Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
A
ASMSA-moved2github
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Requirements
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Locked files
Build
Pipelines
Jobs
Pipeline schedules
Test cases
Artifacts
Deploy
Releases
Package registry
Container registry
Model registry
Operate
Environments
Terraform modules
Monitor
Incidents
Service Desk
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Code review analytics
Issue analytics
Insights
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Aleš Křenek
ASMSA-moved2github
Commits
69d15792
Commit
69d15792
authored
1 year ago
by
Mgr. Aleš Křenek Ph.D.
Browse files
Options
Downloads
Patches
Plain Diff
updatable /opt & /usr/local; import GMX correctly
parent
f2113034
No related branches found
No related tags found
No related merge requests found
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
Dockerfile
+5
-6
5 additions, 6 deletions
Dockerfile
IMAGE
+1
-1
1 addition, 1 deletion
IMAGE
src/asmsa/__init__.py
+2
-0
2 additions, 0 deletions
src/asmsa/__init__.py
with
8 additions
and
7 deletions
Dockerfile
+
5
−
6
View file @
69d15792
...
@@ -19,14 +19,17 @@ RUN . bin/activate && pip3 install /tmp/$DIST
...
@@ -19,14 +19,17 @@ RUN . bin/activate && pip3 install /tmp/$DIST
# select tensorflow gpu image as base
# select tensorflow gpu image as base
FROM
tensorflow/tensorflow:2.13.0-gpu
FROM
tensorflow/tensorflow:2.13.0-gpu
RUN
apt update
&&
apt
install
-y
wget g++ libz-dev tini procps
&&
apt clean
&&
rm
-rf
/var/lib/apt/lists/
*
RUN
apt update
&&
apt
install
-y
wget
curl
g++ libz-dev tini procps
&&
curl
-LO
"https://dl.k8s.io/release/
$(
curl
-L
-s
https://dl.k8s.io/release/stable.txt
)
/bin/linux/amd64/kubectl"
&&
install
-m
755 kubectl /usr/local/bin
&&
apt clean
&&
rm
-rf
/var/lib/apt/lists/
*
RUN
useradd
-m
-u
1000 jovyan
RUN
useradd
-m
-u
1000 jovyan
RUN
mkdir
-p
/opt
&&
chown
jovyan /opt
RUN
mkdir
-p
/opt
COPY
--from=builder /opt /opt
COPY
--from=builder /opt /opt
COPY
--from=builder /usr/local /usr/local
COPY
--from=builder /usr/local /usr/local
RUN
chown
-R
jovyan /opt /usr/local/lib/python
$(
python3
-c
"import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')"
)
USER
jovyan
# apply tensorboard fix
# apply tensorboard fix
#RUN wget https://raw.githubusercontent.com/tensorflow/tensorboard/e59ca8d45746f459d797f4e69377eda4433e1624/tensorboard/notebook.py -O - > /usr/local/lib/python3.8/dist-packages/tensorboard/notebook.py
#RUN wget https://raw.githubusercontent.com/tensorflow/tensorboard/e59ca8d45746f459d797f4e69377eda4433e1624/tensorboard/notebook.py -O - > /usr/local/lib/python3.8/dist-packages/tensorboard/notebook.py
COPY
3142.patch /tmp
COPY
3142.patch /tmp
...
@@ -34,10 +37,6 @@ RUN . /opt/bin/activate && cd /usr/local/lib/python$(python3 -c "import sys; pri
...
@@ -34,10 +37,6 @@ RUN . /opt/bin/activate && cd /usr/local/lib/python$(python3 -c "import sys; pri
RUN
.
/opt/bin/activate
&&
jupyter labextension
enable
nglview
RUN
.
/opt/bin/activate
&&
jupyter labextension
enable
nglview
RUN
apt update
&&
apt
install
-y
curl
&&
curl
-LO
"https://dl.k8s.io/release/
$(
curl
-L
-s
https://dl.k8s.io/release/stable.txt
)
/bin/linux/amd64/kubectl"
&&
install
-m
755 kubectl /usr/local/bin
&&
apt clean
&&
rm
-rf
/var/lib/apt/lists/
*
USER
jovyan
RUN
mkdir
/opt/ASMSA
RUN
mkdir
/opt/ASMSA
COPY
IMAGE prepare.ipynb tune.ipynb train.ipynb md.ipynb /opt/ASMSA/
COPY
IMAGE prepare.ipynb tune.ipynb train.ipynb md.ipynb /opt/ASMSA/
COPY
md.mdp.template *.mdp /opt/ASMSA/
COPY
md.mdp.template *.mdp /opt/ASMSA/
...
...
This diff is collapsed.
Click to expand it.
IMAGE
+
1
−
1
View file @
69d15792
ljocha/asmsa:2023-2
0
ljocha/asmsa:2023-2
1
This diff is collapsed.
Click to expand it.
src/asmsa/__init__.py
+
2
−
0
View file @
69d15792
...
@@ -13,6 +13,8 @@ from .mol_model import MoleculeModel, NBDistancesSparse, NBDistancesDense
...
@@ -13,6 +13,8 @@ from .mol_model import MoleculeModel, NBDistancesSparse, NBDistancesDense
from
.aae_model
import
AAEModel
from
.aae_model
import
AAEModel
from
.aae_hyper_model
import
AAEHyperModel
from
.aae_hyper_model
import
AAEHyperModel
from
.gmx
import
GMX
def
_parse_top
(
top
,
ndx
=
None
):
def
_parse_top
(
top
,
ndx
=
None
):
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment