code/git_download_cesm.ipynb index 36422ad2d..a2c13c154 100644 --- a/notebooks/basics/code/git_download_cesm.ipynb +++ b/notebooks/basics/code/git_download_cesm.ipynb @@ -60,7 +60,7 @@ "
\n", "\n", "```\n", - "cd /glade/work/$USER\n", + "cd /glade/u/home/$USER\n", "mkdir code\n", "```\n", " \n", @@ -86,7 +86,7 @@ "Change the current directory to the code workspace directory:
\n", "\n", "```\n", - "cd /glade/work/$USER/code\n", + "cd /glade/u/home/$USER/code\n", "```\n", "
\n", " \n", @@ -227,7 +227,7 @@ "Exercise: Run the `checkout_externals` command to download all the component models:
\n", "\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code\n", + "cd /glade/u/home/$USER/code/my_cesm_code\n", "./manage_externals/checkout_externals\n", "```\n", "
\n", @@ -251,15 +251,15 @@ "\n", " where `$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", diff --git a/notebooks/basics/exercises/extra.ipynb b/notebooks/basics/exercises/extra.ipynb index 1cfb184b4..61f342479 100644 --- a/notebooks/basics/exercises/extra.ipynb +++ b/notebooks/basics/exercises/extra.ipynb @@ -32,7 +32,7 @@ "
\n", " \n", "```\n", - "cd /glade/work/$USER/cases/b1850.basics/\n", + "cd /glade/u/home/$USER/cases/b1850.basics/\n", "```\n", "
" ] @@ -118,7 +118,7 @@ "
\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", "
" ] diff --git a/notebooks/basics/exercises/first_B1850.ipynb b/notebooks/basics/exercises/first_B1850.ipynb index 99894df55..e19562969 100644 --- a/notebooks/basics/exercises/first_B1850.ipynb +++ b/notebooks/basics/exercises/first_B1850.ipynb @@ -39,7 +39,7 @@ "\n", "Did you already create a `cases` directory where you will put all new cases\n", "```\n", - "cd /glade/work/$USER\n", + "cd /glade/u/home/$USER\n", "mkdir cases\n", "```\n", " \n", @@ -47,7 +47,7 @@ "\n", "You can create a new case with the command:\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", "Make sure you use the correct information for the CASE, RES, and COMPSET inputs.\n", "\n", @@ -86,13 +86,13 @@ " \n", "Create a new case b1850.basics with the command:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts\n", - "./create_newcase --case /glade/work/$USER/cases/b1850.basics --res f19_g17 --compset B1850\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts\n", + "./create_newcase --case /glade/u/home/$USER/cases/b1850.basics --res f19_g17 --compset B1850\n", "```\n", "\n", "Case setup:\n", "``` \n", - "cd /glade/work/$USER/cases/b1850.basics \n", + "cd /glade/u/home/$USER/cases/b1850.basics \n", "./case.setup\n", "```\n", " \n", diff --git a/notebooks/basics/exercises/second_B1850.ipynb b/notebooks/basics/exercises/second_B1850.ipynb index 12a2fcdd9..785d94fe4 100644 --- a/notebooks/basics/exercises/second_B1850.ipynb +++ b/notebooks/basics/exercises/second_B1850.ipynb @@ -73,7 +73,7 @@ " \n", "Go to your b1850.basics case directory:\n", "```\n", - "cd /glade/work/$USER/cases/b1850.basics\n", + "cd /glade/u/home/$USER/cases/b1850.basics\n", "```\n", "\n", "Changing xml files:\n", diff --git a/notebooks/challenge/cam-chem_waccm/exercise_1.ipynb b/notebooks/challenge/cam-chem_waccm/exercise_1.ipynb index 1268cbed8..f359642d8 100644 --- a/notebooks/challenge/cam-chem_waccm/exercise_1.ipynb +++ b/notebooks/challenge/cam-chem_waccm/exercise_1.ipynb @@ -127,7 +127,7 @@ "\n", "Create a new case with the command ``create_newcase``:\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", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET\n", "```\n", "You may need to add ``--project \"UESM0013\"`` when creating a new case.\n", diff --git a/notebooks/challenge/cam-chem_waccm/exercise_2.ipynb b/notebooks/challenge/cam-chem_waccm/exercise_2.ipynb index c6b24d51e..fef70c6ca 100644 --- a/notebooks/challenge/cam-chem_waccm/exercise_2.ipynb +++ b/notebooks/challenge/cam-chem_waccm/exercise_2.ipynb @@ -120,7 +120,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET\n", "```\n", "You may need to add ``--project \"UESM0013\"`` when creating a new case.\n", diff --git a/notebooks/challenge/cam-chem_waccm/exercise_3.ipynb b/notebooks/challenge/cam-chem_waccm/exercise_3.ipynb index 2cf02e099..e4dcf8d98 100644 --- a/notebooks/challenge/cam-chem_waccm/exercise_3.ipynb +++ b/notebooks/challenge/cam-chem_waccm/exercise_3.ipynb @@ -95,7 +95,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET\n", "```\n", "You may need to add ``--project \"UESM0013\"`` when creating a new case.\n", diff --git a/notebooks/challenge/cam/cam.ipynb b/notebooks/challenge/cam/cam.ipynb index e6ae0430b..d7f6ff304 100644 --- a/notebooks/challenge/cam/cam.ipynb +++ b/notebooks/challenge/cam/cam.ipynb @@ -73,11 +73,11 @@ "\n", "If you want to run a different configuration from what you’ve learned here, it is important to learn how to find and/or modify a compset.\n", "\n", - "The tool `query compsets` allows you to find more information about the available. This tool is located in the same directory as `create_newcase` in `/glade/work/$USER/code/my_cesm_code/cime/scripts/`:\n", + "The tool `query compsets` allows you to find more information about the available. This tool is located in the same directory as `create_newcase` in `/glade/u/home/$USER/code/my_cesm_code/cime/scripts/`:\n", "\n", "The command is:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./query_config --compsets\n", "```\n", "\n", @@ -95,7 +95,7 @@ "\n", "The command gives a list of all the compsets available, and what components are included. \n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./query_config --compsets\n", "```\n", "This can show exactly what you ran before, and what is possible. To narrow down your choices:\n", diff --git a/notebooks/challenge/cam/exercise_1.ipynb b/notebooks/challenge/cam/exercise_1.ipynb index 788b21a48..41fd9a133 100644 --- a/notebooks/challenge/cam/exercise_1.ipynb +++ b/notebooks/challenge/cam/exercise_1.ipynb @@ -99,7 +99,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET\n", "```\n", "\n", diff --git a/notebooks/challenge/cam/exercise_2.ipynb b/notebooks/challenge/cam/exercise_2.ipynb index aa9b13681..e76a1b721 100644 --- a/notebooks/challenge/cam/exercise_2.ipynb +++ b/notebooks/challenge/cam/exercise_2.ipynb @@ -104,7 +104,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET --run-unsupported\n", "```\n", "\n", diff --git a/notebooks/challenge/cam/exercise_3.ipynb b/notebooks/challenge/cam/exercise_3.ipynb index e5842df3d..61be62837 100644 --- a/notebooks/challenge/cam/exercise_3.ipynb +++ b/notebooks/challenge/cam/exercise_3.ipynb @@ -112,7 +112,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET --run-unsupported\n", "```\n", "\n", diff --git a/notebooks/challenge/cam/exercise_4.ipynb b/notebooks/challenge/cam/exercise_4.ipynb index c272d28c2..c1248d368 100644 --- a/notebooks/challenge/cam/exercise_4.ipynb +++ b/notebooks/challenge/cam/exercise_4.ipynb @@ -101,7 +101,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET \n", "```\n", "\n", diff --git a/notebooks/challenge/cam/exercise_5.ipynb b/notebooks/challenge/cam/exercise_5.ipynb index 5de298e03..aff3a4602 100644 --- a/notebooks/challenge/cam/exercise_5.ipynb +++ b/notebooks/challenge/cam/exercise_5.ipynb @@ -103,7 +103,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET \n", "```\n", "\n", diff --git a/notebooks/challenge/cam/exercise_6.ipynb b/notebooks/challenge/cam/exercise_6.ipynb index de52d31ed..1534f50c5 100644 --- a/notebooks/challenge/cam/exercise_6.ipynb +++ b/notebooks/challenge/cam/exercise_6.ipynb @@ -101,7 +101,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET \n", "```\n", "\n", @@ -128,7 +128,7 @@ "\n", "- copy `zm_conv.F90` into the `SourceMods/src.cam` directory and modify it\n", "```\n", - "cp /glade/work/$USER/code/my_cesm_code/components/cam/src/physics/cam/zm_conv.F90 SourceMods/src.cam\n", + "cp /glade/u/home/$USER/code/my_cesm_code/components/cam/src/physics/cam/zm_conv.F90 SourceMods/src.cam\n", "```\n", "\n", "- In the subroutine `zm_convr`\n", diff --git a/notebooks/challenge/cice/cice_exercise_1.ipynb b/notebooks/challenge/cice/cice_exercise_1.ipynb index fb6e9440d..645599f3d 100644 --- a/notebooks/challenge/cice/cice_exercise_1.ipynb +++ b/notebooks/challenge/cice/cice_exercise_1.ipynb @@ -119,8 +119,8 @@ " \n", "Create a new case g_control with the command:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", - "./create_newcase --case /glade/work/$USER/cases/g_control --compset G --res T62_g37 \n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", + "./create_newcase --case /glade/u/home/$USER/cases/g_control --compset G --res T62_g37 \n", "```\n", "
\n", "\n", diff --git a/notebooks/challenge/cice/cice_exercise_2.ipynb b/notebooks/challenge/cice/cice_exercise_2.ipynb index 6ac8c1817..cafe133fb 100644 --- a/notebooks/challenge/cice/cice_exercise_2.ipynb +++ b/notebooks/challenge/cice/cice_exercise_2.ipynb @@ -143,14 +143,14 @@ " \n", "Clone a new case g_snowalbedo from your control experiment with the command:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", - "./create_clone --case /glade/work/$USER/cases/g_snowalbedo --clone /glade/work/$USER/cases/g_control\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", + "./create_clone --case /glade/u/home/$USER/cases/g_snowalbedo --clone /glade/u/home/$USER/cases/g_control\n", "```\n", "
\n", "\n", "Case setup:\n", "``` \n", - "cd /glade/work/$USER/cases/g_snowalbedo\n", + "cd /glade/u/home/$USER/cases/g_snowalbedo\n", "./case.setup\n", "```\n", "
\n", diff --git a/notebooks/challenge/cice/cice_exercise_3.ipynb b/notebooks/challenge/cice/cice_exercise_3.ipynb index c1ad4f13d..65a5c5880 100644 --- a/notebooks/challenge/cice/cice_exercise_3.ipynb +++ b/notebooks/challenge/cice/cice_exercise_3.ipynb @@ -35,7 +35,7 @@ " \n", "Set the run length to **1 year**. \n", "\n", - "Go to the main source directory under /glade/work/$USER/code/my_cesm_code/components/cice/src and search for the variable `ksno`.\n", + "Go to the main source directory under /glade/u/home/$USER/code/my_cesm_code/components/cice/src and search for the variable `ksno`.\n", " \n", "Copy the source module from the main CESM code directory into $CASE/SourceMods/src.cice.\n", "\n", @@ -115,14 +115,14 @@ " \n", " Clone a new case g_ksno from your control experiment with the command:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", - "./create_clone --case /glade/work/$USER/cases/g_ksno --clone /glade/work/$USER/cases/g_control\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", + "./create_clone --case /glade/u/home/$USER/cases/g_ksno --clone /glade/u/home/$USER/cases/g_control\n", "```\n", "
\n", "\n", "Case setup:\n", "``` \n", - "cd /glade/work/$USER/cases/g_ksno\n", + "cd /glade/u/home/$USER/cases/g_ksno\n", "./case.setup\n", "```\n", "
\n", @@ -136,9 +136,9 @@ "\n", "Copy the file from the $CODEROOT directory:\n", "```\n", - "cp /glade/work/$USER/code/my_cesm_code/components/cice/src/drivers/cesm/ice_constants.F90 /glade/work/$USER/cases/g_ksno/SourceMods/src.cice\n", + "cp /glade/u/home/$USER/code/my_cesm_code/components/cice/src/drivers/cesm/ice_constants.F90 /glade/u/home/$USER/cases/g_ksno/SourceMods/src.cice\n", "\n", - "vi /glade/work/$USER/cases/g_ksno/SourceMods/src.cice/ice_constants.F90\n", + "vi /glade/u/home/$USER/cases/g_ksno/SourceMods/src.cice/ice_constants.F90\n", "```\n", "
\n", "\n", diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_1.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_1.ipynb index df8606e3f..ba568d4af 100644 --- a/notebooks/challenge/clm_ctsm/clm_exercise_1.ipynb +++ b/notebooks/challenge/clm_ctsm/clm_exercise_1.ipynb @@ -37,7 +37,7 @@ " \n", "Create a new case i.day5.a with the command:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts\n", "./create_newcase --case ~/cases/i.day5.a --compset I2000Clm50Sp --res f09_g17_gl4 --run-unsupported\n", "```\n", "
\n", diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_2.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_2.ipynb index 93c53b903..e07bdace7 100644 --- a/notebooks/challenge/clm_ctsm/clm_exercise_2.ipynb +++ b/notebooks/challenge/clm_ctsm/clm_exercise_2.ipynb @@ -56,7 +56,7 @@ " \n", "Create a new case i.day5.b :\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts\n", "./create_newcase --case ~/cases/i.day5.b --compset IHistClm50BgcCrop --res f09_g17_gl4 --run-unsupported\n", "```\n", "
\n", diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_3.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_3.ipynb index 3dae486b9..99939c22e 100644 --- a/notebooks/challenge/clm_ctsm/clm_exercise_3.ipynb +++ b/notebooks/challenge/clm_ctsm/clm_exercise_3.ipynb @@ -53,7 +53,7 @@ " \n", "Create a clone from the control experiment i.day5.a_pft :\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts\n", "./create_clone --case ~/cases/i.day5.a_pft --clone ~/cases/i.day5.a\n", "```\n", "
\n", diff --git a/notebooks/challenge/mom/mom_exercise_5.ipynb b/notebooks/challenge/mom/mom_exercise_5.ipynb index dd239be2f..0eaf132be 100644 --- a/notebooks/challenge/mom/mom_exercise_5.ipynb +++ b/notebooks/challenge/mom/mom_exercise_5.ipynb @@ -32,7 +32,7 @@ "Change the current directory to the code workspace directory:
\n", "\n", "```\n", - "cd /glade/work/$USER/code\n", + "cd /glade/u/home/$USER/code\n", "```\n", "
\n", " \n", @@ -51,7 +51,7 @@ "
\n", " \n", "```\n", - "cd /glade/work/$USER/code/cesm2_3_beta17\n", + "cd /glade/u/home/$USER/code/cesm2_3_beta17\n", "./manage_externals/checkout_externals -o\n", "```\n", "
\n", @@ -149,8 +149,8 @@ " \n", "Create a new case gmom_jra.run_length with the command:\n", "```\n", - "cd /glade/work/$USER/code/cesm2_3_beta17/cime/scripts/\n", - "./create_newcase --case /glade/work/$USER/cases/gmom_jra.run_length --compset GMOM_JRA --res TL319_t232 \n", + "cd /glade/u/home/$USER/code/cesm2_3_beta17/cime/scripts/\n", + "./create_newcase --case /glade/u/home/$USER/cases/gmom_jra.run_length --compset GMOM_JRA --res TL319_t232 \n", "```\n", "
\n", "\n", diff --git a/notebooks/challenge/paleo/exercise_1.ipynb b/notebooks/challenge/paleo/exercise_1.ipynb index b0e2ad602..9696d2ae9 100644 --- a/notebooks/challenge/paleo/exercise_1.ipynb +++ b/notebooks/challenge/paleo/exercise_1.ipynb @@ -110,7 +110,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET --project $PROJECT\n", "```\n", "\n", diff --git a/notebooks/challenge/paleo/exercise_2.ipynb b/notebooks/challenge/paleo/exercise_2.ipynb index 1c217ee07..49a5caae4 100644 --- a/notebooks/challenge/paleo/exercise_2.ipynb +++ b/notebooks/challenge/paleo/exercise_2.ipynb @@ -125,7 +125,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET --project $PROJECT\n", "```\n", "\n", diff --git a/notebooks/challenge/paleo/exercise_3.ipynb b/notebooks/challenge/paleo/exercise_3.ipynb index 32f29b485..738b84561 100644 --- a/notebooks/challenge/paleo/exercise_3.ipynb +++ b/notebooks/challenge/paleo/exercise_3.ipynb @@ -69,7 +69,7 @@ "Set environment variables with the commands:\n", "\n", "```\n", - "cd /glade/work/$USER/code \n", + "cd /glade/u/home/$USER/code \n", "git clone https://github.com/NCAR/iCESM1.3_iHESP_hires iCESM1.3_iHESP_hires \n", "cd iCESM1.3_iHESP_hires \n", "./manage_externals/checkout_externals \n", @@ -119,7 +119,7 @@ "\n", "Create a new case with the command ``create_newcase``:\n", "```\n", - "cd /glade/work/$USER/code/iCESM1.3_iHESP_hires/cime/scripts/\n", + "cd /glade/u/home/$USER/code/iCESM1.3_iHESP_hires/cime/scripts/\n", "./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET --project $PROJECT --run-unsupported \n", "```\n", "\n", diff --git a/notebooks/challenge/pop/pop_exercise_1.ipynb b/notebooks/challenge/pop/pop_exercise_1.ipynb index 07c1e07a6..ac110d238 100644 --- a/notebooks/challenge/pop/pop_exercise_1.ipynb +++ b/notebooks/challenge/pop/pop_exercise_1.ipynb @@ -89,8 +89,8 @@ " \n", "Create a new case g_control with the command:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", - "./create_newcase --case /glade/work/$USER/cases/g_control --compset G --res T62_g37 \n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", + "./create_newcase --case /glade/u/home/$USER/cases/g_control --compset G --res T62_g37 \n", "```\n", "
\n", "\n", diff --git a/notebooks/challenge/pop/pop_exercise_2.ipynb b/notebooks/challenge/pop/pop_exercise_2.ipynb index 61e72ce81..d40e4dc65 100644 --- a/notebooks/challenge/pop/pop_exercise_2.ipynb +++ b/notebooks/challenge/pop/pop_exercise_2.ipynb @@ -84,13 +84,13 @@ " \n", "Clone a new case g_overflows from your control experiment with the command:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", - "./create_clone --case /glade/work/$USER/cases/g_overflows --clone /glade/work/$USER/cases/g_control\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", + "./create_clone --case /glade/u/home/$USER/cases/g_overflows --clone /glade/u/home/$USER/cases/g_control\n", "```\n", "\n", "Case setup:\n", "``` \n", - "cd /glade/work/$USER/cases/g_overflows\n", + "cd /glade/u/home/$USER/cases/g_overflows\n", "./case.setup\n", "```\n", "\n", diff --git a/notebooks/challenge/pop/pop_exercise_3.ipynb b/notebooks/challenge/pop/pop_exercise_3.ipynb index 5321da323..1681d67a6 100644 --- a/notebooks/challenge/pop/pop_exercise_3.ipynb +++ b/notebooks/challenge/pop/pop_exercise_3.ipynb @@ -79,13 +79,13 @@ " \n", "Clone a new case g_windstress from your control experiment with the command:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", - "./create_clone --case /glade/work/$USER/cases/g_windstress --clone /glade/work/$USER/cases/g_control\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", + "./create_clone --case /glade/u/home/$USER/cases/g_windstress --clone /glade/u/home/$USER/cases/g_control\n", "```\n", "\n", "Case setup:\n", "``` \n", - "cd /glade/work/$USER/cases/g_windstress\n", + "cd /glade/u/home/$USER/cases/g_windstress\n", "./case.setup\n", "```\n", "\n", @@ -97,7 +97,7 @@ " \n", "Copy the forcing_coupled.F90 file from the control case to the ocean SourceMods.\n", "``` \n", - "cp /glade/work/$USER/code/my_cesm_code/components/pop/source/forcing_coupled.F90 /glade/work/$USER/cases/g_windstress/SourceMods/src.pop\n", + "cp /glade/u/home/$USER/code/my_cesm_code/components/pop/source/forcing_coupled.F90 /glade/u/home/$USER/cases/g_windstress/SourceMods/src.pop\n", "``` \n", " \n", "Edit the file forcing_coupled.F90 in the rotate_wind_stress routine after ```SMFT(:,:,1,:)``` is defined:\n", diff --git a/notebooks/challenge/pop/pop_exercise_4.ipynb b/notebooks/challenge/pop/pop_exercise_4.ipynb index e16128ff3..6b2f4c173 100644 --- a/notebooks/challenge/pop/pop_exercise_4.ipynb +++ b/notebooks/challenge/pop/pop_exercise_4.ipynb @@ -86,13 +86,13 @@ " \n", "Create a new case G1850ECO with the command:\n", "```\n", - "cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", - "./create_newcase --case /glade/work/$USER/cases/G1850ECO --compset G1850ECO --res T62_g37\n", + "cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", + "./create_newcase --case /glade/u/home/$USER/cases/G1850ECO --compset G1850ECO --res T62_g37\n", "```\n", "\n", "Case setup:\n", "``` \n", - "cd /glade/work/$USER/cases/G1850ECO \n", + "cd /glade/u/home/$USER/cases/G1850ECO \n", "./case.setup\n", "```\n", " \n", diff --git a/notebooks/diagnostics/additional/uxarray.ipynb b/notebooks/diagnostics/additional/uxarray.ipynb index f33c2d45d..b02ecaf3e 100644 --- a/notebooks/diagnostics/additional/uxarray.ipynb +++ b/notebooks/diagnostics/additional/uxarray.ipynb @@ -207,7 +207,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/glade/work/oero/conda-envs/uxarray-dask/lib/python3.12/site-packages/uxarray/grid/geometry.py:95: UserWarning: Converting to a GeoDataFrame with over 1,000,000 faces may take some time.\n", + "/glade/u/home/oero/conda-envs/uxarray-dask/lib/python3.12/site-packages/uxarray/grid/geometry.py:95: UserWarning: Converting to a GeoDataFrame with over 1,000,000 faces may take some time.\n", " warnings.warn(\n" ] }, diff --git a/notebooks/diagnostics/mom/basics_mom.ipynb b/notebooks/diagnostics/mom/basics_mom.ipynb index 135954736..15ad332bc 100644 --- a/notebooks/diagnostics/mom/basics_mom.ipynb +++ b/notebooks/diagnostics/mom/basics_mom.ipynb @@ -125,7 +125,7 @@ "\n", "
\n", " \n", - "/glade/work/$USER/cases/gmom_jra.run_length/CaseDocs/diag_table\n", + "/glade/u/home/$USER/cases/gmom_jra.run_length/CaseDocs/diag_table\n", "\n", "
\n", "\n", diff --git a/notebooks/modifications/xml/exercises/xml_length_exercise.ipynb b/notebooks/modifications/xml/exercises/xml_length_exercise.ipynb index f84da235c..5b66bff56 100644 --- a/notebooks/modifications/xml/exercises/xml_length_exercise.ipynb +++ b/notebooks/modifications/xml/exercises/xml_length_exercise.ipynb @@ -21,7 +21,9 @@ " \n", "**Part II**:\n", "*Do part II only **after** Part I has finished running*. \n", - "Change the debug level back to 1. Expand Part I to produce a total of 38 months of model run. Remember that you have already run for 1 month. **You should submit this at the end of the day so that it will (hopefully) run overnight and be available the following day.** You can continue with Exercise 2-3 and submit the run later.\n", + "Change the debug level back to 1. Expand Part I to produce a total of 38 months of model run. Remember that you have already run for 1 month. **You should submit this at the end of the day so that it will (hopefully) run overnight and be available the following day. Also you should submit that run in the ``cpu`` queue, so it doesn't interfere with the other exercises** You can continue with Exercise 2-3 and submit the run later.\n", + "\n", + "**VERY IMPORTANT: submit Part II, in the ``cpu`` queue and not the ``tutorial`` queue **\n", "\n", "
" ] @@ -70,18 +72,18 @@ " \n", "\n", " \n", - "From the `SRCROOT` (`/glade/work/$USER/code/my_cesm_code`) directory, create your case:\n", + "From the `SRCROOT` (`/glade/u/home/$USER/code/my_cesm_code`) directory, create your case:\n", " \n", "```\n", - " cd /glade/work/$USER/code/my_cesm_code/cime/scripts\n", - " ./create_newcase --case /glade/work/$USER/cases/b1850.run_length --res f19_g17 --compset B1850\n", + " cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts\n", + " ./create_newcase --case /glade/u/home/$USER/cases/b1850.run_length --res f19_g17 --compset B1850\n", "```\n", "
\n", " \n", "In your case directory, change debugging levels and set runtime variables:\n", "\n", "```\n", - " cd /glade/work/$USER/cases/b1850.run_length\n", + " cd /glade/u/home/$USER/cases/b1850.run_length\n", " ./xmlchange INFO_DBUG=2,STOP_N=3,STOP_OPTION=nmonths\n", " ./xmlchange --subgroup case.run JOB_WALLCLOCK_TIME=2:00:00\n", "```\n", @@ -122,6 +124,7 @@ "1. To continue the run, set `CONTINUE_RUN` to `TRUE`\n", " \n", "```\n", + " cd /glade/u/home/$USER/cases/b1850.run_length\n", " ./xmlchange CONTINUE_RUN=TRUE\n", "```\n", "\n", @@ -143,8 +146,16 @@ " ./xmlchange INFO_DBUG=1\n", "```\n", "\n", + "\n", + "
\n", + "5. Change queue\n", + " \n", + "```\n", + " ./xmlchange JOB_QUEUE=cpu\n", + "```\n", + "\n", "
\n", - "5. Change wallclock time to use the maximum of the allowed wallclock on derecho:\n", + "6. Change wallclock time to use the maximum of the allowed wallclock on derecho:\n", " \n", "```\n", " ./xmlchange --subgroup case.run JOB_WALLCLOCK_TIME=12:00:00\n", @@ -152,7 +163,7 @@ "```\n", "\n", "
\n", - "6. Submit (./case.submit) from your b1850.run_length case directory:\n", + "7. Submit (./case.submit) from your b1850.run_length case directory:\n", "\n", "```\n", " ./case.submit\n", @@ -187,7 +198,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.12" + "version": "3.10.13" } }, "nbformat": 4, diff --git a/notebooks/modifications/xml/exercises/xml_runtype_exercise.ipynb b/notebooks/modifications/xml/exercises/xml_runtype_exercise.ipynb index 69b8ced50..c2de435f3 100644 --- a/notebooks/modifications/xml/exercises/xml_runtype_exercise.ipynb +++ b/notebooks/modifications/xml/exercises/xml_runtype_exercise.ipynb @@ -68,8 +68,8 @@ "1. Create your new case with the command:\n", " \n", "```\n", - " cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", - " ./create_newcase --case /glade/work/$USER/cases/b1850.branch --res f19_g17 --compset B1850\n", + " cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", + " ./create_newcase --case /glade/u/home/$USER/cases/b1850.branch --res f19_g17 --compset B1850\n", "```\n", "
\n", "\n", @@ -77,7 +77,7 @@ "2. In your case directory, change the run type to branch, and change the associated RUN_* variables:\n", "\n", "```\n", - " cd /glade/work/$USER/cases/b1850.branch\n", + " cd /glade/u/home/$USER/cases/b1850.branch\n", " ./xmlchange RUN_TYPE=branch\n", " ./xmlchange RUN_REFCASE=b1850.run_length,RUN_REFDATE=0001-04-01,GET_REFCASE=FALSE\n", "```\n", diff --git a/notebooks/modifications/xml/exercises/xml_timestep_exercise.ipynb b/notebooks/modifications/xml/exercises/xml_timestep_exercise.ipynb index 819312a81..471d52efb 100644 --- a/notebooks/modifications/xml/exercises/xml_timestep_exercise.ipynb +++ b/notebooks/modifications/xml/exercises/xml_timestep_exercise.ipynb @@ -17,7 +17,7 @@ "\n", "Exercise: Change physics timestep in CAM and CLM

\n", "\n", - "**Hybrid** start a fully coupled run under pre-Industrial conditions with a resolution of f19_g17. Use restart and initial files from Exercise 2. Change the physics timestep in the atmosphere and land to 1200 seconds (default is 1800). Run 5 days.\n", + "**Hybrid** start a fully coupled run under pre-Industrial conditions with a resolution of f19_g17. Use restart and initial files from Exercise 1. Change the physics timestep in the atmosphere and land to 1200 seconds (default is 1800). Run 5 days.\n", " \n", "
" ] @@ -60,16 +60,17 @@ "1. From the script directory, create your case:\n", " \n", "```\n", - " cd /glade/work/$USER/code/my_cesm_code/cime/scripts/\n", - " ./create_newcase --case /glade/work/$USER/cases/b1850.timestep --res f19_g17 --compset B1850\n", + " cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/\n", + " ./create_newcase --case /glade/u/home/$USER/cases/b1850.timestep --res f19_g17 --compset B1850\n", "```\n", " \n", "
\n", "2. In your case directory, change run type and runtime variables:\n", " \n", "```\n", - " cd /glade/work/$USER/cases/b1850.timestep\n", - " ./xmlchange RUN_TYPE=hybrid,RUN_REFCASE=b1850.branch,RUN_REFDATE=0001-06-01,GET_REFCASE=FALSE,JOB_WALLCLOCK_TIME=2:00:00\n", + " cd /glade/u/home/$USER/cases/b1850.timestep\n", + " ./xmlchange RUN_TYPE=hybrid\n", + " ./xmlchange RUN_REFCASE=b1850.run_length,RUN_REFDATE=0001-04-01,GET_REFCASE=FALSE,JOB_WALLCLOCK_TIME=2:00:00\n", "```\n", " \n", "
\n", @@ -85,7 +86,7 @@ " \n", "```\n", " ./case.setup\n", - " cp /glade/derecho/scratch/$USER/archive/b1850.branch/rest/0001-06-01-00000/* /glade/derecho/scratch/$USER/b1850.timestep/run/\n", + " cp /glade/derecho/scratch/$USER/archive/b1850.run_length/rest/0001-04-01-00000/* /glade/derecho/scratch/$USER/b1850.timestep/run/\n", "```\n", " \n", "
\n", @@ -127,7 +128,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.12" + "version": "3.10.13" } }, "nbformat": 4, diff --git a/notebooks/modifications/xml/overview.ipynb b/notebooks/modifications/xml/overview.ipynb index 37d127221..e4b65095b 100644 --- a/notebooks/modifications/xml/overview.ipynb +++ b/notebooks/modifications/xml/overview.ipynb @@ -80,7 +80,7 @@ "![CESM xml files](../../../images/modifications/CESM2_xml_files.png)\n", "*

Figure: Overview of the XML file locations

*\n", "For the current tutorial on derecho, the paths are:\n", - "- `$CASEROOT` = `/glade/work/$USER/cases/$CASE`" + "- `$CASEROOT` = `/glade/u/home/$USER/cases/$CASE`" ] }, { diff --git a/notebooks/namelist/exercises/exercise_cam_output.ipynb b/notebooks/namelist/exercises/exercise_cam_output.ipynb index 7125e4a83..46596092d 100644 --- a/notebooks/namelist/exercises/exercise_cam_output.ipynb +++ b/notebooks/namelist/exercises/exercise_cam_output.ipynb @@ -116,7 +116,7 @@ "\n", "Create a new case `b1850_high_freq` with the command:\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", "./create_newcase --case ~/cases/b1850_high_freq --compset B1850 --res f19_g17 \n", "```\n", "\n", diff --git a/notebooks/namelist/exercises/exercise_tuning_parameter.ipynb b/notebooks/namelist/exercises/exercise_tuning_parameter.ipynb index 8a05d7a52..d4d5115b1 100644 --- a/notebooks/namelist/exercises/exercise_tuning_parameter.ipynb +++ b/notebooks/namelist/exercises/exercise_tuning_parameter.ipynb @@ -74,7 +74,7 @@ " \n", "Create a new case `b1850_dcs`with the command:\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", "./create_newcase --case ~/cases/b1850_dcs --compset B1850 --res f19_g17 \n", "```\n", "\n", diff --git a/notebooks/sourcemods/exercises/exercise_add_field.ipynb b/notebooks/sourcemods/exercises/exercise_add_field.ipynb index e56e9c874..56ce325f6 100644 --- a/notebooks/sourcemods/exercises/exercise_add_field.ipynb +++ b/notebooks/sourcemods/exercises/exercise_add_field.ipynb @@ -78,7 +78,7 @@ " \n", "Create a new case `b1850_T750` with the command:\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", "./create_newcase --case ~/cases/b1850_T750 --compset B1850 --res f19_g17 \n", "```\n", "\n", diff --git a/notebooks/troubleshooting/exercises/troubleshooting_cam.ipynb b/notebooks/troubleshooting/exercises/troubleshooting_cam.ipynb index d9e2822e3..29aca109d 100644 --- a/notebooks/troubleshooting/exercises/troubleshooting_cam.ipynb +++ b/notebooks/troubleshooting/exercises/troubleshooting_cam.ipynb @@ -83,7 +83,7 @@ " \n", "Create a new case ``b1850_high_freq_bugfixing`` with the command:\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", " ./create_newcase --case ~/cases/b1850_high_freq_bugfixing --compset B1850 --res f19_g17 \n", "```\n", "\n",