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Add timeout to SSH queue scan command #191

Merged
merged 11 commits into from
Jun 18, 2024
Merged

Add timeout to SSH queue scan command #191

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e2a5ba8
Add timeout to SSH queue scan command
Icemole May 31, 2024
213c745
Chagne Popen/communicate by run
Icemole May 31, 2024
bceb3e2
Add batch mode option to ssh command
Icemole May 31, 2024
3ca38b4
Remove stdout/err pipe
Icemole May 31, 2024
9880e42
Better formatting
Icemole May 31, 2024
d639048
Capture output on subprocess
Icemole May 31, 2024
7679653
Apply fix for AWS and load sharing engines
Icemole May 31, 2024
60fe641
Input instead of stdin
Icemole May 31, 2024
2b67c81
Revert timeout of subprocess to 30 seconds
Icemole Jun 3, 2024
f5fdfc7
Catch `subprocess.TimeoutExpired`
Icemole Jun 13, 2024
a94365a
Properly return when timeout is expired
Icemole Jun 18, 2024
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21 changes: 14 additions & 7 deletions sisyphus/simple_linux_utility_for_resource_management_engine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,16 +86,23 @@ def system_call(self, command, send_to_stdin=None):
"""
if self.gateway:
escaped_command = [shlex.quote(s) for s in command] # parameters need to be shell safe when sending via ssh
system_command = ["ssh", "-x", self.gateway] + [" ".join(["cd", os.getcwd(), "&&"] + escaped_command)]
system_command = ["ssh", "-x", self.gateway, "-o", "BatchMode=yes"] + [
" ".join(["cd", os.getcwd(), "&&"] + escaped_command)
]
else:
# no gateway given, skip ssh local
system_command = command

logging.debug("shell_cmd: %s" % " ".join(system_command))
p = subprocess.Popen(system_command, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
if send_to_stdin:
send_to_stdin = send_to_stdin.encode()
out, err = p.communicate(input=send_to_stdin, timeout=30)
p = subprocess.run(
system_command,
stdin=send_to_stdin,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
timeout=gs.WAIT_PERIOD_BETWEEN_CHECKS,
)
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def fix_output(o):
"""
Expand All @@ -109,9 +116,9 @@ def fix_output(o):
assert False
return o[:-1]

out = fix_output(out)
err = fix_output(err)
retval = p.wait(timeout=30)
out = fix_output(p.stdout)
err = fix_output(p.stderr)
retval = p.returncode

# Check for ssh error
err_ = []
Expand Down Expand Up @@ -289,7 +296,7 @@ def reset_cache(self):
def queue_state(self):
"""Returns list with all currently running tasks in this queue"""

if time.time() - self._task_info_cache_last_update < 30:
if time.time() - self._task_info_cache_last_update < gs.WAIT_PERIOD_BETWEEN_CHECKS:
# use cached value
return self._task_info_cache

Expand Down
21 changes: 14 additions & 7 deletions sisyphus/son_of_grid_engine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,16 +87,23 @@ def system_call(self, command, send_to_stdin=None):
:rtype: list[bytes], list[bytes], int
"""
if self.gateway:
system_command = ["ssh", "-x", self.gateway] + [" ".join(["cd", os.getcwd(), "&&"] + command)]
system_command = ["ssh", "-x", self.gateway, "-o", "BatchMode=yes"] + [
" ".join(["cd", os.getcwd(), "&&"] + command)
]
else:
# no gateway given, skip ssh local
system_command = command

logging.debug("shell_cmd: %s" % " ".join(system_command))
p = subprocess.Popen(system_command, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
if send_to_stdin:
send_to_stdin = send_to_stdin.encode()
out, err = p.communicate(input=send_to_stdin, timeout=30)
p = subprocess.run(
system_command,
stdin=send_to_stdin,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
timeout=gs.WAIT_PERIOD_BETWEEN_CHECKS,
)

def fix_output(o):
"""
Expand All @@ -110,9 +117,9 @@ def fix_output(o):
assert False
return o[:-1]

out = fix_output(out)
err = fix_output(err)
retval = p.wait(timeout=30)
out = fix_output(p.stdout)
err = fix_output(p.stderr)
retval = p.returncode

# Check for ssh error
err_ = []
Expand Down Expand Up @@ -307,7 +314,7 @@ def reset_cache(self):
def queue_state(self):
"""Return s list with all currently running tasks in this queue"""

if time.time() - self._task_info_cache_last_update < 30:
if time.time() - self._task_info_cache_last_update < gs.WAIT_PERIOD_BETWEEN_CHECKS:
# use cached value
return self._task_info_cache

Expand Down
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