From b329c380262b05da4c0da9b555bd7637fa604261 Mon Sep 17 00:00:00 2001
From: Jackson Clark <jclark58@uic.edu>
Date: Mon, 7 Aug 2023 17:29:55 -0500
Subject: [PATCH 1/2] Added conda envirnoments and useful guides.

---
 README.md             |  27 ++++-----
 environment.yml       | 133 ++++++++++++++++++++++++++++++++++++++++++
 environment_gpu.yml   | 133 ++++++++++++++++++++++++++++++++++++++++++
 installation_guide.md |  31 ++++++++++
 4 files changed, 307 insertions(+), 17 deletions(-)
 create mode 100644 environment.yml
 create mode 100644 environment_gpu.yml
 create mode 100644 installation_guide.md

diff --git a/README.md b/README.md
index 1bb1ef5..5cb21b5 100644
--- a/README.md
+++ b/README.md
@@ -29,13 +29,17 @@ larger environments.
 testing a trained model on them. As an example, the trained
 model used in our paper can be found [here](https://drive.google.com/file/d/1AtAeUwLF1Rn_X3b2FHkHi4fI5vveUHF6/view?usp=sharing).
 
-## Before compilation: compile cpp_mstar code
+### Requirements
+- [Anaconda](`https://docs.anaconda.com/free/anaconda/install/index.html`)
+- [Boost](https://www.boost.org/`)
+- If using GPU:
+    - cuDNN 6
+    - CUDA 8
+    - GCC 4.
+- Ubuntu is strongly reccomended
 
-- cd into the od_mstar3 folder.
-- python3 setup.py build_ext (may need --inplace as extra argument).
-- copy so object from build/lib.*/ at the root of the od_mstar3 folder.
-- Check by going back to the root of the git folder,
-running python3 and "import cpp_mstar"
+## Installing dependencies
+- Follow the [Installation Guide](installation_guide.md)
 
 ### Custom testing
 
@@ -51,17 +55,6 @@ Hotkeys:
 - up/down arrows: change size
 - p: pause inference
 
-### Requirements
-- Python 3.4
-- Cython 0.28.4
-- OpenAI Gym 0.9.4
-- Tensorflow 1.3.1
-- Numpy 1.13.3
-- matplotlib
-- imageio (for GIFs creation)
-- tk
-- networkx (if using od_mstar.py and not the C++ version)
-
 ### Authors
 
 [Guillaume Sartoretti](guillaume.sartoretti@gmail.com)
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..efbf626
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,133 @@
+name: primal
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - blas=1.0=mkl
+  - ca-certificates=2023.05.30=h06a4308_0
+  - certifi=2021.5.30=py36h06a4308_0
+  - cycler=0.11.0=pyhd3eb1b0_0
+  - cython=0.28.4=py36hf484d3e_0
+  - dbus=1.13.18=hb2f20db_0
+  - decorator=5.1.1=pyhd3eb1b0_0
+  - defusedxml=0.7.1=pyhd3eb1b0_0
+  - entrypoints=0.4=pyhd8ed1ab_0
+  - expat=2.4.9=h6a678d5_0
+  - fontconfig=2.14.1=h52c9d5c_1
+  - freetype=2.12.1=h4a9f257_0
+  - glib=2.69.1=h4ff587b_1
+  - gst-plugins-base=1.14.1=h6a678d5_1
+  - gstreamer=1.14.1=h5eee18b_1
+  - icu=58.2=he6710b0_3
+  - imageio=2.9.0=pyhd3eb1b0_0
+  - intel-openmp=2022.1.0=h9e868ea_3769
+  - ipykernel=5.5.5=py36hcb3619a_0
+  - ipython=5.8.0=py36_1
+  - ipython_genutils=0.2.0=pyhd3eb1b0_1
+  - ipywidgets=7.6.5=pyhd3eb1b0_1
+  - jinja2=3.0.3=pyhd3eb1b0_0
+  - jpeg=9e=h5eee18b_1
+  - jsonschema=2.6.0=py36_0
+  - jupyter=1.0.0=py36_7
+  - jupyter_client=5.3.4=py36_0
+  - jupyter_console=5.2.0=py36_1
+  - jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
+  - kiwisolver=1.3.1=py36h2531618_0
+  - lcms2=2.12=h3be6417_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - lerc=3.0=h295c915_0
+  - libdeflate=1.17=h5eee18b_0
+  - libffi=3.3=he6710b0_2
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgfortran-ng=7.5.0=ha8ba4b0_17
+  - libgfortran4=7.5.0=ha8ba4b0_17
+  - libgomp=11.2.0=h1234567_1
+  - libpng=1.6.39=h5eee18b_0
+  - libsodium=1.0.18=h7b6447c_0
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libtiff=4.5.0=h6a678d5_2
+  - libuuid=1.41.5=h5eee18b_0
+  - libwebp-base=1.2.4=h5eee18b_1
+  - libxcb=1.15=h7f8727e_0
+  - libxml2=2.9.14=h74e7548_0
+  - lz4-c=1.9.4=h6a678d5_0
+  - markupsafe=2.0.1=py36h27cfd23_0
+  - matplotlib=3.1.1=py36h5429711_0
+  - mistune=0.8.4=py36h7b6447c_0
+  - mkl=2018.0.3=1
+  - mkl_fft=1.0.6=py36h7dd41cf_0
+  - mkl_random=1.0.1=py36h4414c95_1
+  - nbconvert=5.6.1=py36_0
+  - nbformat=5.1.3=pyhd3eb1b0_0
+  - ncurses=6.4=h6a678d5_0
+  - notebook=6.0.1=py36_0
+  - numpy=1.13.3=py36hdbf6ddf_4
+  - olefile=0.46=py36_0
+  - openjpeg=2.4.0=h3ad879b_0
+  - openssl=1.1.1t=h7f8727e_0
+  - packaging=21.3=pyhd3eb1b0_0
+  - pandoc=2.12=h06a4308_3
+  - pandocfilters=1.5.0=pyhd3eb1b0_0
+  - pcre=8.45=h295c915_0
+  - pexpect=4.8.0=pyhd3eb1b0_3
+  - pickleshare=0.7.5=pyhd3eb1b0_1003
+  - pillow=8.3.1=py36h2c7a002_0
+  - pip=21.2.2=py36h06a4308_0
+  - prometheus_client=0.13.1=pyhd3eb1b0_0
+  - prompt_toolkit=1.0.15=py_1
+  - ptyprocess=0.7.0=pyhd3eb1b0_2
+  - pygments=2.11.2=pyhd3eb1b0_0
+  - pyparsing=3.0.4=pyhd3eb1b0_0
+  - pyqt=5.9.2=py36h05f1152_2
+  - python=3.6.13=h12debd9_1
+  - python-dateutil=2.8.2=pyhd3eb1b0_0
+  - python_abi=3.6=2_cp36m
+  - pytz=2021.3=pyhd3eb1b0_0
+  - pyzmq=19.0.2=py36h9947dbf_2
+  - qt=5.9.7=h5867ecd_1
+  - qtconsole=5.2.2=pyhd3eb1b0_0
+  - qtpy=2.0.1=pyhd3eb1b0_0
+  - readline=8.2=h5eee18b_0
+  - scipy=1.1.0=py36hd20e5f9_0
+  - send2trash=1.8.0=pyhd3eb1b0_1
+  - setuptools=58.0.4=py36h06a4308_0
+  - simplegeneric=0.8.1=py36_2
+  - sip=4.19.8=py36hf484d3e_0
+  - six=1.16.0=pyhd3eb1b0_1
+  - sqlite=3.41.2=h5eee18b_0
+  - terminado=0.9.4=py36h06a4308_0
+  - testpath=0.5.0=pyhd3eb1b0_0
+  - tk=8.6.12=h1ccaba5_0
+  - tornado=6.1=py36h27cfd23_0
+  - traitlets=4.3.3=pyhd8ed1ab_2
+  - wcwidth=0.2.5=pyhd3eb1b0_0
+  - webencodings=0.5.1=py36_1
+  - wheel=0.37.1=pyhd3eb1b0_0
+  - widgetsnbextension=3.5.1=py36_0
+  - xz=5.4.2=h5eee18b_0
+  - zeromq=4.3.4=h2531618_0
+  - zlib=1.2.13=h5eee18b_0
+  - zstd=1.5.5=hc292b87_0
+  - pip:
+      - bleach==1.5.0
+      - charset-normalizer==2.0.12
+      - dataclasses==0.8
+      - gym==0.9.4
+      - html5lib==0.9999999
+      - idna==3.4
+      - importlib-metadata==4.8.3
+      - jupyter-core==4.9.2
+      - markdown==3.3.7
+      - protobuf==3.19.6
+      - pyglet==2.0.7
+      - python-version==0.0.2
+      - requests==2.27.1
+      - tensorflow==1.3.0
+      - tensorflow-tensorboard==0.1.8
+      - typing-extensions==4.1.1
+      - urllib3==1.26.16
+      - werkzeug==2.0.3
+      - zipp==3.6.0
+
diff --git a/environment_gpu.yml b/environment_gpu.yml
new file mode 100644
index 0000000..02a84d6
--- /dev/null
+++ b/environment_gpu.yml
@@ -0,0 +1,133 @@
+name: primal
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - blas=1.0=mkl
+  - ca-certificates=2023.05.30=h06a4308_0
+  - certifi=2021.5.30=py36h06a4308_0
+  - cycler=0.11.0=pyhd3eb1b0_0
+  - cython=0.28.4=py36hf484d3e_0
+  - dbus=1.13.18=hb2f20db_0
+  - decorator=5.1.1=pyhd3eb1b0_0
+  - defusedxml=0.7.1=pyhd3eb1b0_0
+  - entrypoints=0.4=pyhd8ed1ab_0
+  - expat=2.4.9=h6a678d5_0
+  - fontconfig=2.14.1=h52c9d5c_1
+  - freetype=2.12.1=h4a9f257_0
+  - glib=2.69.1=h4ff587b_1
+  - gst-plugins-base=1.14.1=h6a678d5_1
+  - gstreamer=1.14.1=h5eee18b_1
+  - icu=58.2=he6710b0_3
+  - imageio=2.9.0=pyhd3eb1b0_0
+  - intel-openmp=2022.1.0=h9e868ea_3769
+  - ipykernel=5.5.5=py36hcb3619a_0
+  - ipython=5.8.0=py36_1
+  - ipython_genutils=0.2.0=pyhd3eb1b0_1
+  - ipywidgets=7.6.5=pyhd3eb1b0_1
+  - jinja2=3.0.3=pyhd3eb1b0_0
+  - jpeg=9e=h5eee18b_1
+  - jsonschema=2.6.0=py36_0
+  - jupyter=1.0.0=py36_7
+  - jupyter_client=5.3.4=py36_0
+  - jupyter_console=5.2.0=py36_1
+  - jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
+  - kiwisolver=1.3.1=py36h2531618_0
+  - lcms2=2.12=h3be6417_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - lerc=3.0=h295c915_0
+  - libdeflate=1.17=h5eee18b_0
+  - libffi=3.3=he6710b0_2
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgfortran-ng=7.5.0=ha8ba4b0_17
+  - libgfortran4=7.5.0=ha8ba4b0_17
+  - libgomp=11.2.0=h1234567_1
+  - libpng=1.6.39=h5eee18b_0
+  - libsodium=1.0.18=h7b6447c_0
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libtiff=4.5.0=h6a678d5_2
+  - libuuid=1.41.5=h5eee18b_0
+  - libwebp-base=1.2.4=h5eee18b_1
+  - libxcb=1.15=h7f8727e_0
+  - libxml2=2.9.14=h74e7548_0
+  - lz4-c=1.9.4=h6a678d5_0
+  - markupsafe=2.0.1=py36h27cfd23_0
+  - matplotlib=3.1.1=py36h5429711_0
+  - mistune=0.8.4=py36h7b6447c_0
+  - mkl=2018.0.3=1
+  - mkl_fft=1.0.6=py36h7dd41cf_0
+  - mkl_random=1.0.1=py36h4414c95_1
+  - nbconvert=5.6.1=py36_0
+  - nbformat=5.1.3=pyhd3eb1b0_0
+  - ncurses=6.4=h6a678d5_0
+  - notebook=6.0.1=py36_0
+  - numpy=1.13.3=py36hdbf6ddf_4
+  - olefile=0.46=py36_0
+  - openjpeg=2.4.0=h3ad879b_0
+  - openssl=1.1.1t=h7f8727e_0
+  - packaging=21.3=pyhd3eb1b0_0
+  - pandoc=2.12=h06a4308_3
+  - pandocfilters=1.5.0=pyhd3eb1b0_0
+  - pcre=8.45=h295c915_0
+  - pexpect=4.8.0=pyhd3eb1b0_3
+  - pickleshare=0.7.5=pyhd3eb1b0_1003
+  - pillow=8.3.1=py36h2c7a002_0
+  - pip=21.2.2=py36h06a4308_0
+  - prometheus_client=0.13.1=pyhd3eb1b0_0
+  - prompt_toolkit=1.0.15=py_1
+  - ptyprocess=0.7.0=pyhd3eb1b0_2
+  - pygments=2.11.2=pyhd3eb1b0_0
+  - pyparsing=3.0.4=pyhd3eb1b0_0
+  - pyqt=5.9.2=py36h05f1152_2
+  - python=3.6.13=h12debd9_1
+  - python-dateutil=2.8.2=pyhd3eb1b0_0
+  - python_abi=3.6=2_cp36m
+  - pytz=2021.3=pyhd3eb1b0_0
+  - pyzmq=19.0.2=py36h9947dbf_2
+  - qt=5.9.7=h5867ecd_1
+  - qtconsole=5.2.2=pyhd3eb1b0_0
+  - qtpy=2.0.1=pyhd3eb1b0_0
+  - readline=8.2=h5eee18b_0
+  - scipy=1.1.0=py36hd20e5f9_0
+  - send2trash=1.8.0=pyhd3eb1b0_1
+  - setuptools=58.0.4=py36h06a4308_0
+  - simplegeneric=0.8.1=py36_2
+  - sip=4.19.8=py36hf484d3e_0
+  - six=1.16.0=pyhd3eb1b0_1
+  - sqlite=3.41.2=h5eee18b_0
+  - terminado=0.9.4=py36h06a4308_0
+  - testpath=0.5.0=pyhd3eb1b0_0
+  - tk=8.6.12=h1ccaba5_0
+  - tornado=6.1=py36h27cfd23_0
+  - traitlets=4.3.3=pyhd8ed1ab_2
+  - wcwidth=0.2.5=pyhd3eb1b0_0
+  - webencodings=0.5.1=py36_1
+  - wheel=0.37.1=pyhd3eb1b0_0
+  - widgetsnbextension=3.5.1=py36_0
+  - xz=5.4.2=h5eee18b_0
+  - zeromq=4.3.4=h2531618_0
+  - zlib=1.2.13=h5eee18b_0
+  - zstd=1.5.5=hc292b87_0
+  - pip:
+      - bleach==1.5.0
+      - charset-normalizer==2.0.12
+      - dataclasses==0.8
+      - gym==0.9.4
+      - html5lib==0.9999999
+      - idna==3.4
+      - importlib-metadata==4.8.3
+      - jupyter-core==4.9.2
+      - markdown==3.3.7
+      - protobuf==3.19.6
+      - pyglet==2.0.7
+      - python-version==0.0.2
+      - requests==2.27.1
+      - tensorflow-gpu==1.3.0
+      - tensorflow-tensorboard==0.1.8
+      - typing-extensions==4.1.1
+      - urllib3==1.26.16
+      - werkzeug==2.0.3
+      - zipp==3.6.0
+
diff --git a/installation_guide.md b/installation_guide.md
new file mode 100644
index 0000000..e855343
--- /dev/null
+++ b/installation_guide.md
@@ -0,0 +1,31 @@
+# PRIMAL Installation directions
+## Prerequisites
+- Git
+- [Anaconda](`https://docs.anaconda.com/free/anaconda/install/index.html`)
+- [Boost](https://www.boost.org/`)
+- If using GPU:
+    - cuDNN 6
+    - CUDA 8
+    - GCC 4.8
+## Installation steps
+- Run this command: `conda env create -f environment.yml` (or, if using a GPU `conda env create -f environment_gpu.yml`) This will create a new conda environment called `primal` that includes all the dependencies
+- Activate the environment with this command: `conda activate primal`
+- Run `cd od_mstar3` and then `python3 setup.py build_ext --inplace`, this builds the cpp_mstar library. (Note: if `python3` in the previous command does not work, try using just `python`)
+- Run `cd ..` to get back in the main directory
+## Installing pre-trained model
+- Make sure you're in the root directory
+- Create a directory called `model_primal` if it does not exist
+- Download this file: `https://drive.google.com/file/d/1AtAeUwLF1Rn_X3b2FHkHi4fI5vveUHF6/view` (it will take some time)
+- Extract the contents of that file to the model_primal directory
+### You're all done!
+## Notes:
+- Training is done by the `DRLMAPF_A3C_RNN.ipynb` notebook. I do reccommend using the pre-trained model instead of retraining. Do not train unless you know what you're doing.
+- To use the map creator, just run `python mapgenerator.py`
+- Hotkeys for map generator:
+    - o: obstacle mode
+    - a: agent mode
+    - g: goal mode, click an agent then click a free tile to place its goal
+    - c: clear agents
+    - r: reset
+    - up/down arrows: change size
+    - p: pause inference
\ No newline at end of file

From ad7fd41dfaf231411b5a89680ee035911797c33c Mon Sep 17 00:00:00 2001
From: Jackson Clark <jclark58@uic.edu>
Date: Wed, 23 Aug 2023 19:32:41 -0500
Subject: [PATCH 2/2] Added example PBS compute job script.

---
 compute_job.sh   | 33 +++++++++++++++++++++++++++++++++
 devel_compute.sh | 28 ++++++++++++++++++++++++++++
 2 files changed, 61 insertions(+)
 create mode 100644 compute_job.sh
 create mode 100644 devel_compute.sh

diff --git a/compute_job.sh b/compute_job.sh
new file mode 100644
index 0000000..aeec476
--- /dev/null
+++ b/compute_job.sh
@@ -0,0 +1,33 @@
+##!/bin/bash
+##This script test different conda environments running on Cascade Lake GPU Nodes
+## This script was adapted from the NAS example for conda environments and needs some changes to the configuration..
+## The actual shell code that is used for the job (below the module statements) should be working well.
+#PBS -q v100@pbspl4
+#PBS -W block=true
+#PBS -lselect=1:ncpus=96:ngpus=8:model=cas_gpu:mem=600g
+#PBS -l place=scatter:exclhost
+#PBS -l walltime=48:00:00
+#PBS -j oe
+#PBS -N model_cas_gpu-check
+#PBS -W group_list=a1509
+
+
+# load analytix modules
+module use -a /swbuild/analytix/tools/modulefiles
+module load miniconda3/v4
+# We might need to load cuda here
+#module load cuda/10.1.243
+#q: How can I specify that cuda 8 is used
+#a: module load cuda/8.0.61
+# module load cuda/8.0.61
+# NOTE: cuda 8 isn't listed as a current module, you might have to ask the NAS on how to use it.
+
+
+# Activate conda environment here:
+source activate primal-deploy
+
+
+## Run script here
+python DRLMAPF_A3C_RNN.py
+
+conda deactivate
\ No newline at end of file
diff --git a/devel_compute.sh b/devel_compute.sh
new file mode 100644
index 0000000..e9a20cd
--- /dev/null
+++ b/devel_compute.sh
@@ -0,0 +1,28 @@
+##!/bin/bash
+##This script test different conda environments running on Cascade Lake GPU Nodes
+#PBS -q v100@pbspl4
+#PBS -lselect=1:ncpus=12:ngpus=2:model=cas_gpu:mem=30g
+#PBS -l place=scatter:exclhost
+#PBS -j oe
+#PBS -N model_cas_gpu-check
+#PBS -W group_list=a1509
+
+
+# load analytix modules
+module use -a /swbuild/analytix/tools/modulefiles
+module load miniconda3/v4
+# We might need to load cuda here
+#module load cuda/10.1.243
+#q: How can I specify that cuda 8 is used
+#a: module load cuda/8.0.61
+# module load cuda/8.0.61
+
+
+# Activate conda environment here:
+source activate primal-deploy
+
+
+## Run script here
+python DRLMAPF_A3C_RNN.py
+
+conda deactivate
\ No newline at end of file