Merge pull request #8 from pabloprf/development_upgrade

Refactored remote execution handler, general improvements and bug fixes in preparation for release
pabloprf · Jan 16, 2024 · d7a1f78 · d7a1f78
2 parents c19778d + 2e4959c
commit d7a1f78
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diff --git a/config/config_user_example.json b/config/config_user_example.json
@@ -20,10 +20,26 @@
         "scratch":    "/Users/exampleusername/scratch/",
         "modules":    ""
     },
+    "perlmutter": {
+        "machine":          "perlmutter.nersc.gov", 
+        "username":         "exampleusername",
+        "scratch":          "/pscratch/sd/p/exampleusername/",
+        "identity":         "$HOME/.ssh/nersc",
+        "slurm": {
+            "account":      "m3195_g",
+            "partition":    "debug",
+            "constraint":   "gpu",
+            "mem":          "4GB",
+            "email":      "optional@email"
+        }
+    },
     "engaging": {
         "machine":          "eofe7.mit.edu", 
         "username":         "exampleusername",
-        "partition":        "sched_mit_psfc",
+        "slurm": {
+            "partition":    "sched_mit_psfc",
+            "exclude":      "node584"
+        },
         "identity":         "~/.ssh/id_rsa",
         "scratch":          "/nobackup1/exampleusername/",
         "modules":    ""
@@ -39,7 +55,6 @@
         "machine":          "mfews02.psfc.mit.edu", 
         "username":         "exampleusername",
         "tunnel":           "mferws01.psfc.mit.edu",
-        "scratch_tunnel":   "/home/exampleusername/scratch/",
         "port":             9224,
         "scratch":          "/home/exampleusername/scratch/",
         "modules":    ""
@@ -48,7 +63,6 @@
         "machine":    "irisa.gat.com", 
         "username":   "exampleusername",
         "tunnel":     "cybele.gat.com",
-        "scratch_tunnel": "/home/exampleusername/scratch/",
         "port":            2039,
         "scratch":    "/cluster-scratch/exampleusername/",
         "modules":    ""

diff --git a/config/machines_sources/aliases.bashrc b/config/machines_sources/aliases.bashrc
@@ -3,23 +3,34 @@
 # ---------------------------------------------------------------------------------------------------------------------
 
 # mitim_tools interfaces: read, run, plot
-alias mitim_plot_gacode="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_gacodes.py --files $1"
-alias mitim_plot_tgyro="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_tgyros.py --folders $1"
-alias mitim_plot_tglf="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_tglf.py --folder $1" 		 # [--suffix _0.55] [--gacode input.gacode]
-alias mitim_plot_eq="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gs_tools/exe/read_eqs.py --files $1"
-alias mitim_read_transp="ipython3 -i -- $MITIM_PATH/src/mitim_tools/transp_tools/exe/read_transp.py --files $1"
-alias mitim_run_tglf="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/run_tglf.py --folder $1 --tglf $2" #[--gacode input.gacode] [--scan RLTS_2] [--drives True]
+
+alias mitim_plot_gacode="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_gacode.py $1"
+alias mitim_plot_tgyro="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_tgyro.py $1"
+alias mitim_plot_tglf="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_tglf.py $1" 		 # [--suffix _0.55] [--gacode input.gacode]
+alias mitim_plot_cgyro="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_cgyro.py $1"
+alias mitim_plot_eq="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gs_tools/exe/read_eq.py $1"
+alias mitim_plot_transp="ipython3 -i -- $MITIM_PATH/src/mitim_tools/transp_tools/exe/read_transp.py $1"
+
+alias mitim_run_tglf="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/run_tglf.py $1 $2" # (folder input.tglf)  [--gacode input.gacode] [--scan RLTS_2] [--drives True]
 
 # Optimizations
-alias mitim_plot_opt="ipython3 -i -- $MITIM_PATH/src/mitim_tools/opt_tools/exe/read.py --type 4 --resolution 20 --folders $1"
-alias mitim_plot_portalsSR="ipython3 -i -- $MITIM_PATH/src/mitim_modules/portals/exe/check_initialization.py $1"
-alias mitim_plot_portals="mitim_plot_opt $1"
+alias mitim_plot_opt="ipython3 -i -- $MITIM_PATH/src/mitim_tools/opt_tools/exe/read.py --type 4 --resolution 20 $1"
+alias mitim_plot_portals="ipython3 -i -- $MITIM_PATH/src/mitim_modules/portals/exe/readMetrics.py $1"
+alias mitim_slurm="python3 $MITIM_PATH/src/mitim_tools/opt_tools/exe/slurm.py $1"
 
 # TRANSP
-alias mitim_trcheck="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_check.py $1"		# mitim_trcheck pablorf
-alias mitim_trclean="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_clean.py $1" 		# mitim_trclean 88664P CMOD --numbers 1,2,3
-alias mitim_trlook="ipython3 -i -- $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_look.py $1" # mitim_trlook 152895P01 CMOD --nofull --plot --remove
+alias mitim_trcheck="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_check.py $1"		        # mitim_trcheck pablorf
+alias mitim_trcheck_p="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_check_periodic.py $1"	# mitim_trcheck_p pablorf
+alias mitim_trclean="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_clean.py $1" 		        # mitim_trclean 88664P CMOD --numbers 1,2,3
+alias mitim_trlook="ipython3 -i -- $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_look.py $1"         # mitim_trlook 152895P01 CMOD --nofull --plot --remove
+
+# To run TRANSP (in folder with required files): transp 88664 P01 CMOD --version tshare --trmpi 32 --toricmpi 32 --ptrmpi 32
+alias transp="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_transp.py"
+
+# IM Aliases
+alias runim="python3 $MITIM_PATH/src/mitim_tools/im_tools/exe/run_im.py ./"             # To run complete IM evaluation:   runim 7 [DebugOption: --debug 0]
+alias runmitim="python3 $MITIM_PATH/mitim_opt/scenarios_tools/routines/runMITIM_BO.py"  # To peform scenario optimization
 
 # Others
 alias compare_nml="python3 $MITIM_PATH/src/mitim_tools/transp_tools/routines/compareNML.py $1"
-alias eff_job="python3 $MITIM_PATH/src/mitim_tools/misc_tools/PARALLELtools.py $1" # Give sbatch.out or slurm_output.dat
+alias eff_job="python3 $MITIM_PATH/src/mitim_tools/misc_tools/PARALLELtools.py $1" # Give mitim.out or slurm_output.dat
diff --git a/config/machines_sources/eofe.bashrc b/config/machines_sources/eofe.bashrc
@@ -1,3 +1,7 @@
+# This is a setup file for the EOFE cluster. Remember (see Installation guide) that this is not
+# stricly necessary. However, it is convenient to have it here, so that you can load the modules
+# with a single command. If you do not want to use this file, you can load the modules manually
+# if you have these lines in your .bashrc (or equivalent)
 
 module use /home/software/psfc/modulefiles/
 
@@ -64,7 +68,7 @@ then
 	# --------------------------------------------------------------------------------
 
 	export GACODE_PLATFORM=PSFC_EOFE_RPP
-	export GACODE_ROOT=/home/$USER/gacode_sparc
+	export GACODE_ROOT=/home/$USER/gacode_rpp
 
 	# --------------------------------------------------------------------------------
 	#               ASTRA

diff --git a/config/machines_sources/iris.bashrc b/config/machines_sources/iris.bashrc
@@ -1,17 +1,19 @@
-# Stuff only for IRIS machine
+# This is a setup file for the IRIS cluster. Remember (see Installation guide) that this is not
+# stricly necessary. However, it is convenient to have it here, so that you can load the modules
+# with a single command. If you do not want to use this file, you can load the modules manually
+# if you have these lines in your .bashrc (or equivalent)
 
 # ------------------------------------------------------------------------------------------------
 #               GACODE
 # ------------------------------------------------------------------------------------------------
 
-# module load atom/pygacode
-
 ! [ -z "$PS1" ] && echo "              * Proceeding to load GACODE modules"
 
 export GACODE_PLATFORM=IRIS
 export GACODE_ROOT=/home/$USER/gacode
-
 . ${GACODE_ROOT}/shared/bin/gacode_setup
+module load ntcc
+
 #. ${GACODE_ROOT}/platform/env/env.${GACODE_PLATFORM}   # IMPORTANT to not do this, otherwise it will then point to atom
 
 if [ $? -eq 124 ]
@@ -20,10 +22,3 @@ then
 else
 	! [ -z "$PS1" ] && echo "                   * GACODE modules loaded"
 fi
-
-# ------------------------------------------------------------------------------------------------
-#               TRANSP/NTCC
-# ------------------------------------------------------------------------------------------------
-
-module load omfit/unstable
-module load ntcc
diff --git a/config/machines_sources/nersc.bashrc b/config/machines_sources/nersc.bashrc
@@ -0,0 +1,20 @@
+# This is a setup file for NERSC Perlmutter. Remember (see Installation guide) that this is not
+# stricly necessary. However, it is convenient to have it here, so that you can load the modules
+# with a single command. If you do not want to use this file, you can load the modules manually
+# if you have these lines in your .bashrc (or equivalent)
+
+if [ "$NERSC_HOST" = perlmutter ]
+then
+	! [ -z "$PS1" ] && echo "              * PERLMUTTER"
+
+    # ------------------------------------------------------------------------------------------------
+    #               GACODE
+    # ------------------------------------------------------------------------------------------------
+
+    export GACODE_PLATFORM=PERLMUTTER_GPU
+    export GACODE_ROOT=$HOME/gacode
+    . $GACODE_ROOT/shared/bin/gacode_setup
+    . ${GACODE_ROOT}/platform/env/env.$GACODE_PLATFORM
+fi
+
+source $MITIM_PATH/config/machines_sources/slurm_aliases.bashrc
diff --git a/config/mitim.bashrc b/config/mitim.bashrc
@@ -40,13 +40,15 @@ then
 elif [ "${HOSTNAME:0:3}" = toki ]
 then
 	source $MITIM_PATH/config/machines_sources/toki.bashrc
+# NERSC
+elif [ "$NERSC_HOST" = perlmutter ]
+then
+	source $MITIM_PATH/config/machines_sources/nersc.bashrc
 # None of the above
 else
 	! [ -z "$PS1" ] && echo "     - No specific environment file loaded"
 fi
 
-
-
 # -------------------------------------------------------------------------------------------------------
 # Aliases for quick tools (plotting, reading)
 # -------------------------------------------------------------------------------------------------------
@@ -55,44 +57,4 @@ fi
 
 source $MITIM_PATH/config/machines_sources/aliases.bashrc
 
-# -------------------------------------------------------------------------------------------------------
-# TRANSP Aliases
-# -------------------------------------------------------------------------------------------------------
-
-# To run TRANSP (in folder with required files): transp 88664 P01 CMOD --version tshare --trmpi 32 --toricmpi 32 --ptrmpi 32
-alias transp="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_transp.py"
-
-# To send and get LOOK or do a FETCH: look 88664P01 CMOD --nofull --plot --remove
-alias look="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_look.py"
-
-# To check the grid: trcheck pablorf
-alias trcheck="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_check.py"
-
-# To check the grid periodically: trcheckp pablorf
-alias trcheckp="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_check_periodic.py"
-
-# To delete runs from TRANSP grid: cleanruns 88664P CMOD --numbers 1 --to 5   OR 88664P CMOD --numbers 1,2,3 
-alias cleanruns="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_clean.py"
-
-# Plot transp: trplot transp.cdf
-alias trplot="ipython3 -i $MITIM_PATH/src/mitim_tools/transp_tools/outputs/exploreCDFs.py"
-
-# -------------------------------------------------------------------------------------------------------
-# IM Aliases
-# -------------------------------------------------------------------------------------------------------
-
-# To run complete IM evaluation:   runim 7 [DebugOption: --debug 0]
-alias runim="python3 $MITIM_PATH/src/mitim_tools/im_tools/exe/run_im.py ./"
-
-# To peform scenario optimization
-alias runmitim="python3 $MITIM_PATH/mitim_opt/scenarios_tools/routines/runMITIM_BO.py"
-
-# -------------------------------------------------------------------------------------------------------
-# Other Useful Aliases
-# -------------------------------------------------------------------------------------------------------
-
-# e.g.: grepy hola
-function grepy { clear; grep -rno "$1" . --color --include \*.py; }
-function grepf90 { clear; grep -rno "$1" . --color --include \*.{f90,F90}; }
-
-! [ -z "$PS1" ] && echo -e "\033[32m>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\033[0m"
+! [ -z "$PS1" ] && echo -e "\033[32m>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\033[0m"
diff --git a/docs/capabilities/portals_capabilities.rst b/docs/capabilities/portals_capabilities.rst
@@ -1,7 +1,7 @@
 PORTALS
 =======
 
-The PORTALS method, described in `P. Rodriguez-Fernandez et al., Nulc. Fusion (2022) <https://iopscience.iop.org/article/10.1088/1741-4326/ac64b2>`_ consists of using Bayesian Optimization techniques to find steady-state solutions of transport codes of arbitrary fidelity.
+The PORTALS method, described in `P. Rodriguez-Fernandez et al.,arXiv (2023) <https://arxiv.org/abs/2312.12610>`_ consists of using Bayesian Optimization techniques to find steady-state solutions of transport codes of arbitrary fidelity.
 
 Once setup has been successful, the following regression test should run smoothly:
 

diff --git a/docs/capabilities/tglf_capabilities.rst b/docs/capabilities/tglf_capabilities.rst
@@ -76,7 +76,8 @@ To generate the input files (input.tglf) to TGLF at each radial location, MITIM
 
 Now, we are ready to run TGLF. Once the ``prep()`` command has finished, one can run TGLF with different settings and assumptions. That is why, at this point, a sub-folder name for this specific run can be provided. Similarly to the ``prep()`` command, a ``restart`` flag can be provided.
 The set of control inputs to TGLF (like saturation rule, electromagnetic effects, etc.) are provided in two ways.
-First, the argument ``TGLFsettings`` (which goes from 1 to 5 as of now) indicates the base case to start with. The user is referred to ``GACODEdefaults.py`` to understand the meaning of each setting.
+First, the argument ``TGLFsettings`` indicates the base case to start with.
+The user is referred to ``templates/input.tglf.models.json`` to understand the meaning of each setting, and ``templates/input.tglf.controls`` for the default setup.
 Second, the argument ``extraOptions`` can be passed as a dictionary of variables to change.
 For example, the following two commands will run TGLF with saturation rule number 2 with and without electromagnetic effets. After each ``run()`` command, a ``read()`` is needed, to populate the *tglf.results* dictionary with the TGLF outputs (``label`` refers to the dictionary key for each run):
 
@@ -96,19 +97,6 @@ For example, the following two commands will run TGLF with saturation rule numbe
 
     tglf.read( label = 'no_em' )
 
-.. note::
-
-    One can change every TGLF input with the ``extraOptions = {}`` dictionary, as shown earlier. However, ``GACODEdefaults.py`` contains a list of presets for TGLF that can be selected by simply passing the argument ``TGLFsettings`` to the ``.run()`` method. Available preset are:
-
-    - TGLFsettings = 0: Minimal working example
-    - TGLFsettings = 1: "Old" ES SAT1
-    - TGLFsettings = 2: ES SAT0
-    - TGLFsettings = 3: ES SAT1 (a.k.a. SAT1geo)
-    - TGLFsettings = 4: ES SAT2
-    - TGLFsettings = 5: EM SAT2
-
-    The user is not limited to use those combinations. One can start with a given ``TGLFsettings`` option, and then modify as many parameters as needed with the ``extraOptions`` dictionary.
-
 .. tip::
 
     In this example, ``tglf.results['yes_em']`` and ``tglf.results['no_em']`` are themselves dictionaries, so please do ``.keys()`` to get all the possible results that have been obtained.
@@ -117,7 +105,7 @@ TGLF results can be plotted together by indicating what labels to plot:
 
 .. code-block:: python
 
-    tglf.plotRun( labels = ['yes_em', 'no_em'] )
+    tglf.plot( labels = ['yes_em', 'no_em'] )
 
 As a result, a TGLF notebook with different tabs will be opened with all relevant output quantities:
 
@@ -162,7 +150,7 @@ Similarly as in the previous section, you need to run the ``prep()`` command, bu
     - **PROFILES_GEN** to generate an *input.gacode* file from the *plasmastate.cdf* and *.geq* files. This file is standard within the GACODE suite and contains all plasma information that is required to run core transport codes.
 
 
-The rest of the workflow is identical to the previous section, including ``.run()``, ``.read()`` and ``.plotRun()``.
+The rest of the workflow is identical to the previous section, including ``.run()``, ``.read()`` and ``.plot()``.
 
 
 Run TGLF from input.tglf file
@@ -182,7 +170,7 @@ If you have a input.tglf file already, you can still use this script to run it.
     tglf = TGLFtools.TGLF()
     tglf.prep_from_tglf( folder, inputtglf_file, input_gacode = inputgacode_file )
 
-The rest of the workflow is identical, including ``.run()``, ``.read()`` and ``.plotRun()``.
+The rest of the workflow is identical, including ``.run()``, ``.read()`` and ``.plot()``.
 
 .. tip::
 
@@ -204,7 +192,7 @@ The rest of the workflow is identical, including ``.run()``, ``.read()`` and ``.
         tglf = TGLFtools.TGLF()
         tglf.prep_from_tglf( folder, inputtglf_file )
         tglf.read (folder = f'{folder}/', label = 'yes_em' )
-        tglf.plotRun( labels = ['yes_em'] )
+        tglf.plot( labels = ['yes_em'] )
 
     Please note that the previous code will only work is TGLF was run using MITIM. This is because MITIM stores the results
     with a suffix that indicates the radial location (``rho``) where the run was performed.
@@ -219,7 +207,10 @@ The rest of the workflow is identical, including ``.run()``, ``.read()`` and ``.
 Run 1D scans of TGLF input parameter
 ------------------------------------
 
-*Nothing here yet*
+*Under Development*
+
+*(In the meantime, please checkout* `tutorials/TGLF_tutorial.py <https://github.com/pabloprf/MITIM-fusion/blob/main/tutorials/PORTALS_tutorial.py>`_ *)*
+
 
 TGLF aliases
 ------------

diff --git a/docs/capabilities/tgyro_capabilities.rst b/docs/capabilities/tgyro_capabilities.rst
@@ -95,7 +95,7 @@ And plot:
 
 .. code-block:: python
 
-	tgyro.plotRun(labels=['run1'])
+	tgyro.plot(labels=['run1'])
 
 As a result, a TGYRO notebook with different tabs will be opened with all relevant output quantities:
 

diff --git a/docs/capabilities/transp_capabilities.rst b/docs/capabilities/transp_capabilities.rst
@@ -91,7 +91,7 @@ If TRANSP has already been run and the .CDF results file already exists (``cdf_f
 
 	transp_results = CDFtools.CDFreactor( cdf_file )
 
-	transp_results.plotRun()
+	transp_results.plot()
 
 .. tip::
 
@@ -114,7 +114,7 @@ If TRANSP has already been run and the .CDF results file already exists (``cdf_f
 
 	.. code-block:: python
 
-		transp_results.plotRun( time = t1 )
+		transp_results.plot( time = t1 )
 
 .. note::
 

diff --git a/docs/faq.rst b/docs/faq.rst
@@ -5,8 +5,8 @@ Frequently Asked Questions
    :local:
    :depth: 1
 
-Issues during MITIM setup
--------------------------
+Issues during MITIM installation
+--------------------------------
 
 .. dropdown:: ``pyqt`` fails to install 
 
@@ -24,6 +24,14 @@ Issues during MITIM setup
       
       pip3 install -e $MITIM_PATH\[pyqt\]
 
+.. dropdown:: ``ERROR: Wheel`` error in pip:
+
+   Make sure you are getting the fresh packages, by using the ``--no-cache`` option:
+
+   .. code-block:: console
+      
+      pip3 install -e $MITIM_PATH\[pyqt\] --no-cache
+
 Issues during MITIM tests
 -------------------------
 
@@ -39,6 +47,8 @@ Issues during MITIM tests
       . $GACODE_ROOT/shared/bin/gacode_setup
       . ${GACODE_ROOT}/platform/env/env.${GACODE_PLATFORM}
 
+      \# Add also modules that are required to run MPI instances in your machine
+
    If you still have problems with MITIM execution of TGLF and you have checked that by manually logging-in to the machine you can run TGLF,
    then it is possible that you have print or echo statements in your ``.bashrc`` or ``.zshrc`` files.
    Please remove them or add the following: