prompt: You will be provided with a partial code base and an issue statement explaining a problem to resolve.
  <issue>
  Job resubmission with job scheduler doesn't work 
  I was not able to find out the reason behind resubmission issue with job scheduler, such as:
  `veros-resubmit -i acc.lowres -n 50 -l 62208000 -c "python acc.py -b bohrium -v debug" --callback "/usr/bin/sbatch /groups/ocean/nutrik/veros_cases/paper/acc/veros_batch.sh"`
  Although jobs with run length of up to 29 days are resubmitted fine, those with longer run length are not resubmitted and no errors or messages are reported.
  
  In fact, jobs are successfully resubmitted without scheduler (`--callback "./veros_batch.sh"`) for any run length.
  
  </issue>
  <code>
  [start of veros/cli/veros_resubmit.py]
  1 #!/usr/bin/env python
  2 
  3 import functools
  4 import subprocess
  5 import shlex
  6 import sys
  7 import os
  8 
  9 import click
  10 
  11 LAST_N_FILENAME = "{identifier}.current_run"
  12 
  13 
  14 class ShellCommand(click.ParamType):
  15     name = "command"
  16 
  17     def convert(self, value, param, ctx):
  18         return shlex.split(value)
  19 
  20 
  21 def get_current_n(filename):
  22     if not os.path.isfile(filename):
  23         return 0
  24 
  25     with open(filename, "r") as f:
  26         return int(f.read())
  27 
  28 
  29 def write_next_n(n, filename):
  30     with open(filename, "w") as f:
  31         f.write(str(n))
  32 
  33 
  34 def call_veros(cmd, name, n, runlen):
  35     identifier = "{name}.{n:0>4}".format(name=name, n=n)
  36     prev_id = "{name}.{n:0>4}".format(name=name, n=n - 1)
  37     args = ["-s", "identifier", identifier, "-s", "restart_output_filename",
  38             "{identifier}.restart.h5", "-s", "runlen", "{}".format(runlen)]
  39     if n:
  40         args += ["-s", "restart_input_filename", "{prev_id}.restart.h5".format(prev_id=prev_id)]
  41     sys.stdout.write("\n >>> {}\n\n".format(" ".join(cmd + args)))
  42     sys.stdout.flush()
  43     try:
  44         subprocess.check_call(cmd + args)
  45     except subprocess.CalledProcessError:
  46         raise RuntimeError("Run {} failed, exiting".format(n))
  47 
  48 
  49 def resubmit(identifier, num_runs, length_per_run, veros_cmd, callback):
  50     """Performs several runs of Veros back to back, using the previous run as restart input.
  51 
  52     Intended to be used with scheduling systems (e.g. SLURM or PBS).
  53 
  54     """
  55     last_n_filename = LAST_N_FILENAME.format(identifier=identifier)
  56 
  57     current_n = get_current_n(last_n_filename)
  58     if current_n >= num_runs:
  59         return
  60 
  61     call_veros(veros_cmd, identifier, current_n, length_per_run)
  62     write_next_n(current_n + 1, last_n_filename)
  63     subprocess.Popen(callback)
  64 
  65 
  66 @click.command("veros-resubmit", short_help="Re-run a Veros setup several times")
  67 @click.option("-i", "--identifier", required=True,
  68               help="Base identifier of the simulation")
  69 @click.option("-n", "--num-runs", type=click.INT, required=True,
  70               help="Total number of runs to execute")
  71 @click.option("-l", "--length-per-run", type=click.FLOAT, required=True,
  72               help="Length (in seconds) of each run")
  73 @click.option("-c", "--veros-cmd", type=ShellCommand(), required=True,
  74               help="The command that is used to call veros (quoted)")
  75 @click.option("--callback", metavar="CMD", type=ShellCommand(), default=None,
  76               help="Command to call after each run has finished (quoted, default: call self)")
  77 @functools.wraps(resubmit)
  78 def cli(*args, **kwargs):
  79     if kwargs["callback"] is None:
  80         kwargs["callback"] = sys.argv
  81     resubmit(*args, **kwargs)
  82 
  83 
  84 if __name__ == "__main__":
  85     cli()
  86
  [end of veros/cli/veros_resubmit.py]
  </code>
  
  I need you to solve this issue by generating a single patch file that I can apply directly to this repository using git apply. Please respond with a single patch file in the following format.
  <patch>
  diff --git a/file.py b/file.py
  --- a/file.py
  +++ b/file.py
  @@ -1,27 +1,35 @@
   def euclidean(a, b):
  -    while b:
  -        a, b = b, a % b
  -    return a
  +    if b == 0:
  +        return a
  +    return euclidean(b, a % b)
   
   
   def bresenham(x0, y0, x1, y1):
       points = []
       dx = abs(x1 - x0)
       dy = abs(y1 - y0)
  -    sx = 1 if x0 < x1 else -1
  -    sy = 1 if y0 < y1 else -1
  -    err = dx - dy
  +    x, y = x0, y0
  +    sx = -1 if x0 > x1 else 1
  +    sy = -1 if y0 > y1 else 1
   
  -    while True:
  -        points.append((x0, y0))
  -        if x0 == x1 and y0 == y1:
  -            break
  -        e2 = 2 * err
  -        if e2 > -dy:
  -            err -= dy
  -            x0 += sx
  -        if e2 < dx:
  -            err += dx
  -            y0 += sy
  +    if dx > dy:
  +        err = dx / 2.0
  +        while x != x1:
  +            points.append((x, y))
  +            err -= dy
  +            if err < 0:
  +                y += sy
  +                err += dx
  +            x += sx
  +    else:
  +        err = dy / 2.0
  +        while y != y1:
  +            points.append((x, y))
  +            err -= dx
  +            if err < 0:
  +                x += sx
  +                err += dy
  +            y += sy
  +
  +    points.append((x, y))
       return points
  
  </patch>
golden_diff: diff --git a/veros/cli/veros_resubmit.py b/veros/cli/veros_resubmit.py
  --- a/veros/cli/veros_resubmit.py
  +++ b/veros/cli/veros_resubmit.py
  @@ -5,10 +5,13 @@
   import shlex
   import sys
   import os
  +import time
   
   import click
   
   LAST_N_FILENAME = "{identifier}.current_run"
  +CHILD_TIMEOUT = 10
  +POLL_DELAY = 0.1
   
   
   class ShellCommand(click.ParamType):
  @@ -60,7 +63,21 @@
   
       call_veros(veros_cmd, identifier, current_n, length_per_run)
       write_next_n(current_n + 1, last_n_filename)
  -    subprocess.Popen(callback)
  +    next_proc = subprocess.Popen(callback)
  +
  +    # catch immediately crashing processes
  +    timeout = CHILD_TIMEOUT
  +
  +    while timeout > 0:
  +        retcode = next_proc.poll()
  +        if retcode is not None:
  +            if retcode > 0:
  +                # process crashed
  +                raise RuntimeError("Callback exited with {}".format(retcode))
  +            else:
  +                break
  +        time.sleep(POLL_DELAY)
  +        timeout -= POLL_DELAY
   
   
   @click.command("veros-resubmit", short_help="Re-run a Veros setup several times")
  @@ -78,6 +95,7 @@
   def cli(*args, **kwargs):
       if kwargs["callback"] is None:
           kwargs["callback"] = sys.argv
  +
       resubmit(*args, **kwargs)
  
verification_info: {"golden_diff": "diff --git a/veros/cli/veros_resubmit.py b/veros/cli/veros_resubmit.py\n--- a/veros/cli/veros_resubmit.py\n+++ b/veros/cli/veros_resubmit.py\n@@ -5,10 +5,13 @@\n import shlex\n import sys\n import os\n+import time\n \n import click\n \n LAST_N_FILENAME = \"{identifier}.current_run\"\n+CHILD_TIMEOUT = 10\n+POLL_DELAY = 0.1\n \n \n class ShellCommand(click.ParamType):\n@@ -60,7 +63,21 @@\n \n     call_veros(veros_cmd, identifier, current_n, length_per_run)\n     write_next_n(current_n + 1, last_n_filename)\n-    subprocess.Popen(callback)\n+    next_proc = subprocess.Popen(callback)\n+\n+    # catch immediately crashing processes\n+    timeout = CHILD_TIMEOUT\n+\n+    while timeout > 0:\n+        retcode = next_proc.poll()\n+        if retcode is not None:\n+            if retcode > 0:\n+                # process crashed\n+                raise RuntimeError(\"Callback exited with {}\".format(retcode))\n+            else:\n+                break\n+        time.sleep(POLL_DELAY)\n+        timeout -= POLL_DELAY\n \n \n @click.command(\"veros-resubmit\", short_help=\"Re-run a Veros setup several times\")\n@@ -78,6 +95,7 @@\n def cli(*args, **kwargs):\n     if kwargs[\"callback\"] is None:\n         kwargs[\"callback\"] = sys.argv\n+\n     resubmit(*args, **kwargs)\n", "issue": "Job resubmission with job scheduler doesn't work \nI was not able to find out the reason behind resubmission issue with job scheduler, such as:\r\n`veros-resubmit -i acc.lowres -n 50 -l 62208000 -c \"python acc.py -b bohrium -v debug\" --callback \"/usr/bin/sbatch /groups/ocean/nutrik/veros_cases/paper/acc/veros_batch.sh\"`\r\nAlthough jobs with run length of up to 29 days are resubmitted fine, those with longer run length are not resubmitted and no errors or messages are reported.\r\n\r\nIn fact, jobs are successfully resubmitted without scheduler (`--callback \"./veros_batch.sh\"`) for any run length.\n", "before_files": [{"content": "#!/usr/bin/env python\n\nimport functools\nimport subprocess\nimport shlex\nimport sys\nimport os\n\nimport click\n\nLAST_N_FILENAME = \"{identifier}.current_run\"\n\n\nclass ShellCommand(click.ParamType):\n    name = \"command\"\n\n    def convert(self, value, param, ctx):\n        return shlex.split(value)\n\n\ndef get_current_n(filename):\n    if not os.path.isfile(filename):\n        return 0\n\n    with open(filename, \"r\") as f:\n        return int(f.read())\n\n\ndef write_next_n(n, filename):\n    with open(filename, \"w\") as f:\n        f.write(str(n))\n\n\ndef call_veros(cmd, name, n, runlen):\n    identifier = \"{name}.{n:0>4}\".format(name=name, n=n)\n    prev_id = \"{name}.{n:0>4}\".format(name=name, n=n - 1)\n    args = [\"-s\", \"identifier\", identifier, \"-s\", \"restart_output_filename\",\n            \"{identifier}.restart.h5\", \"-s\", \"runlen\", \"{}\".format(runlen)]\n    if n:\n        args += [\"-s\", \"restart_input_filename\", \"{prev_id}.restart.h5\".format(prev_id=prev_id)]\n    sys.stdout.write(\"\\n >>> {}\\n\\n\".format(\" \".join(cmd + args)))\n    sys.stdout.flush()\n    try:\n        subprocess.check_call(cmd + args)\n    except subprocess.CalledProcessError:\n        raise RuntimeError(\"Run {} failed, exiting\".format(n))\n\n\ndef resubmit(identifier, num_runs, length_per_run, veros_cmd, callback):\n    \"\"\"Performs several runs of Veros back to back, using the previous run as restart input.\n\n    Intended to be used with scheduling systems (e.g. SLURM or PBS).\n\n    \"\"\"\n    last_n_filename = LAST_N_FILENAME.format(identifier=identifier)\n\n    current_n = get_current_n(last_n_filename)\n    if current_n >= num_runs:\n        return\n\n    call_veros(veros_cmd, identifier, current_n, length_per_run)\n    write_next_n(current_n + 1, last_n_filename)\n    subprocess.Popen(callback)\n\n\n@click.command(\"veros-resubmit\", short_help=\"Re-run a Veros setup several times\")\n@click.option(\"-i\", \"--identifier\", required=True,\n              help=\"Base identifier of the simulation\")\n@click.option(\"-n\", \"--num-runs\", type=click.INT, required=True,\n              help=\"Total number of runs to execute\")\n@click.option(\"-l\", \"--length-per-run\", type=click.FLOAT, required=True,\n              help=\"Length (in seconds) of each run\")\n@click.option(\"-c\", \"--veros-cmd\", type=ShellCommand(), required=True,\n              help=\"The command that is used to call veros (quoted)\")\n@click.option(\"--callback\", metavar=\"CMD\", type=ShellCommand(), default=None,\n              help=\"Command to call after each run has finished (quoted, default: call self)\")\n@functools.wraps(resubmit)\ndef cli(*args, **kwargs):\n    if kwargs[\"callback\"] is None:\n        kwargs[\"callback\"] = sys.argv\n    resubmit(*args, **kwargs)\n\n\nif __name__ == \"__main__\":\n    cli()\n", "path": "veros/cli/veros_resubmit.py"}]}