Merge pull request #66 from NERSC/19-07

19 07

jupyter-base/Dockerfile

@@ -30,9 +30,9 @@ RUN \
 
 RUN \
     curl -s -o /tmp/miniconda3.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh    &&  \
-    bash /tmp/miniconda3.sh -f -b -p /opt/anaconda3         &&  \
+    bash /tmp/miniconda3.sh -b -p /opt/anaconda3            &&  \
     rm -rf /tmp/miniconda3.sh                               &&  \
-    echo "python 3.7.*" >> /opt/anaconda3/conda-meta/pinned &&  \
+    echo "python 3.7.3" >> /opt/anaconda3/conda-meta/pinned &&  \
     /opt/anaconda3/bin/conda update --yes conda             &&  \
     /opt/anaconda3/bin/conda install --yes                      \
         alembic         \

jupyter-nersc/app-notebooks/Dockerfile

@@ -34,7 +34,7 @@ RUN \
 ADD packages2.txt /tmp/packages2.txt
 RUN \
     wget -q -O /tmp/miniconda2.sh https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh  && \
-    bash /tmp/miniconda2.sh -f -b -p /opt/anaconda2             && \
+    bash /tmp/miniconda2.sh -b -p /opt/anaconda2                && \
     rm /tmp/miniconda2.sh                                       && \
     /opt/anaconda2/bin/conda update --yes conda                 && \
     /opt/anaconda2/bin/conda install --yes anaconda             && \
@@ -74,11 +74,12 @@ RUN \
     pip install --no-cache-dir ipympl                               && \
     jupyter nbextension enable --sys-prefix --py widgetsnbextension && \
     jupyter labextension install            \
-        @jupyterlab/hub-extension           \
         @jupyter-widgets/jupyterlab-manager \
         jupyter-matplotlib                  \
         @jupyterlab/toc                     \
-        jupyterlab_bokeh
+        jupyterlab_bokeh                    \
+        jupyterlab-favorites                \
+        jupyterlab-recents
 
 RUN \
     /opt/anaconda2/bin/jupyter nbextension enable --sys-prefix --py widgetsnbextension

jupyter-nersc/app-notebooks/packages2.txt

@@ -1,8 +1,8 @@
 basemap
-beautiful-soup
+beautifulsoup4
 biopython
 netcdf4
-notebook=5.7.8
+notebook
 r-car
 r-essentials
 rpy2

jupyter-nersc/app-notebooks/packages3.txt

@@ -5,7 +5,7 @@ blaze
 jupyter
 jupyterlab
 netcdf4
-notebook=5.7.8
+notebook
 r-essentials
 rpy2
 scipy

jupyter-nersc/web-jupyterhub/Dockerfile

@@ -6,8 +6,6 @@ WORKDIR /srv
 
 # Authenticator and spawner
 
-#   pip install git+https://github.com/nersc/nerscspawner.git                       &&  \
-
 RUN \
     pip install git+https://github.com/nersc/sshapiauthenticator.git        &&  \
     pip install git+https://github.com/jupyterhub/batchspawner.git@4747946  &&  \

jupyter-nersc/web-jupyterhub/docker-entrypoint.sh

@@ -26,5 +26,7 @@ file_env() {
 file_env 'POSTGRES_PASSWORD'
 file_env 'SKEY'
 file_env 'MODS_JUPYTERHUB_API_TOKEN'
+file_env 'CONFIGPROXY_AUTH_TOKEN'
+file_env 'JUPYTERHUB_CRYPT_KEY'
 
 exec "$@"

jupyter-nersc/web-jupyterhub/jupyterhub_config.py

@@ -393,11 +393,11 @@ def comma_split(string):
     {
         'name': 'cull-idle',
         'admin': True,
-        'command': 'cull_idle_servers.py --timeout=86400'.split(),
+        'command': 'cull_idle_servers.py --timeout=57600'.split(),
     },
     {
         'name': 'announcement',
-        'url': 'http://127.0.0.1:8888',
+        'url': 'http://web-jupyterhub:8888',
         'command': ["python", "-m", "announcement"],
     },
     {
@@ -505,6 +505,7 @@ def comma_split(string):
 #  environment variables here. Most, including the default, do not. Consult the
 #  documentation for your spawner to verify!
 #c.Spawner.args = []
+c.Spawner.args = ["--transport=ipc"]
 
 ## The command used for starting the single-user server.
 #  
@@ -706,7 +707,7 @@ def comma_split(string):
 #  JupyterHub modifies its own state accordingly and removes appropriate routes
 #  from the configurable proxy.
 #c.Spawner.poll_interval = 30
-c.Spawner.poll_interval = 900
+c.Spawner.poll_interval = 300
 
 ## The port for single-user servers to listen on.
 #  
@@ -747,7 +748,7 @@ def comma_split(string):
 #  takes longer than this. start should return when the server process is started
 #  and its location is known.
 #c.Spawner.start_timeout = 60
-c.Spawner.start_timeout = 900
+c.Spawner.start_timeout = 120
 
 #------------------------------------------------------------------------------
 # LocalProcessSpawner(Spawner) configuration
@@ -1057,52 +1058,52 @@ def comma_split(string):
     "gerty-shared-node-cpu": (
         "sshspawner.sshspawner.SSHSpawner", {
             "cmd": ["/global/common/cori/das/jupyterhub/jupyter-launcher.sh", 
-                "/global/common/cori/software/python/3.6-anaconda-5.2/bin/jupyter-labhub"],
+                "/usr/common/software/python/3.7-anaconda-2019.07/bin/jupyter-labhub"],
             "environment": {"OMP_NUM_THREADS" : "2"},
-            "remote_hosts": ["gert01.nersc.gov"],
+            "remote_hosts": ["gerty.nersc.gov"],
             "remote_port_command": "/usr/bin/python /global/common/cori/das/jupyterhub/new-get-port.py --ip",
             "hub_api_url": "http://{}:8081/hub/api".format(ip),
-            "path": "/global/common/cori/software/python/3.6-anaconda-5.2/bin:/global/common/cori/das/jupyterhub:/usr/common/usg/bin:/usr/bin:/bin",
+            "path": "/usr/common/software/python/3.7-anaconda-2019.07/bin:/global/common/cori/das/jupyterhub:/usr/common/usg/bin:/usr/bin:/bin",
             "ssh_keyfile": '/certs/{username}.key'
         }
     ),
     "cori-shared-node-cpu": (
         "sshspawner.sshspawner.SSHSpawner", {
             "cmd": ["/global/common/cori/das/jupyterhub/jupyter-launcher.sh", 
-                "/global/common/cori/software/python/3.6-anaconda-5.2/bin/jupyter-labhub"],
+                "/usr/common/software/python/3.7-anaconda-2019.07/bin/jupyter-labhub"],
             "environment": {"OMP_NUM_THREADS" : "2"},
             "remote_hosts": ["corijupyter.nersc.gov"],
             "remote_port_command": "/usr/bin/python /global/common/cori/das/jupyterhub/new-get-port.py --ip",
             "hub_api_url": "http://{}:8081/hub/api".format(ip),
-            "path": "/global/common/cori/software/python/3.6-anaconda-5.2/bin:/global/common/cori/das/jupyterhub:/usr/common/usg/bin:/usr/bin:/bin",
+            "path": "/global/common/cori/software/python/3.7-anaconda-2019.07/bin:/global/common/cori/das/jupyterhub:/usr/common/usg/bin:/usr/bin:/bin",
             "ssh_keyfile": '/certs/{username}.key'
         }
     ),
     "cori-exclusive-node-cpu": (
         "nerscslurmspawner.NERSCExclusiveSlurmSpawner", {
             "cmd": ["/global/common/cori/das/jupyterhub/jupyter-launcher.sh",
-                "/global/common/cori/software/python/3.6-anaconda-5.2/bin/jupyter-labhub"],
+                "/usr/common/software/python/3.7-anaconda-2019.07/bin/jupyter-labhub"],
             "exec_prefix": "/usr/bin/ssh -q -o StrictHostKeyChecking=no -o preferredauthentications=publickey -l {username} -i /certs/{username}.key {remote_host}",
             "http_timeout": 300,
             "startup_poll_interval": 30.0,
             "req_remote_host": "cori19-224.nersc.gov",
             "req_homedir": "/tmp",
             "req_runtime": "240",
             "hub_api_url": "http://{}:8081/hub/api".format(ip),
-            "path": "/global/common/cori/software/python/3.6-anaconda-5.2/bin:/global/common/cori/das/jupyterhub:/usr/common/usg/bin:/usr/bin:/bin",
+            "path": "/global/common/cori/software/python/3.7-anaconda-2019.07/bin:/global/common/cori/das/jupyterhub:/usr/common/usg/bin:/usr/bin:/bin",
         }
     ),
     "cori-exclusive-node-gpu": (
         "nerscslurmspawner.NERSCExclusiveGPUSlurmSpawner", {
             "cmd": ["/global/common/cori/das/jupyterhub/jupyter-launcher.sh",
-                "/global/common/cori/software/python/3.6-anaconda-5.2/bin/jupyter-labhub"],
+                "/usr/common/software/python/3.7-anaconda-2019.07/bin/jupyter-labhub"],
             "exec_prefix": "/usr/bin/ssh -q -o StrictHostKeyChecking=no -o preferredauthentications=publickey -l {username} -i /certs/{username}.key {remote_host}",
             "startup_poll_interval": 30.0,
             "req_remote_host": "cori19-224.nersc.gov",
             "req_homedir": "/tmp",
             "req_runtime": "240",
             "hub_api_url": "http://{}:8081/hub/api".format(ip),
-            "path": "/global/common/cori/software/python/3.6-anaconda-5.2/bin:/global/common/cori/das/jupyterhub:/usr/common/usg/bin:/usr/bin:/bin",
+            "path": "/global/common/cori/software/python/3.7-anaconda-2019.07/bin:/global/common/cori/das/jupyterhub:/usr/common/usg/bin:/usr/bin:/bin",
         }
     ),
     "spin-shared-node-cpu": (
@@ -1121,37 +1122,26 @@ def comma_split(string):
 
 # Pre-spawn myquota check
 
-def space_error(home):
-    """Extra message pointing users to try spawning again from /hub/home.  """
-    home = url_path_join(home, 'home')
-    return ("There is insufficient space in your home directory; please clear up some files and then " +
-            "<a href='{home}'>navigate to the hub home</a> and start your server.".format(home=home))
-
 async def setup(spawner):
     username = spawner.user.name
     remote_host = "corijupyter.nersc.gov"
-#   keyfile = spawner.ssh_keyfile.format(username=username)
     keyfile = "/certs/{username}.key".format(username=username) # NEED to have in NERSCSpawner now
     certfile = keyfile + "-cert.pub"
     k = asyncssh.read_private_key(keyfile)
     c = asyncssh.read_certificate(certfile)
-    # print(username, remote_host, keyfile, certfile)
     async with asyncssh.connect(remote_host, username=username, 
             client_keys=[(k,c)], known_hosts=None) as conn:
-        home = "/global/homes/{}/{}".format(username[0], username)
-        result = await conn.run("myquota -c {}".format(home))
+        result = await conn.run("myquota -c $HOME")
         retcode = result.exit_status
-        # result = await conn.run(spawner.remote_port_command)
-        # remote_port = int(result.stdout)
     if retcode:
-        e = web.HTTPError(507,reason="Insufficient Storage")
-        em = space_error(spawner.hub.base_url)
-        e.my_message = em
+        from jinja2 import Markup
+        e = web.HTTPError(507, reason="Insufficient Storage")
+        e.jupyterhub_message = Markup("<br>Your home directory is over quota! " +
+                "Try moving or archiving and deleting some files from there, " +
+                "then come back and try again.<br>")
         raise e
-    # spawner.remote_host = remote_host
-    # spawner.port = remote_port
 
-# c.Spawner.pre_spawn_hook = setup
+c.Spawner.pre_spawn_hook = setup
 
 ###
 
@@ -1177,43 +1167,3 @@ def auth_state_hook(spawner, auth_state):
 ### Prometheus
 
 c.JupyterHub.authenticate_prometheus = False
-
-
-## c.NERSCSpawner.spawners = [
-##         ("spin", "sshspawner.sshspawner.SSHSpawner", {
-##             "remote_hosts"          : ["jupyter"],
-##             "remote_port"           : "22",
-##             "hub_api_url"           : "http://{}:8081/hub/api".format(ip),
-##             "path"                  : "/opt/anaconda3/bin:/usr/bin:/usr/local/bin:/bin",
-##             "remote_port_command"   : "/opt/anaconda3/bin/get_port.py",
-##             "ssh_keyfile"           : "/tmp/{username}.key",
-##         }),
-##         ("cori-shared", "sshspawner.sshspawner.SSHSpawner", {
-##             "remote_hosts"          : ["cori19-224.nersc.gov"],
-##             "remote_port"           : "22",
-##             "hub_api_url"           : "http://{}:8081/hub/api".format(ip),
-##             "path"                  : bindir + ":/global/common/cori/das/jupyterhub/:/usr/common/usg/bin:/usr/bin:/bin",
-##             "remote_port_command"   : "/global/common/cori/das/jupyterhub/get_port.py",
-##             "ssh_keyfile"           : "/tmp/{username}.key",
-##         }),
-##         ("cori-exclusive-cpu", "nerscspawner.nerscspawner.NERSCSlurmSpawner", {
-##             "exec_prefix"           :
-##                 "/usr/bin/ssh -q -o StrictHostKeyChecking=no -o preferredauthentications=publickey -l {username} -i /tmp/{username}.key {remote_host}",
-##             "startup_poll_interval" : 10.0,
-##             "req_remote_host"       : "cori19-224.nersc.gov",
-##             "req_homedir"           : "/tmp",
-##             "req_runtime"           : "30",
-##             "hub_api_url"           : "http://{}:8081/hub/api".format(ip),
-##             "path"                  : bindir + ":/global/common/cori/das/jupyterhub/:/usr/common/usg/bin:/usr/bin:/bin",
-##         }),
-##         ("cori-config", "nerscspawner.nerscspawner.NERSCSlurmSpawner", {
-##             "exec_prefix"           :
-##                 "/usr/bin/ssh -q -o StrictHostKeyChecking=no -o preferredauthentications=publickey -l {username} -i /tmp/{username}.key {remote_host}",
-##             "startup_poll_interval" : 10.0,
-##             "req_remote_host"       : "cori19-224.nersc.gov",
-##             "req_homedir"           : "/tmp",
-##             "req_runtime"           : "30",
-##             "hub_api_url"           : "http://{}:8081/hub/api".format(ip),
-##             "path"                  : bindir + ":/global/common/cori/das/jupyterhub/:/usr/common/usg/bin:/usr/bin:/bin",
-##         }),
-## ]

jupyter-nersc/web-jupyterhub/nerscslurmspawner.py

@@ -173,7 +173,6 @@ class NERSCExclusiveGPUSlurmSpawner(NERSCSlurmSpawner):
 #SBATCH --constraint=gpu
 #SBATCH --gres=gpu:1
 #SBATCH --job-name=jupyter
-#SBATCH --mem=30GB
 #SBATCH --nodes={{ nodes }}
 #SBATCH --time={{ runtime }}
 {{ env_text }}

jupyter-nersc/web-jupyterhub/nerscspawner.py

@@ -1,7 +1,7 @@
 
 import os
 
-from jupyterhub.spawner import Spawner
+from jupyterhub.spawner import LocalProcessSpawner
 
 from tornado import httpclient, web
 from traitlets import List, Dict, Unicode, observe
@@ -77,10 +77,15 @@ def user_allocations(self, repos=[]):
                 continue
             yield allocation
 
+    def start(self):
+        if self.name not in self.spawners:
+            raise web.HTTPError(404)
+        return super().start()
+
     def select_profile(self, profile):
         self.log.debug("select_profile: " + profile)
         if profile == "":
-            self.child_class, self.child_config = Spawner, {}
+            self.child_class, self.child_config = LocalProcessSpawner, {}
         else:
             try:
                 self.child_class, self.child_config = self.spawners[profile]

jupyter-nersc/web-offline/Dockerfile

@@ -22,26 +22,31 @@ RUN \
     ln -snf /usr/share/zoneinfo/$TZ /etc/localtime  &&  \
     echo $TZ > /etc/timezone
 
-# Add flask and gunicorn
+# Miniconda
 
 RUN \
     curl -s -o /tmp/miniconda3.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh    &&  \
-    bash /tmp/miniconda3.sh -f -b -p /opt/anaconda3         &&  \
+    bash /tmp/miniconda3.sh -b -p /opt/anaconda3            &&  \
     rm -rf /tmp/miniconda3.sh                               &&  \
-    echo "python 3.7.*" >> /opt/anaconda3/conda-meta/pinned &&  \
+    echo "python 3.7.3" >> /opt/anaconda3/conda-meta/pinned &&  \
     /opt/anaconda3/bin/conda update --yes conda             &&  \
-    /opt/anaconda3/bin/conda install --yes                      \
-        flask           \
-        gunicorn                                            &&  \
     /opt/anaconda3/bin/conda clean --yes --all
 
 ENV PATH=/opt/anaconda3/bin:$PATH
 
+# Packages
+
+RUN \
+    conda install --yes         \
+        --channel=conda-forge   \
+        jinja2                  \
+        sanic
+
 # Application
 
 WORKDIR /srv
 ADD app.py /srv/
 ADD templates /srv/templates
 ADD static /srv/static
 
-CMD ["gunicorn", "app:app", "-b", ":8000", "--name", "app", "--workers=4", "--log-file=-"]
+CMD ["python", "-m", "sanic", "app.app", "--host=0.0.0.0", "--workers=4"]

jupyter-nersc/web-offline/app.py

@@ -1,17 +1,25 @@
 import os
 
-from flask import Flask, render_template
+from sanic import Sanic
+from sanic.response import html
 
-app = Flask(__name__)
+from jinja2 import Environment, PackageLoader
 
-@app.route('/', defaults={'path': ''})
+env = Environment(loader=PackageLoader('app', 'templates'))
+
+app = Sanic(__name__)
+app.static("/static", "./static")
+
+@app.route('/')
 @app.route('/<path:path>')
-def catch_all(path):
+async def catch_all(request, path=""):
     default_message = "NERSC's Jupyter service is offline. It will return when maintenance is over. Please try again later."
     message = os.environ.get("MESSAGE", default_message).strip()
     if not message:
         message = default_message
-    return render_template("index.html", message=message), 503
+    template = env.get_template("index.html")
+    content = template.render(message=message, app=app)
+    return html(content, status=503)
 
 if __name__ == '__main__':
-    app.run(host="0.0.0.0")
+    app.run()

jupyter-nersc/web-offline/templates/index.html

@@ -16,10 +16,10 @@
         <div class="container">
             <div class="row">
                 <div class="col-6">
-                    <img src="{{ url_for('static', filename='rectanglelogo-greytext-orangebody-greymoons.png') }}" class="float-left" height="80">
+                    <img src="{{ app.url_for('static', filename='rectanglelogo-greytext-orangebody-greymoons.png') }}" class="float-left" height="80">
                 </div>
                 <div class="col-6">
-                    <img src="{{ url_for('static', filename='logo.png') }}" class="float-right" height="80">
+                    <img src="{{ app.url_for('static', filename='logo.png') }}" class="float-right" height="80">
                 </div>
             </div>
             <hr>