From 3604d6554155a6957ae881ed590ee303d1247489 Mon Sep 17 00:00:00 2001
From: Leonhard Hennig <leonhard.hennig@dfki.de>
Date: Tue, 2 Jul 2024 08:31:25 +0200
Subject: [PATCH 1/5] Update folder locations (resolves
 https://github.com/DFKI-NLP/pegasus-bridle/issues/11)

---
 .env.example | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.env.example b/.env.example
index b830d5f..cfb50ab 100644
--- a/.env.example
+++ b/.env.example
@@ -2,7 +2,7 @@
 
 # choose an Enroot Image
 # IMPORTANT: For the scripts provided here to function correctly, there needs to be conda installed in that image!
-CONTAINER_IMAGE=/netscratch/enroot/nvcr.io_nvidia_pytorch_23.07-py3.sqsh
+CONTAINER_IMAGE=/enroot/nvcr.io_nvidia_pytorch_23.07-py3.sqsh
 
 # chooses a Slurm partition
 PARTITION=batch
@@ -38,7 +38,7 @@ HOST_CONDA_ENVS_DIR=/netscratch/$USER/miniconda3
 # change this if you use another Enroot image with a different conda location
 CONTAINER_CONDA_ENVS_DIR=/opt/conda
 # assemble everything:
-CONTAINER_MOUNTS=/netscratch:/netscratch,/ds:/ds:ro,"$HOST_WORKDIR":"$CONTAINER_WORKDIR","$HOST_CONDA_ENVS_DIR":"$CONTAINER_CONDA_ENVS_DIR","$HOST_CACHEDIR":"/home/$USER/.cache","$HOST_CACHEDIR":/root/.cache,"$HOST_CACHEDIR":/home/root/.cache
+CONTAINER_MOUNTS=/netscratch:/netscratch,/fscratch/$USER:/fscratch/$USER,/ds:/ds:ro,"$HOST_WORKDIR":"$CONTAINER_WORKDIR","$HOST_CONDA_ENVS_DIR":"$CONTAINER_CONDA_ENVS_DIR","$HOST_CACHEDIR":"/home/$USER/.cache","$HOST_CACHEDIR":/root/.cache,"$HOST_CACHEDIR":/home/root/.cache
 
 # Define which conda environment should be activated. Set to $CONDA_DEFAULT_ENV, to use the one that is activated at
 # the host. If not defined, no conda environment will be activated and the base python interpreter will be used.

From 074c9a35081afd3bc0dc958f0e14c133d73d0e0b Mon Sep 17 00:00:00 2001
From: Leonhard Hennig <leonhard.hennig@dfki.de>
Date: Tue, 2 Jul 2024 10:01:16 +0200
Subject: [PATCH 2/5] add conda install

---
 activate_and_execute.sh | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/activate_and_execute.sh b/activate_and_execute.sh
index a8bf547..4b8931b 100644
--- a/activate_and_execute.sh
+++ b/activate_and_execute.sh
@@ -6,6 +6,28 @@ SCRIPT_DIR=$(dirname $0)
 ARGS=( "$@" )
 shift $#
 
+if ! command -v conda > /dev/null 2>&1; then
+    echo "Installing conda..."
+    #wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
+    #bash ~/miniconda.sh -b -p $HOME/miniconda
+    # Following https://docs.conda.io/projects/conda/en/latest/user-guide/install/rpm-debian.html
+    # Install our public GPG key to trusted store
+    curl https://repo.anaconda.com/pkgs/misc/gpgkeys/anaconda.asc | gpg --dearmor > conda.gpg
+    install -o root -g root -m 644 conda.gpg /usr/share/keyrings/conda-archive-keyring.gpg
+    # Check whether fingerprint is correct (will output an error message otherwise)
+    gpg --keyring /usr/share/keyrings/conda-archive-keyring.gpg --no-default-keyring --fingerprint 34161F5BF5EB1D4BFBBB8F0A8AEB4F8B29D82806
+    # Add our Debian repo
+    echo "deb [arch=amd64 signed-by=/usr/share/keyrings/conda-archive-keyring.gpg] https://repo.anaconda.com/pkgs/misc/debrepo/conda stable main" > /etc/apt/sources.list.d/conda.list
+    apt update
+    apt install conda
+    source /opt/conda/etc/profile.d/conda.sh
+    conda -V
+    echo "channels:" > /opt/conda/.condarc
+    echo "  - conda-forge" >> /opt/conda/.condarc
+    echo "channel_priority: strict" >> /opt/conda/.condarc
+fi
+
+
 # activate conda environment, if the variable is defined
 if [ -n "$CONDA_ENV" ]; then
     echo "activate conda environment: $CONDA_ENV"

From d2a45d6e7bca6480386301319343ec5154908820 Mon Sep 17 00:00:00 2001
From: Leonhard Hennig <leonhard.hennig@dfki.de>
Date: Tue, 2 Jul 2024 10:12:02 +0200
Subject: [PATCH 3/5] updated conda install

---
 activate_and_execute.sh | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/activate_and_execute.sh b/activate_and_execute.sh
index 4b8931b..865daf1 100644
--- a/activate_and_execute.sh
+++ b/activate_and_execute.sh
@@ -18,10 +18,9 @@ if ! command -v conda > /dev/null 2>&1; then
     gpg --keyring /usr/share/keyrings/conda-archive-keyring.gpg --no-default-keyring --fingerprint 34161F5BF5EB1D4BFBBB8F0A8AEB4F8B29D82806
     # Add our Debian repo
     echo "deb [arch=amd64 signed-by=/usr/share/keyrings/conda-archive-keyring.gpg] https://repo.anaconda.com/pkgs/misc/debrepo/conda stable main" > /etc/apt/sources.list.d/conda.list
-    apt update
-    apt install conda
+    apt -qy update
+    apt -qy install conda
     source /opt/conda/etc/profile.d/conda.sh
-    conda -V
     echo "channels:" > /opt/conda/.condarc
     echo "  - conda-forge" >> /opt/conda/.condarc
     echo "channel_priority: strict" >> /opt/conda/.condarc

From a8b63857393c61e48c55085806d975927de3f76f Mon Sep 17 00:00:00 2001
From: Leonhard Hennig <leonhard.hennig@dfki.de>
Date: Tue, 2 Jul 2024 10:14:36 +0200
Subject: [PATCH 4/5] updated conda install

---
 activate_and_execute.sh | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/activate_and_execute.sh b/activate_and_execute.sh
index 865daf1..1f82b2e 100644
--- a/activate_and_execute.sh
+++ b/activate_and_execute.sh
@@ -7,10 +7,8 @@ ARGS=( "$@" )
 shift $#
 
 if ! command -v conda > /dev/null 2>&1; then
-    echo "Installing conda..."
-    #wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
-    #bash ~/miniconda.sh -b -p $HOME/miniconda
     # Following https://docs.conda.io/projects/conda/en/latest/user-guide/install/rpm-debian.html
+    echo "Installing conda..."
     # Install our public GPG key to trusted store
     curl https://repo.anaconda.com/pkgs/misc/gpgkeys/anaconda.asc | gpg --dearmor > conda.gpg
     install -o root -g root -m 644 conda.gpg /usr/share/keyrings/conda-archive-keyring.gpg

From 4a0ecd76d7507e1f7d57b296c38f56920daf5477 Mon Sep 17 00:00:00 2001
From: Leonhard Hennig <leonhard.hennig@dfki.de>
Date: Tue, 2 Jul 2024 10:17:23 +0200
Subject: [PATCH 5/5] updated conda install

---
 activate_and_execute.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/activate_and_execute.sh b/activate_and_execute.sh
index 1f82b2e..2de1562 100644
--- a/activate_and_execute.sh
+++ b/activate_and_execute.sh
@@ -16,8 +16,8 @@ if ! command -v conda > /dev/null 2>&1; then
     gpg --keyring /usr/share/keyrings/conda-archive-keyring.gpg --no-default-keyring --fingerprint 34161F5BF5EB1D4BFBBB8F0A8AEB4F8B29D82806
     # Add our Debian repo
     echo "deb [arch=amd64 signed-by=/usr/share/keyrings/conda-archive-keyring.gpg] https://repo.anaconda.com/pkgs/misc/debrepo/conda stable main" > /etc/apt/sources.list.d/conda.list
-    apt -qy update
-    apt -qy install conda
+    apt update
+    apt install conda
     source /opt/conda/etc/profile.d/conda.sh
     echo "channels:" > /opt/conda/.condarc
     echo "  - conda-forge" >> /opt/conda/.condarc