From 2fdf92694e2ca411cc2233498aeb513cf49ae936 Mon Sep 17 00:00:00 2001
From: Jay Qi <jayqi@users.noreply.github.com>
Date: Thu, 8 Aug 2024 22:05:16 -0400
Subject: [PATCH] Fix dockerfiles

---
 Makefile                | 15 ++++---
 runtime/Dockerfile      | 17 ++++++--
 runtime/Dockerfile-lock | 14 ++-----
 runtime/pixi.lock       | 88 +++++++++++++++++++++--------------------
 4 files changed, 68 insertions(+), 66 deletions(-)

diff --git a/Makefile b/Makefile
index 293f9ff..6fd50b5 100644
--- a/Makefile
+++ b/Makefile
@@ -120,15 +120,14 @@ build:
 ## Updates runtime environment lockfile using Docker
 update-lockfile:
 	@echo Generating the lockfile for CPU and GPU within Docker
-	cd runtime && \
-	docker build . \
-		--file Dockerfile-lock \
-		--build-arg CPU_OR_GPU=${CPU_OR_GPU} \
+	docker build runtime \
+		--file runtime/Dockerfile-lock \
 		--tag pixi-lock:local
-	@echo Copying lockfile to host
-	docker create --name dummy pixi-lock:local
-	docker cp dummy:/tmp/pixi.lock runtime/pixi.lock
-	docker rm -f dummy
+	@echo Running lock container
+	docker run \
+		--mount type=bind,source="$(shell pwd)"/runtime,target=/tmp \
+		--rm \
+		pixi-lock:local
 
 ## Ensures that your locally built image can import all the Python packages successfully when it runs
 test-container: _check_image _echo_image _submission_write_perms
diff --git a/runtime/Dockerfile b/runtime/Dockerfile
index 1dc98af..e0ae1ad 100644
--- a/runtime/Dockerfile
+++ b/runtime/Dockerfile
@@ -10,6 +10,15 @@ ENV DEBIAN_FRONTEND=noninteractive \
     PYTHONUNBUFFERED=1 \
     SHELL=/bin/bash
 
+# Create user andset permissions
+ENV RUNTIME_USER=runtimeuser
+ENV RUNTIME_UID=1000
+ENV RUNTIME_GID=1000
+
+RUN echo "Creating ${RUNTIME_USER} user..." \
+    && groupadd --gid ${RUNTIME_UID} ${RUNTIME_USER}  \
+    && useradd --create-home --gid ${RUNTIME_UID} --no-log-init --uid ${RUNTIME_UID} ${RUNTIME_USER}
+
 COPY apt.txt apt.txt
 RUN apt-get update --fix-missing \
     && apt-get install -y apt-utils 2> /dev/null \
@@ -17,18 +26,18 @@ RUN apt-get update --fix-missing \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /apt.txt
 
-COPY --chown=$MAMBA_USER:$MAMBA_USER pixi.lock /tmp/pixi.lock
-COPY --chown=$MAMBA_USER:$MAMBA_USER pixi.toml /tmp/pixi.toml
+COPY --chown=$RUNTIME_USER:$RUNTIME_USER pixi.lock /tmp/pixi.lock
+COPY --chown=$RUNTIME_USER:$RUNTIME_USER pixi.toml /tmp/pixi.toml
 RUN pixi install --manifest-path /tmp/pixi.toml -e ${CPU_OR_GPU} && \
     pixi clean --manifest-path /tmp/pixi.toml -e ${CPU_OR_GPU}
 
 RUN mkdir /code_execution
-RUN chown -R ${MAMBA_USER}:${MAMBA_USER} /code_execution
+RUN chown -R ${RUNTIME_USER}:${RUNTIME_USER} /code_execution
 
 COPY tests /code_execution/tests
 COPY entrypoint.sh /entrypoint.sh
 
 WORKDIR /code_execution
-USER ${MAMBA_USER}
+USER ${RUNTIME_USER}
 
 CMD ["bash", "/entrypoint.sh"]
diff --git a/runtime/Dockerfile-lock b/runtime/Dockerfile-lock
index d133a82..48e36a7 100644
--- a/runtime/Dockerfile-lock
+++ b/runtime/Dockerfile-lock
@@ -2,15 +2,7 @@ FROM ghcr.io/prefix-dev/pixi:0.26.1-bookworm-slim
 
 USER root
 
-ARG CPU_OR_GPU=gpu
-
-ENV DEBIAN_FRONTEND=noninteractive \
-    LANG=C.UTF-8  \
-    LC_ALL=C.UTF-8 \
-    PYTHONUNBUFFERED=1 \
-    SHELL=/bin/bash
-
-COPY --chown=$MAMBA_USER:$MAMBA_USER pixi.lock /tmp/pixi.lock
-COPY --chown=$MAMBA_USER:$MAMBA_USER pixi.toml /tmp/pixi.toml
-RUN pixi tree --manifest-path /tmp/pixi.toml --platform linux-64
+RUN mkdir -p /tmp
+WORKDIR /tmp
 
+ENTRYPOINT ["pixi", "tree", "--manifest-path", "pixi.toml", "--platform", "linux-64", "-v"]
diff --git a/runtime/pixi.lock b/runtime/pixi.lock
index 998272a..98a45da 100644
--- a/runtime/pixi.lock
+++ b/runtime/pixi.lock
@@ -18,7 +18,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.3.1-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/astunparse-1.6.3-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/async-timeout-4.0.3-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-24.1.0-pyh71513ae_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-24.2.0-pyh71513ae_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.7.3-h28f7589_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.6.1-hc309b26_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.0-hd590300_0.conda
@@ -44,7 +44,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/cachetools-5.4.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/catalogue-2.0.10-py310hff52083_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.7.4-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.16.0-py310h2fee648_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.17.0-py310h2fdcea3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cloudpathlib-0.16.0-pyhd8ed1ab_0.conda
@@ -74,7 +74,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gmpy2-2.1.5-py310hc7909c9_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/google-api-core-2.19.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-2.32.0-pyhff2d567_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-2.33.0-pyhff2d567_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-oauthlib-1.0.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/google-pasta-0.2.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/googleapis-common-protos-1.63.2-pyhd8ed1ab_0.conda
@@ -211,7 +211,7 @@ environments:
       - conda: https://conda.anaconda.org/pytorch/noarch/pytorch-mutex-1.0-cpu.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pyu2f-0.1.5-pyhd8ed1ab_0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.1-py310h2372a71_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.2-py310h5b4e0ec_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ray-core-2.8.1-py310h2ca9b2b_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ray-default-2.8.1-py310ha1e06c9_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/rdma-core-28.9-h59595ed_1.conda
@@ -222,7 +222,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.3-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/requests-oauthlib-2.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/rich-13.7.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.19.1-py310h42e942d_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.20.0-py310h42e942d_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/rsa-4.9-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/s2n-1.3.49-h06160fa_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/sacremoses-0.0.53-pyhd8ed1ab_0.tar.bz2
@@ -305,7 +305,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.3.1-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/astunparse-1.6.3-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/async-timeout-4.0.3-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-24.1.0-pyh71513ae_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-24.2.0-pyh71513ae_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.7.3-h28f7589_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.6.1-hc309b26_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.0-hd590300_0.conda
@@ -331,7 +331,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/cachetools-5.4.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/catalogue-2.0.10-py310hff52083_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.7.4-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.16.0-py310h2fee648_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.17.0-py310h2fdcea3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cloudpathlib-0.16.0-pyhd8ed1ab_0.conda
@@ -371,7 +371,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gmpy2-2.1.5-py310hc7909c9_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/google-api-core-2.19.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-2.32.0-pyhff2d567_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-2.33.0-pyhff2d567_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-oauthlib-1.0.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/google-pasta-0.2.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/googleapis-common-protos-1.63.2-pyhd8ed1ab_0.conda
@@ -518,7 +518,7 @@ environments:
       - conda: https://conda.anaconda.org/pytorch/noarch/pytorch-mutex-1.0-cuda.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pyu2f-0.1.5-pyhd8ed1ab_0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.1-py310h2372a71_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.2-py310h5b4e0ec_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ray-core-2.8.1-py310h2ca9b2b_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ray-default-2.8.1-py310ha1e06c9_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/rdma-core-28.9-h59595ed_1.conda
@@ -529,7 +529,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.3-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/requests-oauthlib-2.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/rich-13.7.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.19.1-py310h42e942d_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.20.0-py310h42e942d_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/rsa-4.9-pyhd8ed1ab_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/s2n-1.3.49-h06160fa_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/sacremoses-0.0.53-pyhd8ed1ab_0.tar.bz2
@@ -755,19 +755,19 @@ packages:
   timestamp: 1691763717537
 - kind: conda
   name: attrs
-  version: 24.1.0
+  version: 24.2.0
   build: pyh71513ae_0
   subdir: noarch
   noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/attrs-24.1.0-pyh71513ae_0.conda
-  sha256: fe47984d3e453c763ff7b4b854837f0bf4fe233a2cd162be82504a19c4ec1457
-  md5: 1f2d47df5c1127313066a8651fe9288d
+  url: https://conda.anaconda.org/conda-forge/noarch/attrs-24.2.0-pyh71513ae_0.conda
+  sha256: 28dba85a7e0f7fb57d7315e13f603d1e41b83c5b88aa2a602596b52c833a2ff8
+  md5: 6732fa52eb8e66e5afeb32db8701a791
   depends:
   - python >=3.7
   license: MIT
   license_family: MIT
-  size: 56327
-  timestamp: 1722715555247
+  size: 56048
+  timestamp: 1722977241383
 - kind: conda
   name: aws-c-auth
   version: 0.7.3
@@ -1198,13 +1198,14 @@ packages:
   timestamp: 1720458053074
 - kind: conda
   name: cffi
-  version: 1.16.0
-  build: py310h2fee648_0
+  version: 1.17.0
+  build: py310h2fdcea3_0
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.16.0-py310h2fee648_0.conda
-  sha256: 007e7f69ab45553b7bf11f2c1b8d3f3a13fd42997266a0d57795f41c7d38df36
-  md5: 45846a970e71ac98fd327da5d40a0a2c
+  url: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.17.0-py310h2fdcea3_0.conda
+  sha256: 082a0c2aee928cdc4fc41320a61a530d10b4c13c886f0de8f6d57e7daacfc1b1
+  md5: 6ac912f6208a15d35955ab73a4e5efda
   depends:
+  - __glibc >=2.17,<3.0.a0
   - libffi >=3.4,<4.0a0
   - libgcc-ng >=12
   - pycparser
@@ -1212,8 +1213,8 @@ packages:
   - python_abi 3.10.* *_cp310
   license: MIT
   license_family: MIT
-  size: 241339
-  timestamp: 1696001848492
+  size: 242409
+  timestamp: 1723018481932
 - kind: conda
   name: charset-normalizer
   version: 3.3.2
@@ -1882,13 +1883,13 @@ packages:
   timestamp: 1719307111090
 - kind: conda
   name: google-auth
-  version: 2.32.0
+  version: 2.33.0
   build: pyhff2d567_0
   subdir: noarch
   noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/google-auth-2.32.0-pyhff2d567_0.conda
-  sha256: ed1ba42553e213245f6f5f8cb417996525f10ba7c88b5819de3f521e110bbf5a
-  md5: 985a17f06e617d6c8dab825a39a39d00
+  url: https://conda.anaconda.org/conda-forge/noarch/google-auth-2.33.0-pyhff2d567_0.conda
+  sha256: 4898e99b92a16b4900696dad12d7b201e6940f6cd20fabfe8f0a059fef9f5b87
+  md5: 5a750d3f2f4bfb378322dda0d8a02018
   depends:
   - aiohttp >=3.6.2,<4.0.0
   - cachetools >=2.0.0,<6.0
@@ -1901,8 +1902,8 @@ packages:
   - rsa >=3.1.4,<5
   license: Apache-2.0
   license_family: Apache
-  size: 110849
-  timestamp: 1720518449305
+  size: 111747
+  timestamp: 1723018880178
 - kind: conda
   name: google-auth-oauthlib
   version: 1.0.0
@@ -4443,22 +4444,22 @@ packages:
   timestamp: 1604249020971
 - kind: conda
   name: pyyaml
-  version: 6.0.1
-  build: py310h2372a71_1
-  build_number: 1
+  version: 6.0.2
+  build: py310h5b4e0ec_0
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.1-py310h2372a71_1.conda
-  sha256: aa78ccddb0a75fa722f0f0eb3537c73ee1219c9dd46cea99d6b9eebfdd780f3d
-  md5: bb010e368de4940771368bc3dc4c63e7
+  url: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.2-py310h5b4e0ec_0.conda
+  sha256: e7b3d6ee96fedc29b49a3705401765743082e79ea9f6359fdc6d3a2245fd6747
+  md5: ad8de7b4ac482217959cc1e8fe0cc56d
   depends:
+  - __glibc >=2.17,<3.0.a0
   - libgcc-ng >=12
   - python >=3.10,<3.11.0a0
   - python_abi 3.10.* *_cp310
   - yaml >=0.2.5,<0.3.0a0
   license: MIT
   license_family: MIT
-  size: 170627
-  timestamp: 1695373587159
+  size: 181235
+  timestamp: 1723018382019
 - kind: conda
   name: ray-core
   version: 2.8.1
@@ -4665,12 +4666,12 @@ packages:
   timestamp: 1709150578093
 - kind: conda
   name: rpds-py
-  version: 0.19.1
+  version: 0.20.0
   build: py310h42e942d_0
   subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.19.1-py310h42e942d_0.conda
-  sha256: bded054638611b028d354b581d70e4353be5f4bd43a331c2d9bb829f80a18f1b
-  md5: e475e081b969944abf635b7484b8661e
+  url: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.20.0-py310h42e942d_0.conda
+  sha256: 77a800f5a37bcaefad09b46b19f2d17357bc46eff7514f8db570c885e9369477
+  md5: 825361e63187e65a9da05a8b4274a0e1
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc-ng >=12
@@ -4680,8 +4681,8 @@ packages:
   - __glibc >=2.17
   license: MIT
   license_family: MIT
-  size: 331102
-  timestamp: 1721861153079
+  size: 334195
+  timestamp: 1723039241464
 - kind: conda
   name: rsa
   version: '4.9'
@@ -4749,6 +4750,7 @@ packages:
   constrains:
   - __glibc >=2.17
   license: Apache-2.0
+  license_family: APACHE
   size: 400960
   timestamp: 1722937971905
 - kind: conda