fix failed pre-commit checks

backends/htcondor/run.sh

@@ -1,9 +1,8 @@
 #!/usr/bin/bash
 
 # apparently this vodoo kills all processes opened in this script
-trap "trap - SIGTERM && kill -- -$$" SIGINT SIGTERM EXIT
+# trap "trap - SIGTERM && kill -- -$$" SIGINT SIGTERM EXIT
+# ssh -N -L 8080:localhost:8080 lxplus7103 &
+# sleep 10
 
-ssh -N -L 8080:localhost:8080 lxplus7103 &
-
-sleep 10
-/afs/cern.ch/work/j/jheuel/zoidberg/target/debug/zoidberg_client http://localhost:8080
+/home/home4/institut_1b/jheuel/repositories/zoidberg/target/release/zoidberg_client

backends/htcondor/worker.submit

@@ -6,9 +6,10 @@ error        = output/stderr.$(Process)
 log          = output/log.$(Process)
 
 request_cpus   = 1
-#request_memory = 1024
+request_memory = 4096
 #request_disk   = 10240
 
+getenv = True
 should_transfer_files = no
 
-queue 150
+queue 20

submitters/snakemake/zoidberg/grid-status.py

@@ -2,8 +2,17 @@
 
 import sys
 import requests
+from os import environ
 
-resp = requests.post("http://localhost:8080/status", json=[{"id": int(sys.argv[1])}])
+def print_and_exit(s):
+    print(s)
+    exit(0)
+
+resp = requests.post(
+    "http://localhost:8080/status",
+    json=[{"id": int(sys.argv[1])}],
+    headers={"cookie": environ["ZOIDBERG_SECRET"]},
+)
 
 translation = {
     "Submitted": "running",
@@ -11,4 +20,12 @@ translation = {
     "Failed": "failed",
 }
 
-print(translation[resp.json()[0]["status"]])
+j = resp.json()
+
+if len(j) == 0:
+    print_and_exit("failed")
+
+if "Running" in j[0]["status"]:
+    print_and_exit("running")
+
+print_and_exit(translation[resp.json()[0]["status"]])

submitters/snakemake/zoidberg/grid-submit.py

@@ -2,14 +2,25 @@
 
 import sys
 import requests
+from os import environ
+
+from snakemake.utils import read_job_properties
 
 jobscript = sys.argv[1]
+job_properties = read_job_properties(jobscript)
+
+payload = {
+    "cmd": jobscript
+}
+
+payload["threads"] = job_properties.get("threads", 1)
 
 resp = requests.post(
     "http://localhost:8080/submit",
     json=[
-        {"cmd": jobscript},
+        payload,
     ],
+    headers={"cookie": environ["ZOIDBERG_SECRET"]},
 )
 assert resp.ok, "http request failed"
 

zoidberg_client/src/main.rs

@@ -1,4 +1,4 @@
-use clap::{App, Arg};
+use clap::{arg, value_parser, App, Arg};
 use env_logger::Env;
 use futures::future::{AbortHandle, Abortable};
 use log;
@@ -16,7 +16,7 @@ use zoidberg_lib::types::{
 const VERSION: &str = env!("CARGO_PKG_VERSION");
 
 fn build_client(secret: &str) -> Client {
-    let cookie = format!("{}", secret);
+    let cookie = secret.to_string();
 
     let mut headers = header::HeaderMap::new();
     headers.insert(
@@ -37,10 +37,11 @@ struct Worker {
     id: String,
     secret: String,
     server: String,
+    threads: i32,
 }
 
 impl Worker {
-    async fn new(server: &str, secret: &str) -> Result<Worker, Box<dyn Error>> {
+    async fn new(server: &str, secret: &str, threads: i32) -> Result<Worker, Box<dyn Error>> {
         let res = build_client(secret)
             .get(format!("{}/register", server))
             .send()
@@ -50,9 +51,10 @@ impl Worker {
         let r: RegisterResponse = serde_json::from_str(&body)?;
         log::info!("registered worker with id: {}", &r.id);
         Ok(Worker {
-            id: r.id.to_string(),
+            id: r.id,
             secret: secret.to_string(),
             server: server.to_string(),
+            threads,
         })
     }
 
@@ -83,6 +85,7 @@ impl Worker {
             .post(format!("{}/fetch", self.server))
             .json(&FetchRequest {
                 worker_id: self.id.clone(),
+                threads: self.threads,
             })
             .send()
             .await?;
@@ -129,22 +132,34 @@ async fn main() -> Result<(), Box<dyn Error>> {
 
     let matches = App::new("Zoidberg client")
         .version(VERSION)
-        .author("Johannes Heuel")
+        .author("by Johannes Heuel")
         .arg(
             Arg::with_name("server")
                 .takes_value(true)
-                .required(true)
                 .help("Set Zoidberg server address"),
         )
+        .arg(
+            arg!(-j --threads <VALUE> "Sets number of threads")
+                .required(false)
+                .value_parser(value_parser!(i32)),
+        )
         .get_matches();
-    let server = matches.value_of("server").unwrap();
+    let threads: i32 = if let Some(t) = matches.get_one::<i32>("threads") {
+        *t
+    } else {
+        1
+    };
+
     let secret = std::env::var("ZOIDBERG_SECRET").unwrap_or_else(|_| {
         eprintln!("Please set the $ZOIDBERG_SECRET environment variable");
         std::process::exit(1);
     });
 
+    let server = std::env::var("ZOIDBERG_SERVER")
+        .unwrap_or_else(|_| String::from(matches.value_of("server").unwrap()));
+
     let client = Arc::new(
-        Worker::new(server, &secret)
+        Worker::new(&server, &secret, threads)
             .await
             .expect("Could not create client"),
     );

zoidberg_lib/src/types.rs

@@ -46,6 +46,8 @@ pub struct Job {
     pub cmd: String,
     #[serde(default = "Status::default")]
     pub status: Status,
+    #[serde(default)]
+    pub threads: i32,
 }
 
 #[derive(Serialize, Deserialize)]
@@ -61,6 +63,8 @@ pub struct RegisterResponse {
 #[derive(Serialize, Deserialize)]
 pub struct FetchRequest {
     pub worker_id: String,
+    #[serde(default)]
+    pub threads: i32,
 }
 
 #[derive(Serialize, Deserialize)]

zoidberg_server/src/auth.rs

@@ -0,0 +1,24 @@
+use actix_web::{dev, error::ErrorBadRequest, Error, FromRequest, HttpRequest, Result};
+use futures::future::{err, ok, Ready};
+
+pub struct Authorization {}
+
+impl FromRequest for Authorization {
+    type Error = Error;
+    type Future = Ready<Result<Self, Self::Error>>;
+
+    fn from_request(req: &HttpRequest, _payload: &mut dev::Payload) -> Self::Future {
+        if let Some(head) = req.headers().get("cookie") {
+            if let Ok(cookie) = head.to_str() {
+                if let Some(secret) = req.app_data::<String>() {
+                    if secret == cookie {
+                        return ok(Authorization {});
+                    } else {
+                        return err(ErrorBadRequest("no auth"));
+                    }
+                }
+            }
+        }
+        err(ErrorBadRequest("no auth"))
+    }
+}

zoidberg_server/src/main.rs

@@ -1,13 +1,9 @@
-use actix_web::error::ErrorBadRequest;
 use actix_web::{
-    dev, get, middleware::Logger, post, web, App, Error, FromRequest, HttpRequest, HttpResponse,
-    HttpServer, Responder, Result,
+    get, middleware::Logger, post, web, App, HttpResponse, HttpServer, Responder, Result,
 };
 use chrono::Utc;
-use clap;
 use env_logger::Env;
-use futures::future::{err, ok, Ready};
-use log;
+
 use std::sync::Mutex;
 use std::time::Duration;
 use uuid::Uuid;
@@ -16,8 +12,11 @@ use zoidberg_lib::types::{
     Worker,
 };
 
+mod auth;
 mod webpage;
 
+use auth::Authorization;
+
 const VERSION: &str = env!("CARGO_PKG_VERSION");
 
 struct State {
@@ -38,33 +37,17 @@ impl State {
     }
 }
 
-struct Authorization {}
-
-impl FromRequest for Authorization {
-    type Error = Error;
-    type Future = Ready<Result<Self, Self::Error>>;
-
-    fn from_request(req: &HttpRequest, _payload: &mut dev::Payload) -> Self::Future {
-        if let Some(head) = req.headers().get("cookie") {
-            if let Ok(cookie) = head.to_str() {
-                if let Some(secret) = req.app_data::<String>() {
-                    if secret == cookie {
-                        return ok(Authorization {});
-                    } else {
-                        return err(ErrorBadRequest("no auth"));
-                    }
-                }
-            }
-        }
-        err(ErrorBadRequest("no auth"))
-    }
-}
-
 #[get("/")]
 async fn index(data: web::Data<State>) -> impl Responder {
     let workers = data.workers.lock().unwrap();
-    let new_jobs = data.new_jobs.lock().unwrap();
-    let page = webpage::render(&*new_jobs, &*workers);
+    let jobs = data.jobs.lock().unwrap();
+    let filtered_jobs: Vec<Job> = jobs
+        .to_vec()
+        .iter()
+        .filter(|x| !matches!(x.status, Status::Completed))
+        .cloned()
+        .collect();
+    let page = webpage::render(&filtered_jobs, &*workers);
     HttpResponse::Ok().body(page)
 }
 
@@ -87,7 +70,9 @@ async fn fetch(
     f: web::Json<FetchRequest>,
     _: Authorization,
 ) -> Result<impl Responder> {
-    let requesting_worker = f.into_inner().worker_id;
+    let f = f.into_inner();
+    let requesting_worker = f.worker_id;
+    let threads = f.threads;
     {
         let workers = data.workers.lock().unwrap();
         if workers.iter().filter(|w| w.id == requesting_worker).count() != 1 {
@@ -97,15 +82,24 @@ async fn fetch(
         }
     }
     let mut new_jobs = data.new_jobs.lock().unwrap();
-    if let Some(j) = new_jobs.pop() {
+    new_jobs.sort_by(|a, b| b.threads.cmp(&a.threads));
+
+    if let Some(j) = new_jobs
+        .iter()
+        .filter(|x| x.threads <= threads)
+        .cloned()
+        .collect::<Vec<Job>>()
+        .first()
+    {
         let mut jobs = data.jobs.lock().unwrap();
         for cj in jobs.iter_mut() {
             if cj.id == j.id {
                 cj.status = Status::Running(requesting_worker.clone())
             }
         }
-        return Ok(web::Json(FetchResponse::Jobs(vec![j])));
-    }
+        new_jobs.retain(|x| x.id != j.id);
+        return Ok(web::Json(FetchResponse::Jobs(vec![j.clone()])));
+    };
     Ok(web::Json(FetchResponse::Nop))
 }
 
@@ -156,7 +150,7 @@ async fn heartbeat(
     data: web::Data<State>,
     _: Authorization,
 ) -> Result<String> {
-    log::info!("Heartbeat from worker {}", heartbeat.id);
+    log::debug!("Heartbeat from worker {}", heartbeat.id);
     let mut workers = data.workers.lock().unwrap();
     for w in workers.iter_mut() {
         if w.id == heartbeat.id {
@@ -204,7 +198,7 @@ async fn main() -> std::io::Result<()> {
 
     let _matches = clap::App::new("Zoidberg server")
         .version(VERSION)
-        .author("Johannes Heuel")
+        .author("by Johannes Heuel")
         .get_matches();
 
     let state = web::Data::new(State::new());
@@ -213,12 +207,24 @@ async fn main() -> std::io::Result<()> {
     tokio::spawn(async move {
         loop {
             tokio::time::sleep(Duration::from_secs(10)).await;
+            {
                 let mut workers = s.workers.lock().unwrap();
                 workers.retain(|w| match w.last_heartbeat {
                     None => true,
                     Some(t) => Utc::now().timestamp() - t < 60,
                 })
             }
+            let workers = s.workers.lock().unwrap();
+            let mut jobs = s.jobs.lock().unwrap();
+            for job in jobs.iter_mut() {
+                if let Status::Running(w) = &job.status {
+                    let exists = workers.iter().filter(|x| &x.id == w).count() > 0;
+                    if !exists {
+                        job.status = Status::Failed;
+                    }
+                }
+            }
+        }
     });
 
     HttpServer::new(move || {
@@ -234,7 +240,7 @@ async fn main() -> std::io::Result<()> {
             .service(heartbeat)
             .service(submit)
     })
-    .bind(("127.0.0.1", 8080))?
+    .bind(("0.0.0.0", 8080))?
     .run()
     .await
 }
@@ -272,31 +278,53 @@ mod tests {
             .uri("/register")
             .to_request();
         let resp: RegisterResponse = test::call_and_read_body_json(&app, req).await;
-        assert_eq!(resp.id, 1);
+        assert!(!resp.id.is_empty());
     }
 
     #[actix_web::test]
     async fn test_fetch() {
         let cmd = String::from("hi");
+        let jobid = 11;
         let app = test::init_service(
             App::new()
                 .app_data(String::from("secret"))
                 .app_data(web::Data::new(State {
-                    counter_workers: Mutex::new(0),
                     counter_jobs: Mutex::new(0),
-                    workers: Mutex::new(Vec::new()),
-                    new_jobs: Mutex::new(vec![Job {
-                        id: 0,
+                    workers: Mutex::new(vec![Worker {
+                        id: "some_worker".to_string(),
+                        last_heartbeat: None,
+                    }]),
+                    new_jobs: Mutex::new(vec![
+                        Job {
+                            id: jobid,
                             cmd: cmd.clone(),
                             status: Status::Submitted,
-                    }]),
+                            threads: 1,
+                        },
+                        Job {
+                            id: jobid + 1,
+                            cmd: cmd.clone(),
+                            status: Status::Submitted,
+                            threads: 2,
+                        },
+                        Job {
+                            id: jobid + 2,
+                            cmd: cmd.clone(),
+                            status: Status::Submitted,
+                            threads: 3,
+                        },
+                    ]),
                     jobs: Mutex::new(Vec::new()),
                 }))
                 .service(fetch),
         )
         .await;
-        let req = test::TestRequest::get()
+        let req = test::TestRequest::post()
             .append_header(("cookie", "secret"))
+            .set_json(FetchRequest {
+                worker_id: "some_worker".to_string(),
+                threads: 1,
+            })
             .uri("/fetch")
             .to_request();
         let resp: FetchResponse = test::call_and_read_body_json(&app, req).await;
@@ -308,7 +336,7 @@ mod tests {
                 panic!("did not expect FetchResponse::Terminate from worker {}", w)
             }
             FetchResponse::Jobs(new_jobs) => {
-                assert_eq!(new_jobs[0].id, 0);
+                assert_eq!(new_jobs[0].id, jobid);
                 assert_eq!(new_jobs[0].cmd, cmd);
             }
         }
@@ -317,18 +345,19 @@ mod tests {
     #[actix_web::test]
     async fn test_status() {
         let cmd = String::from("hi");
+        let jobid = 1;
         let app = test::init_service(
             App::new()
                 .app_data(String::from("secret"))
                 .app_data(web::Data::new(State {
-                    counter_workers: Mutex::new(0),
                     counter_jobs: Mutex::new(0),
                     workers: Mutex::new(Vec::new()),
                     new_jobs: Mutex::new(Vec::new()),
                     jobs: Mutex::new(vec![Job {
-                        id: 1,
+                        id: jobid,
                         cmd: cmd.clone(),
-                        status: Status::Running(0),
+                        status: Status::Submitted,
+                        threads: 1,
                     }]),
                 }))
                 .service(status),
@@ -336,11 +365,11 @@ mod tests {
         .await;
         let req = test::TestRequest::post()
             .append_header(("cookie", "secret"))
-            .set_json(vec![StatusRequest { id: 1 }])
+            .set_json(vec![StatusRequest { id: jobid }])
             .uri("/status")
             .to_request();
         let resp: Vec<Job> = test::call_and_read_body_json(&app, req).await;
-        assert_eq!(resp[0].id, 1);
+        assert_eq!(resp[0].id, jobid);
     }
 
     #[actix_web::test]
@@ -355,9 +384,9 @@ mod tests {
         let req = test::TestRequest::post()
             .append_header(("cookie", "secret"))
             .set_json(vec![Update {
-                worker: 0,
+                worker: "some_worker".to_string(),
                 job: 0,
-                status: Status::Running(0),
+                status: Status::Submitted,
             }])
             .uri("/update")
             .to_request();
@@ -379,7 +408,8 @@ mod tests {
             .set_json(vec![Job {
                 id: 0,
                 cmd: String::from("hi"),
-                status: Status::Running(0),
+                status: Status::Submitted,
+                threads: 1,
             }])
             .uri("/submit")
             .to_request();

zoidberg_server/src/webpage.rs

@@ -4,12 +4,12 @@ use zoidberg_lib::types::{Job, Worker};
 // TODO: write nicer frontend
 pub fn render(jobs: &[Job], workers: &[Worker]) -> String {
     let jobs_html: String = String::from("<table class=\"table is-hoverable\">")
-        + "<thead><tr><th><td>ID</td><td>command</td><td>status</td></th></tr></thead><tbody>"
+        + "<thead><tr><th>ID</th><th style=\"width: 150px;\">command</th><th>status</th></tr></thead><tbody>"
         + &jobs
             .iter()
             .map(|j| {
                 format!(
-                    "<tr><th></th><td>{}</td><td>{}</td><td>{}</td></tr>",
+                    "<tr><td>{}</td><td>{}</td><td>{}</td></tr>",
                     j.id, j.cmd, j.status
                 )
             })
@@ -18,7 +18,7 @@ pub fn render(jobs: &[Job], workers: &[Worker]) -> String {
         + "</tbody></table>";
 
     let workers_html: String = String::from("<table class=\"table is-hoverable\">")
-        + "<thead><tr><th><td>ID</td><td>last heartbeat</td></th></tr></thead><tbody>"
+        + "<thead><tr><th>ID</th><th>last heartbeat</th></tr></thead><tbody>"
         + &workers
             .iter()
             .map(|w| {
@@ -27,12 +27,19 @@ pub fn render(jobs: &[Job], workers: &[Worker]) -> String {
                 } else {
                     String::from("")
                 };
-                format!("<tr><th></th><td>{}</td><td>{}</td></tr>", w.id, ts)
+                format!("<tr><td>{}</td><td>{}</td></tr>", w.id, ts)
             })
             .collect::<Vec<String>>()
             .join("\n")
         + "</tbody></table>";
 
+    let style = r#"<style>
+      td {
+        max-width: 40vw;
+        word-wrap: break-word;
+      }
+    </style>"#;
+
     let _debug_html = r#"<style>
       *:not(path):not(g) {{
         color:                    hsla(210, 100%, 100%, 0.9) !important;
@@ -52,9 +59,11 @@ pub fn render(jobs: &[Job], workers: &[Worker]) -> String {
     <meta charset="utf-8">
     <meta name="viewport" content="width=device-width, initial-scale=1">
     <title>Zoidberg</title>
-    <link rel="icon" href="data:,">
+    <link rel="icon" href="data:image/svg+xml,%3Csvg%20xmlns='http://www.w3.org/2000/svg'%20viewBox='0%200%2016%2016'%3E%3Ctext%20x='0'%20y='14'%3E🦀%3C/text%3E%3C/svg%3E" type="image/svg+xml" />
+
     <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bulma@0.9.4/css/bulma.min.css">
     {}
+    {}
   </head>
   <body>
   <section class="section">
@@ -82,7 +91,7 @@ pub fn render(jobs: &[Job], workers: &[Worker]) -> String {
   </body>
 </html>
 "#,
-        _debug_html, jobs_html, workers_html
+        style, _debug_html, jobs_html, workers_html
     );
     page
 }