Merge remote-tracking branch 'origin/master' into rc1.5.11

codalab/model/bundle_model.py

@@ -1003,6 +1003,11 @@ def transition_bundle_running(self, bundle, worker_run, row, user_id, worker_id,
             'memory_usage': memory_usage,
         }
 
+        # Increment user time as we go to ensure user doesn't go over time quota.
+        if user_id == self.root_user_id and hasattr(bundle.metadata, 'time'):
+            time_increment = worker_run.container_time_total - bundle.metadata.time
+            self.increment_user_time_used(bundle.owner_id, time_increment)
+
         if worker_run.docker_image is not None:
             metadata_update['docker_image'] = worker_run.docker_image
 
@@ -1066,7 +1071,7 @@ def transition_bundle_worker_offline(self, bundle):
             self.update_bundle(bundle, bundle_update, connection)
         return True
 
-    def transition_bundle_finalizing(self, bundle, worker_run, connection):
+    def transition_bundle_finalizing(self, bundle, worker_run, user_id, connection):
         """
         Transitions bundle to FINALIZING state:
             Saves the failure message and exit code from the worker
@@ -1076,6 +1081,11 @@ def transition_bundle_finalizing(self, bundle, worker_run, connection):
         failure_message, exitcode = worker_run.failure_message, worker_run.exitcode
         if failure_message is None and exitcode is not None and exitcode != 0:
             failure_message = 'Exit code %d' % exitcode
+
+        if user_id == self.root_user_id:
+            time_increment = worker_run.container_time_total - bundle.metadata.time
+            self.increment_user_time_used(bundle.owner_id, time_increment)
+
         # Build metadata
         metadata = {}
         if failure_message is not None:
@@ -1098,15 +1108,11 @@ def transition_bundle_finished(self, bundle, bundle_location):
         failure_message = metadata.get('failure_message', None)
         exitcode = metadata.get('exitcode', 0)
         state = State.FAILED if failure_message or exitcode else State.READY
-        if failure_message == 'Kill requested':
+        if failure_message and 'Kill requested' in failure_message:
             state = State.KILLED
 
         worker = self.get_bundle_worker(bundle.uuid)
 
-        # Increment the amount of time used for the user whose bundles run on CodaLab's public instances
-        if worker['user_id'] == self.root_user_id:
-            self.increment_user_time_used(bundle.owner_id, metadata.get('time', 0))
-
         if worker['shared_file_system']:
             # TODO(Ashwin): fix for --link.
             self.update_disk_metadata(bundle, bundle_location)
@@ -1170,7 +1176,7 @@ def bundle_checkin(self, bundle, worker_run, user_id, worker_id):
                 self.transition_bundle_running(
                     bundle, worker_run, row, user_id, worker_id, connection
                 )
-                return self.transition_bundle_finalizing(bundle, worker_run, connection)
+                return self.transition_bundle_finalizing(bundle, worker_run, user_id, connection)
 
             if worker_run.state in [State.PREPARING, State.RUNNING]:
                 return self.transition_bundle_running(

codalab/rest/workers.py

@@ -5,6 +5,7 @@
 import http.client
 import json
 from datetime import datetime
+import logging
 
 from bottle import abort, get, local, post, request, response
 
@@ -14,6 +15,8 @@
 from codalab.worker.bundle_state import BundleCheckinState
 from codalab.worker.main import DEFAULT_EXIT_AFTER_NUM_RUNS
 
+logger = logging.getLogger(__name__)
+
 
 @post("/workers/<worker_id>/checkin", name="worker_checkin", apply=AuthenticatedProtectedPlugin())
 def checkin(worker_id):
@@ -42,16 +45,27 @@ def checkin(worker_id):
         request.json.get("preemptible", False),
     )
 
+    messages = []
     for run in request.json["runs"]:
         try:
             worker_run = BundleCheckinState.from_dict(run)
             bundle = local.model.get_bundle(worker_run.uuid)
             local.model.bundle_checkin(bundle, worker_run, request.user.user_id, worker_id)
-        except Exception:
-            pass
+
+            if local.model.get_user_time_quota_left(bundle.owner_id) <= 0:
+                # Then, user has gone over their time quota and we kill the job.
+                kill_message = (
+                    'Kill requested: User time quota exceeded. To apply for more quota, please visit the following link: '
+                    'https://codalab-worksheets.readthedocs.io/en/latest/FAQ/#how-do-i-request-more-disk-quota-or-time-quota'
+                )
+                messages.append({'type': 'kill', 'uuid': bundle.uuid, 'kill_message': kill_message})
+        except Exception as e:
+            logger.info("Exception in REST checkin: {}".format(e))
 
     with closing(local.worker_model.start_listening(socket_id)) as sock:
-        return local.worker_model.get_json_message(sock, WAIT_TIME_SECS)
+        messages.append(local.worker_model.get_json_message(sock, WAIT_TIME_SECS))
+    response.content_type = 'application/json'
+    return json.dumps(messages)
 
 
 def check_reply_permission(worker_id, socket_id):

codalab/worker/worker.py

@@ -451,29 +451,37 @@ def checkin(self):
         # Stop processing any new runs received from server
         if not response or self.terminate_and_restage or self.terminate:
             return
-        action_type = response['type']
-        logger.debug('Received %s message: %s', action_type, response)
-        if action_type == 'run':
-            self.initialize_run(response['bundle'], response['resources'])
-        else:
-            uuid = response['uuid']
-            socket_id = response.get('socket_id', None)
-            if uuid not in self.runs:
-                if action_type in ['read', 'netcat']:
-                    self.read_run_missing(socket_id)
-                return
-            if action_type == 'kill':
-                self.kill(uuid)
-            elif action_type == 'mark_finalized':
-                self.mark_finalized(uuid)
-            elif action_type == 'read':
-                self.read(socket_id, uuid, response['path'], response['read_args'])
-            elif action_type == 'netcat':
-                self.netcat(socket_id, uuid, response['port'], response['message'])
-            elif action_type == 'write':
-                self.write(uuid, response['subpath'], response['string'])
+        if type(response) is not list:
+            response = [response]
+        for action in response:
+            if not action:
+                continue
+            action_type = action['type']
+            logger.debug('Received %s message: %s', action_type, action)
+            if action_type == 'run':
+                self.initialize_run(action['bundle'], action['resources'])
             else:
-                logger.warning("Unrecognized action type from server: %s", action_type)
+                uuid = action['uuid']
+                socket_id = action.get('socket_id', None)
+                if uuid not in self.runs:
+                    if action_type in ['read', 'netcat']:
+                        self.read_run_missing(socket_id)
+                    return
+                if action_type == 'kill':
+                    kill_message = 'Kill requested'
+                    if 'kill_message' in action:
+                        kill_message = action['kill_message']
+                    self.kill(uuid, kill_message)
+                elif action_type == 'mark_finalized':
+                    self.mark_finalized(uuid)
+                elif action_type == 'read':
+                    self.read(socket_id, uuid, action['path'], action['read_args'])
+                elif action_type == 'netcat':
+                    self.netcat(socket_id, uuid, action['port'], action['message'])
+                elif action_type == 'write':
+                    self.write(uuid, action['subpath'], action['string'])
+                else:
+                    logger.warning("Unrecognized action type from server: %s", action_type)
 
     def process_runs(self):
         """ Transition each run then filter out finished runs """
@@ -680,11 +688,11 @@ def initialize_run(self, bundle, resources):
                 file=sys.stdout,
             )
 
-    def kill(self, uuid):
+    def kill(self, uuid, kill_message='Kill requested'):
         """
         Marks the run as killed so that the next time its state is processed it is terminated.
         """
-        self.runs[uuid] = self.runs[uuid]._replace(kill_message='Kill requested', is_killed=True)
+        self.runs[uuid] = self.runs[uuid]._replace(kill_message=kill_message, is_killed=True)
 
     def restage_bundle(self, uuid):
         """

docker_config/compose_files/docker-compose.dev.yml

@@ -11,6 +11,8 @@ services:
     stdin_open: true
     tty: true
   rest-server:
+    stdin_open: true
+    tty: true
     volumes:
       # Mount the alembic directory so that we can create new database migrations with the alembic version files mounted.
       - ./../../alembic/:/opt/codalab-worksheets/alembic/
@@ -19,3 +21,11 @@ services:
       - ./../../tests/:/opt/codalab-worksheets/tests/
       - ./../../scripts/:/opt/codalab-worksheets/scripts/
       - ./../../codalab/:/opt/codalab-worksheets/codalab/
+
+  # Allow developers to use PDB to debug programs in Docker containers.
+  bundle-manager:
+    stdin_open: true
+    tty: true
+  worker:
+    stdin_open: true
+    tty: true

docs/FAQ.md

@@ -40,9 +40,9 @@ If you have used up your disk quota and want to reduce your disk usage, here are
 - If you have intermediate bundles whose contents you don't need, you can use `cl rm -d <bundle>` to delete only the contents of the bundle but keep the metadata.  This way, you keep the provenance and can regenerate this bundle in the future.
 - If there are selected files that you wish to keep in a bundle, you can use `cl make <bundle>/<important-file>` to make a new bundle that only has a copy of the desired file and then you can do `cl rm -d <bundle>` to remove all the other files in that bundle.
 
-### How do I request more disk quota?
+### How do I request more disk quota or time quota?
 
-If you have tried the steps above and still need more disk quota, please fill out this [form](https://docs.google.com/forms/d/e/1FAIpQLSdS22MaLyE1kx0JL-w2a8f8IasDyc36H_ZuidNBVAE_afMCpw/viewform).
+If you have tried the steps above and still need more **disk quota** or **time quota**, please fill out this [form](https://docs.google.com/forms/d/e/1FAIpQLSebCBrglB7z2R7OeHJ_NsVWcUcHVMAW4AQnFxNt0YvTS-rDNA/viewform).
 
 ### How do I upload large bundles?
 

frontend/src/components/worksheets/Worksheet/Worksheet.js

@@ -237,10 +237,7 @@ class Worksheet extends React.Component {
             ) {
                 return;
             }
-            if (!(uuid in bundlesCount)) {
-                bundlesCount[uuid] = 0;
-            }
-            bundlesCount[uuid] += 1;
+            bundlesCount[uuid] = 1;
             let checkedBundles = this.state.checkedBundles;
             if (!(uuid in checkedBundles)) {
                 checkedBundles[uuid] = {};

frontend/src/components/worksheets/items/TableItem/TableItem.js

@@ -2,6 +2,9 @@
 import React, { useEffect } from 'react';
 import classNames from 'classnames';
 import { withStyles } from '@material-ui/core';
+import Checkbox from '@material-ui/core/Checkbox';
+import CheckBoxOutlineBlankIcon from '@material-ui/icons/CheckBoxOutlineBlank';
+import CheckBoxIcon from '@material-ui/icons/CheckBox';
 import Table from '@material-ui/core/Table';
 import TableHead from '@material-ui/core/TableHead';
 import TableCell from './TableCell';
@@ -39,6 +42,7 @@ class TableItem extends React.Component<{
             indeterminateCheckState: false,
             curSchemaNames: this.props.item.using_schemas.join(' '),
             openSchemaTextBox: false,
+            tableIsSelected: false,
         };
         this.copyCheckedBundleRows = this.copyCheckedBundleRows.bind(this);
         this.showCheckedBundleRowsContents = this.showCheckedBundleRowsContents.bind(this);
@@ -57,6 +61,7 @@ class TableItem extends React.Component<{
             childrenCheckState: childrenStatus,
             indeterminateCheckState: false,
             checked: false,
+            tableIsSelected: false,
         });
     };
 
@@ -131,6 +136,26 @@ class TableItem extends React.Component<{
         });
     };
 
+    toggleTableSelect = () => {
+        const bundles = this.props.item.bundles_spec.bundle_infos;
+        const tableIsSelected = !this.state.tableIsSelected;
+
+        // update the table checkbox state
+        this.setState({ tableIsSelected });
+
+        // update the checkbox state for each bundle row
+        bundles.forEach((bundle, i) => {
+            const identifier = Math.random() * 10000; // see handleCheckBundle() for identifier implementation details
+            this.props.handleCheckBundle(
+                bundle.uuid,
+                identifier,
+                tableIsSelected,
+                this.refreshCheckBox,
+            );
+            this.childrenCheck(i, tableIsSelected);
+        });
+    };
+
     // BULK OPERATION RELATED CODE ABOVE
 
     updateRowIndex = (rowIndex) => {
@@ -150,6 +175,7 @@ class TableItem extends React.Component<{
             this.showCheckedBundleRowsContents,
         );
         let tableClassName = this.props.focused ? 'table focused' : 'table';
+        let checkboxVariant = this.props.focused || this.state.hovered ? 'action' : 'disabled';
         let item = this.props.item;
         let bundleInfos = item.bundles_spec.bundle_infos;
         let headerItems = item.header;
@@ -169,26 +195,40 @@ class TableItem extends React.Component<{
                     style={
                         index === 0
                             ? {
-                                  paddingLeft: editPermission ? '30px' : '70px',
+                                  paddingLeft: editPermission ? '6px' : '70px',
                                   paddingBottom: 0,
                                   paddingTop: 0,
                               }
                             : {}
                     }
                 >
                     {editPermission && index === 0 && (
-                        <Tooltip title={'Change the schemas of this table'}>
-                            <IconButton>
-                                <ViewListIcon
-                                    style={{ padding: '0px', height: 15 }}
-                                    onClick={() => {
-                                        this.setState({
-                                            openSchemaTextBox: !this.state.openSchemaTextBox,
-                                        });
-                                    }}
-                                />
-                            </IconButton>
-                        </Tooltip>
+                        <>
+                            <Checkbox
+                                icon={
+                                    <CheckBoxOutlineBlankIcon
+                                        color={checkboxVariant}
+                                        fontSize='small'
+                                    />
+                                }
+                                checkedIcon={<CheckBoxIcon fontSize='small' />}
+                                classes={{ root: classes.tableCheckbox }}
+                                onChange={this.toggleTableSelect}
+                                checked={this.state.tableIsSelected}
+                            />
+                            <Tooltip title={'Change the schemas of this table'}>
+                                <IconButton>
+                                    <ViewListIcon
+                                        style={{ padding: '0px', height: 15 }}
+                                        onClick={() => {
+                                            this.setState({
+                                                openSchemaTextBox: !this.state.openSchemaTextBox,
+                                            });
+                                        }}
+                                    />
+                                </IconButton>
+                            </Tooltip>
+                        </>
                     )}
                     {item}
                     {showStateTooltip && <BundleStateTooltip />}
@@ -217,7 +257,7 @@ class TableItem extends React.Component<{
                     worksheetUUID={worksheetUUID}
                     item={rowItem}
                     rowIndex={rowIndex}
-                    focused={rowFocused}
+                    focused={this.state.tableIsSelected || rowFocused}
                     focusIndex={this.props.focusIndex}
                     setFocus={setFocus}
                     showNewRerun={this.props.showNewRerun}
@@ -379,6 +419,9 @@ const styles = () => ({
         color: '#000000',
         height: 26,
     },
+    tableCheckbox: {
+        paddingRight: 2,
+    },
 });
 
 const TableContainer = withStyles(styles)(_TableContainer);