+++ /dev/null
-{% comment %}
-Copyright (C) The Arvados Authors. All rights reserved.
-
-SPDX-License-Identifier: CC-BY-SA-3.0
-{% endcomment %}
-
-<notextile>
-<pre>
-$ <span class="userinput">cd ~/keep/by_id/3229739b505d2b878b62aed09895a55a+142</span>
-$ <span class="userinput">ls *.fastq</span>
-$ <span class="userinput">arv-run grep -H -n ATTGGAGGAAAGATGAGTGAC \< *.fastq \> output.txt</span>
-[...]
- 1 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq > output.txt
- 2 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_2.fastq > output.txt
- 2 stderr run-command: completed with exit code 0 (success)
- 2 stderr run-command: the following output files will be saved to keep:
- 2 stderr run-command: 121 ./output.txt
- 2 stderr run-command: start writing output to keep
- 1 stderr run-command: completed with exit code 0 (success)
- 1 stderr run-command: the following output files will be saved to keep:
- 1 stderr run-command: 363 ./output.txt
- 1 stderr run-command: start writing output to keep
- 2 stderr upload wrote 121 total 121
- 1 stderr upload wrote 363 total 363
-[..]
-</pre>
-</notextile>
(3840 * 0.95) - 256 = 3392 MiB
To run on this instance type, the container can request at most 3392 MiB of working RAM.
-
-h2. Job API (deprecated)
-
-# To submit work, create a "job":{{site.baseurl}}/api/methods/jobs.html . If the same job has been submitted in the past, it will return an existing job in @Completed@ state.
-# The dispatcher process will notice a new job in @Queued@ state and attempt to allocate nodes to run the job.
-# The job executes.
-# Retrieve the @output@ field with the portable data hash of the collection with the output files of the job.
Default 3.
</pre>
</notextile>
-
-
-h3(#arv-pipeline-run). arv pipeline run
-
-WARNING: this uses the obsolete "job" API. Don't use this. You should use @arvados-cwl-runner@ instead.
-
-@arv pipeline run@ can be used to start a pipeline run from the command line.
-
-The User Guide has a page with a bit more information on "using arv pipeline run":{{site.baseurl}}/user/topics/running-pipeline-command-line.html.
-
-<notextile>
-<pre>
-$ <code class="userinput">arv pipeline run --help</code>
-Options:
- --dry-run, -n: Do not start any new jobs or wait for existing jobs to
- finish. Just find out whether jobs are finished,
- queued, or running for each component.
- --status-text <s>: Store plain text status in given file. (Default:
- /dev/stdout)
- --status-json <s>: Store json-formatted pipeline in given file. (Default:
- /dev/null)
- --no-wait: Do not wait for jobs to finish. Just look up status,
- submit new jobs if needed, and exit.
- --no-reuse: Do not reuse existing jobs to satisfy pipeline
- components. Submit a new job for every component.
- --debug, -d: Print extra debugging information on stderr.
- --debug-level <i>: Set debug verbosity level.
- --template <s>: UUID of pipeline template, or path to local pipeline
- template file.
- --instance <s>: UUID of pipeline instance.
- --submit: Submit the pipeline instance to the server, and exit.
- Let the Crunch dispatch service satisfy the components
- by finding/running jobs.
- --run-pipeline-here: Manage the pipeline instance in-process. Submit jobs
- to Crunch as needed. Do not exit until the pipeline
- finishes (or fails).
- --run-jobs-here: Run jobs in the local terminal session instead of
- submitting them to Crunch. Implies
- --run-pipeline-here. Note: this results in a
- significantly different job execution environment, and
- some Crunch features are not supported. It can be
- necessary to modify a pipeline in order to make it run
- this way.
- --run-here: Synonym for --run-jobs-here.
- --description <s>: Description for the pipeline instance.
- --version, -v: Print version and exit
- --help, -h: Show this message
-</pre>
-</notextile>
-
-h3(#arv-run). arv run
-
-WARNING: this uses the obsolete "job" API. Don't use this. You should use @arvados-cwl-runner@ instead.
-
-The @arv-run@ command creates Arvados pipelines at the command line that fan out to multiple concurrent tasks across Arvados compute nodes.
-
-The User Guide has a page on "using arv-run":{{site.baseurl}}/user/topics/arv-run.html.
-
-<notextile>
-<pre>
-$ <code class="userinput">arv run --help</code>
-usage: arv-run [-h] [--retries RETRIES] [--dry-run] [--local]
- [--docker-image DOCKER_IMAGE] [--ignore-rcode] [--no-reuse]
- [--no-wait] [--project-uuid PROJECT_UUID] [--git-dir GIT_DIR]
- [--repository REPOSITORY] [--script-version SCRIPT_VERSION]
- ...
-
-positional arguments:
- args
-
-optional arguments:
- -h, --help show this help message and exit
- --retries RETRIES Maximum number of times to retry server requests that
- encounter temporary failures (e.g., server down).
- Default 3.
- --dry-run Print out the pipeline that would be submitted and
- exit
- --local Run locally using arv-run-pipeline-instance
- --docker-image DOCKER_IMAGE
- Docker image to use, otherwise use instance default.
- --ignore-rcode Commands that return non-zero return codes should not
- be considered failed.
- --no-reuse Do not reuse past jobs.
- --no-wait Do not wait and display logs after submitting command,
- just exit.
- --project-uuid PROJECT_UUID
- Parent project of the pipeline
- --git-dir GIT_DIR Git repository passed to arv-crunch-job when using
- --local
- --repository REPOSITORY
- repository field of component, default 'arvados'
- --script-version SCRIPT_VERSION
- script_version field of component, default 'master'
-</pre>
-</notextile>
"normalize": externalCmd{"arv-normalize"},
"docker": externalCmd{"arv-keepdocker"},
})
- Pipeline = cmd.Multi(map[string]cmd.Handler{
- "run": externalCmd{"arv-run-pipeline-instance"},
- })
// user, group, container, specimen, etc.
APICall = apiCallCmd{}
)
return 1
case *exec.Error:
fmt.Fprintln(stderr, err)
- if ec.prog == "arv" || ec.prog == "arv-run-pipeline-instance" {
+ if ec.prog == "arv" {
fmt.Fprint(stderr, rubyInstallHints)
} else if strings.HasPrefix(ec.prog, "arv-") {
fmt.Fprint(stderr, pythonInstallHints)
"Containers.DefaultKeepCacheRAM": true,
"Containers.DispatchPrivateKey": false,
"Containers.JobsAPI": true,
- "Containers.JobsAPI.CrunchJobUser": false,
- "Containers.JobsAPI.CrunchJobWrapper": false,
- "Containers.JobsAPI.CrunchRefreshTrigger": false,
- "Containers.JobsAPI.DefaultDockerImage": false,
"Containers.JobsAPI.Enable": true,
"Containers.JobsAPI.GitInternalDir": false,
- "Containers.JobsAPI.ReuseJobIfOutputsDiffer": false,
"Containers.Logging": false,
"Containers.LogReuseDecisions": false,
"Containers.MaxComputeVMs": false,
puts "Available methods: ls, get, put, docker"
end
abort
- when 'pipeline'
- sub = remaining_opts.shift
- if sub == 'run'
- exec_bin "arv-run-pipeline-instance", remaining_opts
- else
- puts "Usage: arv pipeline [method] [--parameters]\n"
- puts "Use 'arv pipeline [method] --help' to get more information about specific methods.\n\n"
- puts "Available methods: run"
- end
- abort
end
end
end
def cancel(cascade: false, need_transaction: true)
- if need_transaction
- ActiveRecord::Base.transaction do
- cancel(cascade: cascade, need_transaction: false)
- end
- return
- end
-
- if self.state.in?([RunningOnServer, RunningOnClient])
- self.state = Paused
- self.save!
- elsif self.state != Paused
- raise InvalidStateTransitionError
- end
-
- return if !cascade
-
- # cancel all child jobs
- children = self.components.andand.collect{|_, c| c['job']}.compact.collect{|j| j['uuid']}.compact
-
- return if children.empty?
-
- Job.where(uuid: children, state: [Job::Queued, Job::Running]).each do |job|
- job.cancel(cascade: cascade, need_transaction: false)
- end
+ raise "No longer supported"
end
protected
projects / arvados.git / commitdiff