From 7922bd57f1c00f92bc29bb807f95c849df772a19 Mon Sep 17 00:00:00 2001
From: Jennifer Wei <jennifer.wei@omsf.io>
Date: Mon, 16 Oct 2023 10:22:43 -0700
Subject: [PATCH 01/28] Removes conda installation from installation script.

---
 environment.yml                             |  5 ++-
 scripts/install_third_party_dependencies.sh | 39 +++++----------------
 2 files changed, 12 insertions(+), 32 deletions(-)

diff --git a/environment.yml b/environment.yml
index 8f92655..ff0c090 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,14 +7,16 @@ dependencies:
   - conda-forge::python=3.9
   - conda-forge::setuptools=59.5.0
   - conda-forge::pip
+  - conda-forge::cudatoolkit==11.3.*
   - conda-forge::openmm=7.5.1
   - conda-forge::pdbfixer
-  - conda-forge::cudatoolkit==11.3.*
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
   - pytorch::pytorch=1.12.*
   - pip:
+      - packaging
+      - ninja==1.11.1
       - biopython==1.79
       - deepspeed==0.5.10
       - dm-tree==0.1.6
@@ -29,3 +31,4 @@ dependencies:
       - wandb==0.12.21
       - modelcif==0.7
       - git+https://github.com/NVIDIA/dllogger.git
+      - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8bef
diff --git a/scripts/install_third_party_dependencies.sh b/scripts/install_third_party_dependencies.sh
index e334159..3c49003 100755
--- a/scripts/install_third_party_dependencies.sh
+++ b/scripts/install_third_party_dependencies.sh
@@ -1,33 +1,8 @@
 #!/bin/bash
-CONDA_INSTALL_URL=${CONDA_INSTALL_URL:-"https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"}
-
-source scripts/vars.sh
-
-# Install Miniconda locally
-rm -rf lib/conda
-rm -f /tmp/Miniconda3-latest-Linux-x86_64.sh
-wget -P /tmp \
-    "${CONDA_INSTALL_URL}" \
-    && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p lib/conda \
-    && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
-
-# Grab conda-only packages
-export PATH=lib/conda/bin:$PATH
-lib/conda/bin/python3 -m pip install nvidia-pyindex
-conda env create --name=${ENV_NAME} -f environment.yml
-source scripts/activate_conda_env.sh
-
-echo "Attempting to install FlashAttention"
-git clone https://github.com/HazyResearch/flash-attention
-CUR_DIR=$PWD
-cd flash-attention
-git checkout 5b838a8bef
-python3 setup.py install
-cd $CUR_DIR
 
 # Install DeepMind's OpenMM patch
 OPENFOLD_DIR=$PWD
-pushd lib/conda/envs/$ENV_NAME/lib/python3.9/site-packages/ \
+pushd $CONDA_DEFAULT_ENV/lib/python3.9/site-packages/ \
     && patch -p0 < $OPENFOLD_DIR/lib/openmm.patch \
     && popd
 
@@ -39,11 +14,13 @@ wget --no-check-certificate -P openfold/resources \
 mkdir -p tests/test_data/alphafold/common
 ln -rs openfold/resources/stereo_chemical_props.txt tests/test_data/alphafold/common
 
-echo "Downloading OpenFold parameters..."
-bash scripts/download_openfold_params.sh openfold/resources
-
-echo "Downloading AlphaFold parameters..."
-bash scripts/download_alphafold_params.sh openfold/resources
+# echo "Downloading OpenFold parameters..."
+# bash scripts/download_openfold_params.sh openfold/resources
+# 
+# echo "Downloading AlphaFold parameters..."
+# bash scripts/download_alphafold_params.sh openfold/resources
 
 # Decompress test data
 gunzip -c tests/test_data/sample_feats.pickle.gz > tests/test_data/sample_feats.pickle
+
+python setup.py install

From 4fde713c05eb216f56e1a38863cf0392bf544cac Mon Sep 17 00:00:00 2001
From: Jennifer Wei <jennifer.wei@omsf.io>
Date: Tue, 17 Oct 2023 08:22:46 -0700
Subject: [PATCH 02/28] update installation scripts.

---
 environment.yml                             | 2 +-
 scripts/install_third_party_dependencies.sh | 8 +-------
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/environment.yml b/environment.yml
index ff0c090..3d5631c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -8,7 +8,7 @@ dependencies:
   - conda-forge::setuptools=59.5.0
   - conda-forge::pip
   - conda-forge::cudatoolkit==11.3.*
-  - conda-forge::openmm=7.5.1
+  - conda-forge::openmm=7.7.0
   - conda-forge::pdbfixer
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
diff --git a/scripts/install_third_party_dependencies.sh b/scripts/install_third_party_dependencies.sh
index 3c49003..d158228 100755
--- a/scripts/install_third_party_dependencies.sh
+++ b/scripts/install_third_party_dependencies.sh
@@ -1,13 +1,7 @@
 #!/bin/bash
 
-# Install DeepMind's OpenMM patch
-OPENFOLD_DIR=$PWD
-pushd $CONDA_DEFAULT_ENV/lib/python3.9/site-packages/ \
-    && patch -p0 < $OPENFOLD_DIR/lib/openmm.patch \
-    && popd
-
 # Download folding resources
-wget --no-check-certificate -P openfold/resources \
+wget -N --no-check-certificate -P openfold/resources \
     https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
 
 # Certain tests need access to this file

From 705c26773d0cf862320a248e19498c9ef34ef123 Mon Sep 17 00:00:00 2001
From: Jennifer Wei <jennifer.wei@omsf.io>
Date: Tue, 17 Oct 2023 09:10:49 -0700
Subject: [PATCH 03/28] Updating $LD_LIBRARY_PATH to include conda environment
 library.

---
 scripts/install_third_party_dependencies.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/install_third_party_dependencies.sh b/scripts/install_third_party_dependencies.sh
index d158228..de6ee6d 100755
--- a/scripts/install_third_party_dependencies.sh
+++ b/scripts/install_third_party_dependencies.sh
@@ -18,3 +18,6 @@ ln -rs openfold/resources/stereo_chemical_props.txt tests/test_data/alphafold/co
 gunzip -c tests/test_data/sample_feats.pickle.gz > tests/test_data/sample_feats.pickle
 
 python setup.py install
+
+# Setup LD_LIBRARY_PATH to include conda directory:
+export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`

From fb34a0cb62e02c9e3ae238ee7013b61915d79b78 Mon Sep 17 00:00:00 2001
From: Jennifer <whereisthelux@gmail.com>
Date: Tue, 17 Oct 2023 17:10:24 -0400
Subject: [PATCH 04/28] Remove openmm patches

---
 lib/openmm.patch                    | 42 -----------------------------
 openfold/np/relax/amber_minimize.py | 16 +++--------
 openfold/np/relax/cleanup.py        | 10 ++-----
 openfold/np/relax/utils.py          | 10 ++-----
 4 files changed, 8 insertions(+), 70 deletions(-)
 delete mode 100644 lib/openmm.patch

diff --git a/lib/openmm.patch b/lib/openmm.patch
deleted file mode 100644
index cc09e9c..0000000
--- a/lib/openmm.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Index: simtk/openmm/app/topology.py
-===================================================================
---- simtk.orig/openmm/app/topology.py
-+++ simtk/openmm/app/topology.py
-@@ -356,19 +356,35 @@
-         def isCyx(res):
-             names = [atom.name for atom in res._atoms]
-             return 'SG' in names and 'HG' not in names
-+        # This function is used to prevent multiple di-sulfide bonds from being
-+        # assigned to a given atom. This is a DeepMind modification.
-+        def isDisulfideBonded(atom):
-+            for b in self._bonds:
-+                if (atom in b and b[0].name == 'SG' and
-+                    b[1].name == 'SG'):
-+                    return True
-+
-+            return False
- 
-         cyx = [res for res in self.residues() if res.name == 'CYS' and isCyx(res)]
-         atomNames = [[atom.name for atom in res._atoms] for res in cyx]
-         for i in range(len(cyx)):
-             sg1 = cyx[i]._atoms[atomNames[i].index('SG')]
-             pos1 = positions[sg1.index]
-+            candidate_distance, candidate_atom = 0.3*nanometers, None
-             for j in range(i):
-                 sg2 = cyx[j]._atoms[atomNames[j].index('SG')]
-                 pos2 = positions[sg2.index]
-                 delta = [x-y for (x,y) in zip(pos1, pos2)]
-                 distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2])
--                if distance < 0.3*nanometers:
--                    self.addBond(sg1, sg2)
-+                if distance < candidate_distance and not isDisulfideBonded(sg2):
-+                    candidate_distance = distance
-+                    candidate_atom = sg2
-+            # Assign bond to closest pair.
-+            if candidate_atom:
-+                self.addBond(sg1, candidate_atom)
-+
-+
- 
- class Chain(object):
-     """A Chain object represents a chain within a Topology."""
diff --git a/openfold/np/relax/amber_minimize.py b/openfold/np/relax/amber_minimize.py
index 6448e15..3cfbf22 100644
--- a/openfold/np/relax/amber_minimize.py
+++ b/openfold/np/relax/amber_minimize.py
@@ -28,18 +28,10 @@ import openfold.utils.loss as loss
 from openfold.np.relax import cleanup, utils
 import ml_collections
 import numpy as np
-try:
-    # openmm >= 7.6
-    import openmm
-    from openmm import unit
-    from openmm import app as openmm_app
-    from openmm.app.internal.pdbstructure import PdbStructure
-except ImportError:
-    # openmm < 7.6 (requires DeepMind patch)
-    from simtk import openmm
-    from simtk import unit
-    from simtk.openmm import app as openmm_app
-    from simtk.openmm.app.internal.pdbstructure import PdbStructure
+import openmm
+from openmm import unit
+from openmm import app as openmm_app
+from openmm.app.internal.pdbstructure import PdbStructure
 
 ENERGY = unit.kilocalories_per_mole
 LENGTH = unit.angstroms
diff --git a/openfold/np/relax/cleanup.py b/openfold/np/relax/cleanup.py
index 472068b..a435692 100644
--- a/openfold/np/relax/cleanup.py
+++ b/openfold/np/relax/cleanup.py
@@ -20,14 +20,8 @@ cases like removing chains of length one (see clean_structure).
 import io
 
 import pdbfixer
-try:
-    # openmm >= 7.6
-    from openmm import app
-    from openmm.app import element
-except ImportError:
-    # openmm < 7.6 (requires DeepMind patch)
-    from simtk.openmm import app
-    from simtk.openmm.app import element
+from openmm import app
+from openmm.app import element
 
 
 def fix_pdb(pdbfile, alterations_info):
diff --git a/openfold/np/relax/utils.py b/openfold/np/relax/utils.py
index b844953..fc19a91 100644
--- a/openfold/np/relax/utils.py
+++ b/openfold/np/relax/utils.py
@@ -18,14 +18,8 @@ import io
 from openfold.np import residue_constants
 from Bio import PDB
 import numpy as np
-try:
-    # openmm >= 7.6
-    from openmm import app as openmm_app
-    from openmm.app.internal.pdbstructure import PdbStructure
-except ImportError:
-    # openmm < 7.6 (requires DeepMind patch)
-    from simtk.openmm import app as openmm_app
-    from simtk.openmm.app.internal.pdbstructure import PdbStructure
+from openmm import app as openmm_app
+from openmm.app.internal.pdbstructure import PdbStructure
 
 
 def overwrite_pdb_coordinates(pdb_str: str, pos) -> str:

From fcba33580eab1c6dc559a3f245cd742538e1a944 Mon Sep 17 00:00:00 2001
From: Jennifer Wei <jennifer.wei@omsf.io>
Date: Fri, 20 Oct 2023 06:48:05 -0700
Subject: [PATCH 05/28] - Moves python packages to conda installation   instead
 of pip - Adds helper line to automatically prepend conda library to  
 $LD_LIBRARY_PATH

---
 environment.yml                             | 18 ++++++++++--------
 scripts/install_third_party_dependencies.sh | 13 +++++--------
 2 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/environment.yml b/environment.yml
index 3d5631c..7bb387f 100644
--- a/environment.yml
+++ b/environment.yml
@@ -10,23 +10,25 @@ dependencies:
   - conda-forge::cudatoolkit==11.3.*
   - conda-forge::openmm=7.7.0
   - conda-forge::pdbfixer
+  - conda-forge::awscli
+  - conda-forge::biopython==1.79
+  - conda-forge::ninja
+  - conda-forge::numpy==1.21.2
+  - conda-forge::scipy==1.7.1
+  - conda-forge::pyyaml==5.4.1
+  - conda-forge::packaging
+  - conda-forge::tqdm==4.62.2
+  - conda-forge::typing-extensions==3.10.0.2
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
+  - bioconda::aria2
   - pytorch::pytorch=1.12.*
   - pip:
-      - packaging
-      - ninja==1.11.1
-      - biopython==1.79
       - deepspeed==0.5.10
       - dm-tree==0.1.6
       - ml-collections==0.1.0
-      - numpy==1.21.2
-      - PyYAML==5.4.1
       - requests==2.26.0
-      - scipy==1.7.1
-      - tqdm==4.62.2
-      - typing-extensions==3.10.0.2
       - pytorch_lightning==1.5.10
       - wandb==0.12.21
       - modelcif==0.7
diff --git a/scripts/install_third_party_dependencies.sh b/scripts/install_third_party_dependencies.sh
index de6ee6d..62fb620 100755
--- a/scripts/install_third_party_dependencies.sh
+++ b/scripts/install_third_party_dependencies.sh
@@ -8,16 +8,13 @@ wget -N --no-check-certificate -P openfold/resources \
 mkdir -p tests/test_data/alphafold/common
 ln -rs openfold/resources/stereo_chemical_props.txt tests/test_data/alphafold/common
 
-# echo "Downloading OpenFold parameters..."
-# bash scripts/download_openfold_params.sh openfold/resources
-# 
-# echo "Downloading AlphaFold parameters..."
-# bash scripts/download_alphafold_params.sh openfold/resources
-
 # Decompress test data
 gunzip -c tests/test_data/sample_feats.pickle.gz > tests/test_data/sample_feats.pickle
 
 python setup.py install
 
-# Setup LD_LIBRARY_PATH to include conda directory:
-export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH`
+export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
+
+# The following will prepend conda library environment to $LD_LIBRARY_PATH
+# upon conda library activation 
+# conda env config vars set LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH

From 3e3f07c7f2d0d111dc497d029ecf31bd8dc38fb4 Mon Sep 17 00:00:00 2001
From: Jennifer Wei <jennifer.wei@omsf.io>
Date: Fri, 20 Oct 2023 07:02:11 -0700
Subject: [PATCH 06/28] Updates installation instructions in the README.

---
 README.md | 36 ++++++++----------------------------
 1 file changed, 8 insertions(+), 28 deletions(-)

diff --git a/README.md b/README.md
index fbcdd61..e5b41f6 100644
--- a/README.md
+++ b/README.md
@@ -48,37 +48,17 @@ and one of {`jackhmmer`, [MMseqs2](https://github.com/soedinglab/mmseqs2) (night
 installed on on your system. You'll need `git-lfs` to download OpenFold parameters. 
 Finally, some download scripts require `aria2c` and `aws`.
 
-For convenience, we provide a script that installs Miniconda locally, creates a 
-`conda` virtual environment, installs all Python dependencies, and downloads
-useful resources, including both sets of model parameters. Run:
+This package is currently supported for CUDA 11 and Pytorch 1.12
 
-```bash
-scripts/install_third_party_dependencies.sh
-```
+To install:
+1. Clone the repository, e.g. `git clone https://github.com/aqlaboratory/openfold.git`
+1. From the `openfold` repo: 
+    - Create an [Anaconda/Mamba](https://docs.anaconda.com/free/anaconda/install/index.html) environment, e.g. `conda env create -n openfold_env`
+    - Activate the environment, e.g `conda activate openfold_env` 
+1. Run `scripts/install_third_party_dependencies.sh` to configure kernels and folding resources.
 
-To activate the environment, run:
+For some systems, it may help to append the Conda environment library path to `$LD_LIBRARY_PATH`. The `install_third_party_dependencies.sh` script does this once, but you may need this for each bash instance.
 
-```bash
-source scripts/activate_conda_env.sh
-```
-
-To deactivate it, run:
-
-```bash
-source scripts/deactivate_conda_env.sh
-```
-
-With the environment active, compile OpenFold's CUDA kernels with
-
-```bash
-python3 setup.py install
-```
-
-To install the HH-suite to `/usr/bin`, run
-
-```bash
-# scripts/install_hh_suite.sh
-```
 
 ## Usage
 

From b3a118fc83de2079924393f57997263fd35bad77 Mon Sep 17 00:00:00 2001
From: Jennifer Wei <jennifer.wei@omsf.io>
Date: Fri, 20 Oct 2023 09:20:35 -0700
Subject: [PATCH 07/28] Updates Dockerfile to not use OpenMM patches.

---
 Dockerfile | 2 --
 1 file changed, 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 4a9f647..207a3b0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -28,9 +28,7 @@ COPY scripts /opt/openfold/scripts
 COPY run_pretrained_openfold.py /opt/openfold/run_pretrained_openfold.py
 COPY train_openfold.py /opt/openfold/train_openfold.py
 COPY setup.py /opt/openfold/setup.py
-COPY lib/openmm.patch /opt/openfold/lib/openmm.patch
 RUN wget -q -P /opt/openfold/openfold/resources \
     https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
-RUN patch -p0 -d /opt/conda/lib/python3.9/site-packages/ < /opt/openfold/lib/openmm.patch
 WORKDIR /opt/openfold
 RUN python3 setup.py install

From d6ae9f58944bbc952dee6618a6ae049410fe1e00 Mon Sep 17 00:00:00 2001
From: jnwei <jennifer.wei@omsf.io>
Date: Fri, 20 Oct 2023 15:44:34 -0400
Subject: [PATCH 08/28] Remove conda env config setting and update to README

---
 README.md                                   | 3 ++-
 scripts/install_third_party_dependencies.sh | 4 ----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index e5b41f6..25bd605 100644
--- a/README.md
+++ b/README.md
@@ -53,7 +53,8 @@ This package is currently supported for CUDA 11 and Pytorch 1.12
 To install:
 1. Clone the repository, e.g. `git clone https://github.com/aqlaboratory/openfold.git`
 1. From the `openfold` repo: 
-    - Create an [Anaconda/Mamba](https://docs.anaconda.com/free/anaconda/install/index.html) environment, e.g. `conda env create -n openfold_env`
+    - Create an [Anaconda/Mamba](https://docs.anaconda.com/free/anaconda/install/index.html) environment, e.g. 
+        `conda env create -n openfold_env -f environment.yml`
     - Activate the environment, e.g `conda activate openfold_env` 
 1. Run `scripts/install_third_party_dependencies.sh` to configure kernels and folding resources.
 
diff --git a/scripts/install_third_party_dependencies.sh b/scripts/install_third_party_dependencies.sh
index 62fb620..86d5ee8 100755
--- a/scripts/install_third_party_dependencies.sh
+++ b/scripts/install_third_party_dependencies.sh
@@ -14,7 +14,3 @@ gunzip -c tests/test_data/sample_feats.pickle.gz > tests/test_data/sample_feats.
 python setup.py install
 
 export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
-
-# The following will prepend conda library environment to $LD_LIBRARY_PATH
-# upon conda library activation 
-# conda env config vars set LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH

From 0c20e3c98938e62fece153ac1c61924c733b7fa0 Mon Sep 17 00:00:00 2001
From: Gustaf Ahdritz <gahdritz@gmail.com>
Date: Thu, 19 Oct 2023 18:44:01 -0400
Subject: [PATCH 09/28] Update BibTex

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 25bd605..62aa9fa 100644
--- a/README.md
+++ b/README.md
@@ -442,7 +442,7 @@ Please cite our paper:
 
 ```bibtex
 @article {Ahdritz2022.11.20.517210,
-	author = {Ahdritz, Gustaf and Bouatta, Nazim and Kadyan, Sachin and Xia, Qinghui and Gerecke, William and O{\textquoteright}Donnell, Timothy J and Berenberg, Daniel and Fisk, Ian and Zanichelli, Niccolò and Zhang, Bo and Nowaczynski, Arkadiusz and Wang, Bei and Stepniewska-Dziubinska, Marta M and Zhang, Shang and Ojewole, Adegoke and Guney, Murat Efe and Biderman, Stella and Watkins, Andrew M and Ra, Stephen and Lorenzo, Pablo Ribalta and Nivon, Lucas and Weitzner, Brian and Ban, Yih-En Andrew and Sorger, Peter K and Mostaque, Emad and Zhang, Zhao and Bonneau, Richard and AlQuraishi, Mohammed},
+	author = {Ahdritz, Gustaf and Bouatta, Nazim and Floristean, Christina and Kadyan, Sachin and Xia, Qinghui and Gerecke, William and O{\textquoteright}Donnell, Timothy J and Berenberg, Daniel and Fisk, Ian and Zanichelli, Niccolò and Zhang, Bo and Nowaczynski, Arkadiusz and Wang, Bei and Stepniewska-Dziubinska, Marta M and Zhang, Shang and Ojewole, Adegoke and Guney, Murat Efe and Biderman, Stella and Watkins, Andrew M and Ra, Stephen and Lorenzo, Pablo Ribalta and Nivon, Lucas and Weitzner, Brian and Ban, Yih-En Andrew and Sorger, Peter K and Mostaque, Emad and Zhang, Zhao and Bonneau, Richard and AlQuraishi, Mohammed},
 	title = {{O}pen{F}old: {R}etraining {A}lpha{F}old2 yields new insights into its learning mechanisms and capacity for generalization},
 	elocation-id = {2022.11.20.517210},
 	year = {2022},

From 6bf5c8cea1fac91f37dd475259da1ad0161b025f Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 23 Oct 2023 15:37:36 -0500
Subject: [PATCH 10/28] Update environment YAML

---
 environment.yml | 42 +++++++++++++++++++++---------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/environment.yml b/environment.yml
index 8f92655..ea1ab30 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,30 +2,30 @@ name: openfold_venv
 channels:
   - conda-forge
   - bioconda
-  - pytorch
 dependencies:
-  - conda-forge::python=3.9
-  - conda-forge::setuptools=59.5.0
-  - conda-forge::pip
-  - conda-forge::openmm=7.5.1
-  - conda-forge::pdbfixer
-  - conda-forge::cudatoolkit==11.3.*
+  - python=3.9
+  - setuptools=59.5.0
+  - pip
+  - openmm=7.7
+  - pdbfixer
+  - cudatoolkit==11.3.*
+  - pytorch=1.12.*
+  - pytorch_lightning==1.5.10
+  - biopython==1.79
+  - numpy==1.21
+  - PyYAML==5.4.1
+  - requests
+  - scipy==1.7
+  - tqdm==4.62.2
+  - typing-extensions==3.10
+  - wandb==0.12.21
+  - modelcif==0.7
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
-  - pytorch::pytorch=1.12.*
   - pip:
-      - biopython==1.79
-      - deepspeed==0.5.10
-      - dm-tree==0.1.6
-      - ml-collections==0.1.0
-      - numpy==1.21.2
-      - PyYAML==5.4.1
-      - requests==2.26.0
-      - scipy==1.7.1
-      - tqdm==4.62.2
-      - typing-extensions==3.10.0.2
-      - pytorch_lightning==1.5.10
-      - wandb==0.12.21
-      - modelcif==0.7
+      - deepspeed==0.5.10  # can this be updated?
+      - dm-tree==0.1.6  # 0.1.6 yanked from conda-forge - update?
+      - ml-collections==0.1.0  # 0.1.1 is oldest available on conda-forge - update?
       - git+https://github.com/NVIDIA/dllogger.git
+      - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8bef

From f86d42f40ef14ae1795a007a510ed6d95041dfd1 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 23 Oct 2023 15:45:33 -0500
Subject: [PATCH 11/28] Switch to Miniforge3

---
 Dockerfile | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 4a9f647..fe6b6d1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,24 +13,22 @@ RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/
 
 RUN apt-get update && apt-get install -y wget libxml2 cuda-minimal-build-11-3 libcusparse-dev-11-3 libcublas-dev-11-3 libcusolver-dev-11-3 git
 RUN wget -P /tmp \
-    "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" \
-    && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
-    && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
+    "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" \
+    && bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/conda \
+    && rm /tmp/Miniforge3-Linux-x86_64.sh
 ENV PATH /opt/conda/bin:$PATH
 
 COPY environment.yml /opt/openfold/environment.yml
 
 # installing into the base environment since the docker container wont do anything other than run openfold
-RUN conda env update -n base --file /opt/openfold/environment.yml && conda clean --all
+RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all
 
 COPY openfold /opt/openfold/openfold
 COPY scripts /opt/openfold/scripts
 COPY run_pretrained_openfold.py /opt/openfold/run_pretrained_openfold.py
 COPY train_openfold.py /opt/openfold/train_openfold.py
 COPY setup.py /opt/openfold/setup.py
-COPY lib/openmm.patch /opt/openfold/lib/openmm.patch
 RUN wget -q -P /opt/openfold/openfold/resources \
     https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
-RUN patch -p0 -d /opt/conda/lib/python3.9/site-packages/ < /opt/openfold/lib/openmm.patch
 WORKDIR /opt/openfold
 RUN python3 setup.py install

From 32c11376d726a7bc51d2bb239eba14a8939a59ff Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 23 Oct 2023 15:52:39 -0500
Subject: [PATCH 12/28] Update checkout action

---
 .github/workflows/docker-image.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
index b8ce53b..44a422a 100644
--- a/.github/workflows/docker-image.yml
+++ b/.github/workflows/docker-image.yml
@@ -10,6 +10,6 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Build the Docker image
       run: docker build . --file Dockerfile --tag openfold:$(date +%s)
\ No newline at end of file

From 736d668741fee86b4cbe69a81b5b6f9d0fa6969b Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 23 Oct 2023 15:53:34 -0500
Subject: [PATCH 13/28] Add Dependabot for Actions

---
 .github/dependabot.yml | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..ae992e3
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

From 582103505d7c38ef6d21006abf90c7e65254f03c Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 23 Oct 2023 16:01:16 -0500
Subject: [PATCH 14/28] Update name to `pytorch-lightning`

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index ea1ab30..3111fdd 100644
--- a/environment.yml
+++ b/environment.yml
@@ -10,7 +10,7 @@ dependencies:
   - pdbfixer
   - cudatoolkit==11.3.*
   - pytorch=1.12.*
-  - pytorch_lightning==1.5.10
+  - pytorch-lightning==1.5.10
   - biopython==1.79
   - numpy==1.21
   - PyYAML==5.4.1

From 7666c802723e97640b5d0387f0d05054ae5335a3 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 23 Oct 2023 16:13:16 -0500
Subject: [PATCH 15/28] Use conventional "short hash" style

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 3111fdd..0190405 100644
--- a/environment.yml
+++ b/environment.yml
@@ -28,4 +28,4 @@ dependencies:
       - dm-tree==0.1.6  # 0.1.6 yanked from conda-forge - update?
       - ml-collections==0.1.0  # 0.1.1 is oldest available on conda-forge - update?
       - git+https://github.com/NVIDIA/dllogger.git
-      - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8bef
+      - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8

From a90da39554ca10f2f43d61727f4dd9e8c8aa30c5 Mon Sep 17 00:00:00 2001
From: jnwei <jennifer.wei@omsf.io>
Date: Tue, 24 Oct 2023 13:50:32 -0400
Subject: [PATCH 16/28] Test flash-attention v0.2.1 on docker CI

---
 environment.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/environment.yml b/environment.yml
index ecb2bc8..33accb3 100644
--- a/environment.yml
+++ b/environment.yml
@@ -21,13 +21,14 @@ dependencies:
   - wandb==0.12.21
   - modelcif==0.7
   - awscli
+  - ml-collections
   - bioconda::aria2
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
   - pip:
-      - deepspeed==0.5.10  # can this be updated?
-      - dm-tree==0.1.6  # 0.1.6 yanked from conda-forge - update?
-      - ml-collections==0.1.0  # 0.1.1 is oldest available on conda-forge - update?
+      - deepspeed==0.5.10
+      - dm-tree==0.1.6
       - git+https://github.com/NVIDIA/dllogger.git
-      - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8
+      - git+https://github.com/Dao-AILab/flash-attention.git=0.2.1
+      # - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8

From f06657fe8ab44820e39bf4463b58bab76bbeabbf Mon Sep 17 00:00:00 2001
From: Jennifer Wei <jennifer.wei@omsf.io>
Date: Tue, 24 Oct 2023 13:54:21 -0700
Subject: [PATCH 17/28] Add git to environment.yml

---
 environment.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index 33accb3..4c94a81 100644
--- a/environment.yml
+++ b/environment.yml
@@ -22,7 +22,8 @@ dependencies:
   - modelcif==0.7
   - awscli
   - ml-collections
-  - bioconda::aria2
+  - aria2
+  - git
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
@@ -30,5 +31,5 @@ dependencies:
       - deepspeed==0.5.10
       - dm-tree==0.1.6
       - git+https://github.com/NVIDIA/dllogger.git
-      - git+https://github.com/Dao-AILab/flash-attention.git=0.2.1
+      - git+https://github.com/Dao-AILab/flash-attention.git@v0.2.1
       # - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8

From a5a86d4323487858ef2285632a507c8df18ece88 Mon Sep 17 00:00:00 2001
From: jnwei <jennifer.wei@omsf.io>
Date: Tue, 24 Oct 2023 18:07:06 -0400
Subject: [PATCH 18/28] update flash-attention-version

---
 environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 4c94a81..e183bb6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -32,4 +32,3 @@ dependencies:
       - dm-tree==0.1.6
       - git+https://github.com/NVIDIA/dllogger.git
       - git+https://github.com/Dao-AILab/flash-attention.git@v0.2.1
-      # - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8

From 3817d9409881c1295181cf1da7acd7be2510b4ac Mon Sep 17 00:00:00 2001
From: jnwei <jennifer.wei@omsf.io>
Date: Tue, 24 Oct 2023 18:09:42 -0400
Subject: [PATCH 19/28] Update Dockerfile to add conda path to $LD_LIBRARY_PATH

---
 Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile b/Dockerfile
index fe6b6d1..6a2d674 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -22,6 +22,7 @@ COPY environment.yml /opt/openfold/environment.yml
 
 # installing into the base environment since the docker container wont do anything other than run openfold
 RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all
+EXPORT LD_LIBRARY_PATH=${CONDA_PREFIX}/lib:${LD_LIBRARY_PATH}
 
 COPY openfold /opt/openfold/openfold
 COPY scripts /opt/openfold/scripts

From 5efba4425aa8763e8e9bcee1d3410aae63310274 Mon Sep 17 00:00:00 2001
From: jnwei <jennifer.wei@omsf.io>
Date: Tue, 24 Oct 2023 18:31:13 -0400
Subject: [PATCH 20/28] Fix export statement

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 6a2d674..cac5ee8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -22,7 +22,7 @@ COPY environment.yml /opt/openfold/environment.yml
 
 # installing into the base environment since the docker container wont do anything other than run openfold
 RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all
-EXPORT LD_LIBRARY_PATH=${CONDA_PREFIX}/lib:${LD_LIBRARY_PATH}
+RUN export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib:${LD_LIBRARY_PATH}
 
 COPY openfold /opt/openfold/openfold
 COPY scripts /opt/openfold/scripts

From 6fe34248b2825be27757b60d27a06dbe35d3e687 Mon Sep 17 00:00:00 2001
From: jnwei <jennifer.wei@omsf.io>
Date: Tue, 24 Oct 2023 19:32:15 -0400
Subject: [PATCH 21/28] Test nvidia image 11.4.3-cudnn8-runtime-unbuntu18.04

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index cac5ee8..63091de 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nvidia/cuda:11.3.1-cudnn8-runtime-ubuntu18.04
+FROM nvidia/cuda:11.4.3-cudnn8-runtime-ubuntu18.04
 
 # metainformation
 LABEL org.opencontainers.image.version = "1.0.0"

From e2bb3c4b906f5f424a489794358a65ee68158bab Mon Sep 17 00:00:00 2001
From: jnwei <jennifer.wei@omsf.io>
Date: Tue, 24 Oct 2023 19:43:58 -0400
Subject: [PATCH 22/28] Change docker image to use cudnn devel environment

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 63091de..6e8fa41 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nvidia/cuda:11.4.3-cudnn8-runtime-ubuntu18.04
+FROM nvidia/cuda:11.4.3-cudnn8-devel-ubuntu18.04
 
 # metainformation
 LABEL org.opencontainers.image.version = "1.0.0"

From a5c69a79c638a83156648cadf5f84dd113c05f39 Mon Sep 17 00:00:00 2001
From: jnwei <jennifer.wei@omsf.io>
Date: Tue, 24 Oct 2023 19:55:58 -0400
Subject: [PATCH 23/28] Test docker image
 nvidia/11.7.1-cudnn8-devel-ubuntu18.04

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 6e8fa41..03678d6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nvidia/cuda:11.4.3-cudnn8-devel-ubuntu18.04
+FROM nvidia/cuda:11.7.1-cudnn8-devel-ubuntu18.04
 
 # metainformation
 LABEL org.opencontainers.image.version = "1.0.0"

From f68a6c694b1556e2e73a76f2ce2ac1d3377ee2ab Mon Sep 17 00:00:00 2001
From: jnwei <jennifer.wei@omsf.io>
Date: Wed, 25 Oct 2023 08:51:58 -0400
Subject: [PATCH 24/28] Update readme, also reset flash attention version to
 0.2.1 in environment.yml

---
 Dockerfile | 2 +-
 README.md  | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 03678d6..c7d9483 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nvidia/cuda:11.7.1-cudnn8-devel-ubuntu18.04
+FROM nvidia/cuda:11.3.1-cudnn8-devel-ubuntu18.04
 
 # metainformation
 LABEL org.opencontainers.image.version = "1.0.0"
diff --git a/README.md b/README.md
index 62aa9fa..c3adadd 100644
--- a/README.md
+++ b/README.md
@@ -53,8 +53,9 @@ This package is currently supported for CUDA 11 and Pytorch 1.12
 To install:
 1. Clone the repository, e.g. `git clone https://github.com/aqlaboratory/openfold.git`
 1. From the `openfold` repo: 
-    - Create an [Anaconda/Mamba](https://docs.anaconda.com/free/anaconda/install/index.html) environment, e.g. 
-        `conda env create -n openfold_env -f environment.yml`
+    - Create a [Mamba]("https://github.com/conda-forge/miniforge/releases/latest/download/) environment, e.g. 
+        `mamba env create -n openfold_env -f environment.yml`
+      Mamba is recommended as the dependencies required by OpenFold are quite large and mamba can speed up the process.
     - Activate the environment, e.g `conda activate openfold_env` 
 1. Run `scripts/install_third_party_dependencies.sh` to configure kernels and folding resources.
 

From 13f0f6fe165dc0cb8af29662b9137bfa26d8349e Mon Sep 17 00:00:00 2001
From: Jennifer Wei <jennifer.wei@omsf.io>
Date: Fri, 27 Oct 2023 11:30:53 -0700
Subject: [PATCH 25/28] Adds libgcc and pytorch::pytorch to environment.yml

---
 environment.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index e183bb6..49d9050 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,15 +1,16 @@
-name: openfold_venv
+name: openfold-venv
 channels:
   - conda-forge
   - bioconda
+  - pytorch
 dependencies:
   - python=3.9
+  - libgcc=7.2
   - setuptools=59.5.0
   - pip
   - openmm=7.7
   - pdbfixer
   - cudatoolkit==11.3.*
-  - pytorch=1.12.*
   - pytorch-lightning==1.5.10
   - biopython==1.79
   - numpy==1.21
@@ -27,8 +28,9 @@ dependencies:
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
+  - pytorch::pytorch=1.12.*
   - pip:
       - deepspeed==0.5.10
       - dm-tree==0.1.6
       - git+https://github.com/NVIDIA/dllogger.git
-      - git+https://github.com/Dao-AILab/flash-attention.git@v0.2.1
+      - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8

From e3716118cda704a2432e44b46a0714bf35ca4b05 Mon Sep 17 00:00:00 2001
From: Jennifer Wei <jennifer.wei@omsf.io>
Date: Fri, 27 Oct 2023 12:04:15 -0700
Subject: [PATCH 26/28] Adds KMP_AFFINITY to conda environment.

---
 scripts/install_third_party_dependencies.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/install_third_party_dependencies.sh b/scripts/install_third_party_dependencies.sh
index 86d5ee8..3756a87 100755
--- a/scripts/install_third_party_dependencies.sh
+++ b/scripts/install_third_party_dependencies.sh
@@ -14,3 +14,5 @@ gunzip -c tests/test_data/sample_feats.pickle.gz > tests/test_data/sample_feats.
 python setup.py install
 
 export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
+# This setting is used to fix a worker assignment issue during data loading
+conda env config vars set KMP_AFFINITY=none

From 13728b120333820e560dc43cc9e4be79b3f57b4c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Oct 2023 19:25:04 +0000
Subject: [PATCH 27/28] Bump actions/checkout from 2 to 4

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v2...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/undefined_names.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/undefined_names.yml b/.github/workflows/undefined_names.yml
index 8ff9f24..07cb311 100644
--- a/.github/workflows/undefined_names.yml
+++ b/.github/workflows/undefined_names.yml
@@ -4,7 +4,7 @@ jobs:
   undefined_names:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v2
       - run: pip install --upgrade pip
       - run: pip install flake8

From dcd809d9c290d163168776e219223e29b440087f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 30 Oct 2023 14:55:31 +0000
Subject: [PATCH 28/28] Bump actions/setup-python from 2 to 4

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 4.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v2...v4)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/undefined_names.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/undefined_names.yml b/.github/workflows/undefined_names.yml
index 07cb311..a689751 100644
--- a/.github/workflows/undefined_names.yml
+++ b/.github/workflows/undefined_names.yml
@@ -5,7 +5,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
       - run: pip install --upgrade pip
       - run: pip install flake8
       - run: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics