From ccbcc2113c52de435a24569e081d808058f62847 Mon Sep 17 00:00:00 2001 From: Bowen Li Date: Fri, 16 Feb 2024 14:54:24 +0000 Subject: [PATCH 1/6] Update .readthedocs.yml --- .readthedocs.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.readthedocs.yml b/.readthedocs.yml index f5b5350b84..d73fbb812c 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -10,6 +10,8 @@ build: os: ubuntu-22.04 tools: python: "latest" + commands: + - pip install sphinx-rtd-theme # Build documentation in the docs/ directory with Sphinx sphinx: From d25ddbadc932c851be2e292864bffc4adf9d9b7d Mon Sep 17 00:00:00 2001 From: Bowen Li Date: Fri, 16 Feb 2024 14:57:33 +0000 Subject: [PATCH 2/6] Update conf.py --- docs/source/conf.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index f1cda0d303..ba6d2f6617 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -12,9 +12,9 @@ # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # -import os -import sys -sys.path.insert(0, os.path.abspath('../../')) +# import os +# import sys +# sys.path.insert(0, os.path.abspath('../../')) # -- Project information ----------------------------------------------------- @@ -87,7 +87,7 @@ # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] +html_static_path = [""] # Custom sidebar templates, must be a dictionary that maps document names # to template names. From e3dbf70a54c05e0a0f3c1c625ce7bed0adfe08d4 Mon Sep 17 00:00:00 2001 From: Bowen Li Date: Fri, 16 Feb 2024 15:01:53 +0000 Subject: [PATCH 3/6] Update .readthedocs.yml --- .readthedocs.yml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index d73fbb812c..e3c057fc1b 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -7,12 +7,17 @@ version: 2 # Set the version of Python and other tools you might need build: - os: ubuntu-22.04 + os: ubuntu-20.04 tools: - python: "latest" - commands: - - pip install sphinx-rtd-theme + python: "3.9" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/source/conf.py + +python: + install: + - method: pip + path: . + extra_requirements: + - docs From f8ba41df92488179eaca30d926cbdd9657bfff80 Mon Sep 17 00:00:00 2001 From: Bowen Li Date: Mon, 19 Feb 2024 12:22:30 +0000 Subject: [PATCH 4/6] Update .readthedocs.yml --- .readthedocs.yml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index e3c057fc1b..6e8052aac0 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -7,17 +7,15 @@ version: 2 # Set the version of Python and other tools you might need build: - os: ubuntu-20.04 + os: "ubuntu-22.04" tools: - python: "3.9" + python: "3.12" # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/source/conf.py +# Explicitly set the version of Python and its requirements python: - install: - - method: pip - path: . - extra_requirements: - - docs + install: + - requirements: docs/requirements.txt From 341459a852c5070664ebd41f4d4ad00ebb8a4b90 Mon Sep 17 00:00:00 2001 From: Bowen Li Date: Mon, 19 Feb 2024 12:22:54 +0000 Subject: [PATCH 5/6] Create requirements.txt --- docs/requirements.txt | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000000..3f775f1cf6 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,3 @@ +sphinx==5.3.0 +sphinx_rtd_theme==1.1.1 +readthedocs-sphinx-search==0.1.1 From 50ff11867cb6b8f076038336480e7a30c5337b5c Mon Sep 17 00:00:00 2001 From: Bowen Li Date: Mon, 29 Apr 2024 11:52:14 +0100 Subject: [PATCH 6/6] Update user manual --- docs/source/install.rst | 3 +-- docs/source/run_nufeb.rst | 18 +++++++++--------- 2 files changed, 10 insertions(+), 11 deletions(-) diff --git a/docs/source/install.rst b/docs/source/install.rst index 406c30f506..6155444bdf 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -124,8 +124,7 @@ will allow NUFEB simulation to output both vtk and hdf5 data formats. When the installation finished, you should have an executable ``nufeb_mpi`` or ``nufeb_serial`` or ``nufeb_gpu`` in -``NUFEB-2`` directory deponeding on configuration. The path to the executable -will be automatically added to the system (.bashrc). +``NUFEB-2`` directory deponeding on configuration. .. note:: For convenience, the executables built from install.sh are limited to mpi, gpu (cuda + mpi), and serial versions. diff --git a/docs/source/run_nufeb.rst b/docs/source/run_nufeb.rst index b4eab8afe7..eb80fae6c1 100644 --- a/docs/source/run_nufeb.rst +++ b/docs/source/run_nufeb.rst @@ -25,23 +25,23 @@ NUFEB provides numbers of examples available in the ``NUFEB-2/examples`` directo For example: .. parsed-literal:: - cd NUFEB-2/examples/biofilm-het - mpirun -np 4 nufeb_mpi -in nufeb.in + cd NUFEB-2/examples/biofilm-heterotroph + mpirun -np 4 ../../nufeb_mpi -in inputscript.nufeb -The above commands will run the input script ``nufeb.in`` in the ``NUFEB-dev/biofilm-het`` directory using NUFEB MPI executable with 4 CPU processors. +The above commands will run the input script ``inputscript.nufeb`` in the ``NUFEB-dev/biofilm-heterotroph`` directory using NUFEB MPI executable with 4 CPU processors. `mpirun -np X` command-line switch to specify the numbers of processors to run the simulation. .. parsed-literal:: - cd NUFEB-2/examples/biofilm-het/ - nufeb_serial -in nufeb.in + cd NUFEB-2/examples/biofilm-heterotroph + ../../nufeb_serial -in inputscript.nufeb -The above commands will run the ``NUFEB-dev/biofilm-het`` example using NUFEB serial executable with single processor. +The above commands will run the ``NUFEB-dev/biofilm-heterotroph`` example using NUFEB serial executable with single processor. .. parsed-literal:: - cd NUFEB-2/examples/biofilm-het/ - mpirun -np 2 nufeb_gpu -k on g 2 -sf kk -pk kokkos newton off neigh half binsize 2e-6 -in nufeb.in + cd NUFEB-2/examples/biofilm-heterotroph + mpirun -np 2 ../../nufeb_gpu -k on g 2 -sf kk -pk kokkos newton off neigh half binsize 2e-6 -in inputscript.nufeb -The above commands will run the ``NUFEB-dev/biofilm-het`` examaple using NUFEB GPU executable with 2 GPUs and 2 CPUs. +The above commands will run the ``NUFEB-dev/biofilm-heterotroph`` example using NUFEB GPU executable with 2 GPUs and 2 CPUs. In particular, the `-k on` command-line switch enable Kokkos support; `g 2` specify the use of 2 GPUs to run the simulation. `-sf kk` enables NUFEB to use Kokkos variant styles of any commands defined in the inputscript; `-pk kokkos newton off neigh half binsize 2e-6` re-define the setting in the inputscript.