Add depends on

.devcontainer/Dockerfile

@@ -12,6 +12,10 @@ ENV USER_GID=${USER_GID}
 USER root
 RUN apt-get update && apt-get install -y less python3-pip
 
+# "Install" the frobnicator plugin
+RUN wget https://raw.githubusercontent.com/researchapps/flux-core/add-dependency-frob-plugin/src/bindings/python/flux/job/frobnicator/plugins/dependency.py && \
+    mv dependency.py /usr/lib/python3.10/site-packages/flux/job/frobnicator/plugins/
+
 # Add the group and user that match our ids
 RUN groupadd -g ${USER_GID} ${USERNAME} && \
     adduser --disabled-password --uid ${USER_UID} --gid ${USER_GID} --gecos "" ${USERNAME} && \

docs/docs/commands.md

@@ -10,7 +10,7 @@ Here is an example that assumes receiving a Jobspec on a flux cluster.
 
 We are prototyping user-space subsystems, for which we do a satisfy request of a contender jobspec against a directory of user space subsystem files, which each should
 be JGF (json graph format) graphs. While this can be paired with run (to determine if the run should proceed) we provide a separate "satisfy" command to test and prototype the tool.
-We also provide a set of example user subsystems in `examples/subsystems` for each of environment modules and spack. This means we can do satsify requests of jobspecs against the subsystem directory as follows. Here is an example that is satisfied:
+We also provide a set of example user subsystems in `examples/subsystems` for each of environment modules and spack. This means we can do satisfy requests of jobspecs against the subsystem directory as follows. Here is an example that is satisfied:
 
 ```bash
 $ jobspec satisfy ./examples/subsystems/jobspec-spack-subystem-satisfied.yaml --subsystem-dir ./examples/subsystems
@@ -192,4 +192,11 @@ Just for fun (posterity) I briefly tried having emoji here:
 
 ![assets/img/emoji.png](assets/img/emoji.png)
 
+
+#### 4. Depends On
+
+We have support for depends on, but it requires a custom frobnicator plugin to create a dependency based on job name. You
+can see the small tutorial [here](https://github.com/compspec/jobspec/tree/main/examples/depends_on) where you can run the entire thing in the VSCode developer environment.
+
+
 [home](/README.md#jobspec)

examples/depends_on/README.md

@@ -0,0 +1,83 @@
+# JobSpec Nextgen with Depends On
+
+We are going to use jobspec nextgen to run a small workflow with depends on. Note that this requires:
+
+ - The [frobnicator plugin](https://github.com/flux-framework/flux-core/pull/5982) to set a dependency name. This comes with the Developer Environment VSCode container.
+ - You will need to get the hostname of the container and update the [broker.toml](broker.toml) here. Also generate a curve certificate and R lite file:
+
+## 1. Setup
+
+First, install a developer version of jobspec (from the root):
+
+```bash
+pip install -e .
+```
+
+Next, update [broker.toml](broker.toml) to have the hostname of your container (this is in `examples/depends_on` relative to the root). Then:
+
+```bash
+flux R encode --local > /tmp/R
+flux keygen /tmp/curve.cert
+```
+
+You should then be able to start your sub-instance:
+
+```bash
+flux start -o --config=./broker.toml 
+```
+```console
+vscode@c970303f1b79:/workspaces/iflux/jobspec$ flux resource list
+     STATE NNODES   NCORES    NGPUS NODELIST
+      free      1       10        0 c970303f1b79
+ allocated      0        0        0 
+      down      0        0        0 
+```
+
+Check that the frobnicator plugin is installed.
+
+```bash
+$ flux job-frobnicator --list-plugins
+```
+```console
+Available plugins:
+constraints           Apply constraints to incoming jobspec based on broker config.
+defaults              Apply defaults to incoming jobspec based on broker config.
+dependency            Translate dependency.name into a job id for dependency.afterok
+```
+
+Try submitting a job - it should work.
+
+```bash
+flux run hostname
+```
+
+## 2. Test Depends On
+
+We can now submit a simple jobspec that has depends_on, which is included in [jobspec.yaml](jobspec.yaml).
+
+```bash
+jobspec run ./jobspec.yaml
+```
+
+The second task (task-2) depends on task-1, and the first task will sleep for a minute, so at first you'll see:
+
+```bash
+$ flux jobs -a
+       JOBID USER     NAME       ST NTASKS NNODES     TIME INFO
+   ƒ3sL5KeV5 vscode   task-2      D      4      1        - depends:after-success=6329825492992
+   ƒ3sGt1CFy vscode   task-1      R      4      1   13.91s 747b0768eb45
+```
+
+And then after a minute:
+
+```bash
+$ flux jobs -a
+       JOBID USER     NAME       ST NTASKS NNODES     TIME INFO
+   ƒ3sL5KeV5 vscode   task-2     CD      4      1   3.035s 747b0768eb45
+   ƒ3sGt1CFy vscode   task-1     CD      4      1   1.001m 747b0768eb45
+```
+
+Tada! And that's it. You can obviously do more complex things, but this is a great start! 
+Note that we also keep the plugin [dependency.py](dependency.py) here in case the pull request branch
+is lost. You basically need to start a broker that has it enabled, and then put it in the Python flux install 
+at `flux/job/frobnicator/plugins`.

examples/depends_on/broker.toml

@@ -0,0 +1,30 @@
+[access]
+allow-guest-user = true
+allow-root-owner = true
+
+# Point to resource definition generated with flux-R(1).
+[resource]
+path = "/tmp/R"
+
+[bootstrap]
+curve_cert = "/tmp/curve.cert"
+default_port = 8050
+default_bind = "tcp://eth0:%p"
+default_connect = "tcp://%h:%p"
+
+# CHANGE THIS TO YOUR HOSTNAME (or container hostname)
+hosts = [
+{ host="747b0768eb45"},
+]		
+
+
+[archive]
+dbpath = "/tmp/job-archive.sqlite"
+period = "1m"
+busytimeout = "50s"
+
+[ingest.frobnicator]
+plugins = [ "defaults", "constraints", "dependency" ]
+
+[sched-fluxion-qmanager]
+queue-policy = "fcfs"

examples/depends_on/dependency.py

@@ -0,0 +1,65 @@
+##############################################################
+# Copyright 2022 Lawrence Livermore National Security, LLC
+# (c.f. AUTHORS, NOTICE.LLNS, COPYING)
+#
+# This file is part of the Flux resource manager framework.
+# For details, see https://github.com/flux-framework.
+#
+# SPDX-License-Identifier: LGPL-3.0
+##############################################################
+
+"""Translate dependency.name into a job id for dependency.afterok
+
+"""
+
+from flux.job.frobnicator import FrobnicatorPlugin
+
+
+class DependencyAdder:
+    """Get the system attribute for dependency.name and add a
+    task dependency. Raise an error if we can't find it.
+    """
+
+    def __init__(self, config={}):
+        # We don't need this for anything, just saving
+        # for the heck
+        self.config = config
+
+    def add_dependency(self, jobspec):
+        """We need to translate a dependency name into a job id. We will:
+        1. Get the desired name from system attribute dependency.name
+        2. list all flux jobs (I know, I know) and get the job id
+        3. Update the jobspec to have it.
+        4. Raise error if the name does not exist.
+
+        Bullet 2 is a bad design and thus this is only for experimentation.
+        """
+        dependency_name = jobspec.attributes["system"].get("dependency", {}).get("name")
+        if not dependency_name:
+            return
+
+        # We are going to add the first matched job as a dependency
+        import flux
+        import flux.job
+
+        handle = flux.Flux()
+        for job in flux.job.list.job_list(handle).get()["jobs"]:
+            if job["name"] == dependency_name:
+                jobspec.attributes["system"]["dependencies"] = [
+                    {"scheme": "afterok", "value": str(job["id"])}
+                ]
+                return
+
+        raise ValueError(f"Job with name {dependency_name} is not known")
+
+
+class Frobnicator(FrobnicatorPlugin):
+    def __init__(self, parser):
+        super().__init__(parser)
+
+    def configure(self, args, config):
+        self.config = DependencyAdder(config)
+
+    def frob(self, jobspec, user, urgency, flags):
+        """This frobber is looking for an attribute "dependency.name"""
+        self.config.add_dependency(jobspec)

examples/depends_on/jobspec.yaml

@@ -0,0 +1,28 @@
+version: 1
+
+# This is the same example as hello-world-jobspec.yaml
+# But without the slot
+resources:
+  sleep-resources:  
+    type: node
+    count: 1
+    with:
+    - type: core
+      count: 4
+
+tasks:
+- name: task-1
+  command:
+    - bash
+    - -c
+    - "echo Starting task 1; sleep 60; echo Finishing task 1"
+
+  resources: sleep-resources
+- name: task-2
+  depends_on: ["task-1"]
+  command:
+      - bash
+      - -c
+      - "echo Starting task 2; sleep 3; echo Finishing task 2"
+
+  resources: sleep-resources

examples/flux/jobspec.yaml

@@ -17,7 +17,6 @@ tasks:
   resources: single-node
 
 - name: task-2
-  depends_on: ["task-1"]
   command:
       - bash
       - -c

examples/group-with-group.yaml

@@ -18,10 +18,9 @@ groups:
     - group: group-2
 
 - name: group-2
-  depends_on: ["group-1"]
   resources: common
   tasks:
     - command:
       - bash
       - -c
-      - "echo Starting task 1 in group 2; sleep 3; echo Finishing task 1 in group 2"
+      - "echo Starting task 1 in group 2; sleep 3; echo Finishing task 1 in group 2"

examples/hello-world-jobspec.yaml

@@ -22,7 +22,6 @@ tasks:
 
   resources: sleep-resources
 - name: task-2
-  depends_on: ["task-1"]
   command:
       - bash
       - -c

examples/task-with-group.yaml

@@ -9,7 +9,6 @@ resources:
 
 groups:
 - name: task-2
-  depends_on: ["task-1"]
   resources: common
   tasks:
     - command:
@@ -27,4 +26,4 @@ tasks:
     - "echo Starting task 1; sleep 3; echo Finishing task 1"
 
   # flux batch...
-- group: task-2
+- group: task-2

jobspec/transformer/flux/steps.py

@@ -100,10 +100,10 @@ def prepare(self, command=None, waitable=False):
         cwd = attributes.get("cwd")
         watch = attributes.get("watch")
 
-        # We can't support this yet because it needs the jobid
-        # That design to require to get it seems fragile
-        # for depends_on in task.get("depends_on") or []:
-        #    cmd += [f"--dependency={depends_on}"]
+        # Note that you need to install our frobnicator plugin
+        # for this to work. See the examples/depends_on directory
+        for depends_on in task.get("depends_on") or []:
+            cmd += [f"--setattr=dependency.name={depends_on}"]
 
         if cwd is not None:
             cmd += ["--cwd", cwd]

jobspec/version.py

@@ -1,4 +1,4 @@
-__version__ = "0.1.13"
+__version__ = "0.1.14"
 AUTHOR = "Vanessa Sochat"
 AUTHOR_EMAIL = "[email protected]"
 NAME = "jobspec"