Merge pull request #150 from PalNilsson/next

3.9.1.13

PILOTVERSION

@@ -1 +1 @@
-3.9.0.17
+3.9.1.13

pilot/control/job.py

@@ -470,7 +470,7 @@ def send_state(job: Any, args: Any, state: str, xml: str = "", metadata: str = "
     return False
 
 
-def get_job_status_from_server(job_id: int, url: str, port: str) -> (str, int, int):
+def get_job_status_from_server(job_id: int, url: str, port: int) -> (str, int, int):
     """
     Return the current status of job <jobId> from the dispatcher.
 
@@ -482,7 +482,7 @@ def get_job_status_from_server(job_id: int, url: str, port: str) -> (str, int, i
     In the case of time-out, the dispatcher will be asked one more time after 10 s.
 
     :param job_id: PanDA job id (int)
-    :param url: PanDA server URL (str
+    :param url: PanDA server URL (int)
     :param port: PanDA server port (str)
     :return: status (string; e.g. holding), attempt_nr (int), status_code (int).
     """
@@ -1512,10 +1512,6 @@ def get_dispatcher_dictionary(args: Any, taskid: str = "") -> dict:
     if 'HARVESTER_WORKER_ID' in os.environ:
         data['worker_id'] = os.environ.get('HARVESTER_WORKER_ID')
 
-#    instruction_sets = has_instruction_sets(['AVX', 'AVX2'])
-#    if instruction_sets:
-#        data['cpuConsumptionUnit'] = instruction_sets
-
     return data
 
 

pilot/control/monitor.py

@@ -89,6 +89,9 @@ def control(queues: namedtuple, traces: Any, args: object):  # noqa: C901
     last_minute_check = t_0
 
     queuedata = get_queuedata_from_job(queues)
+    if not queuedata:
+        logger.warning('queuedata could not be extracted from queues')
+
     push = args.harvester and args.harvester_submitmode.lower() == 'push'
     try:
         # overall loop counter (ignoring the fact that more than one job may be running)
@@ -103,7 +106,7 @@ def control(queues: namedtuple, traces: Any, args: object):  # noqa: C901
                 break
 
             # check if the OIDC token needs to be refreshed
-            if tokendownloadchecktime:
+            if tokendownloadchecktime and queuedata:
                 if int(time.time() - last_token_check) > tokendownloadchecktime:
                     last_token_check = time.time()
                     if 'no_token_renewal' in queuedata.catchall:

pilot/user/atlas/proxy.py

@@ -31,7 +31,10 @@
 
 # from pilot.user.atlas.setup import get_file_system_root_path
 from pilot.common.errorcodes import ErrorCodes
-from pilot.util.container import execute
+from pilot.util.container import (
+    execute,
+    execute_nothreads
+)
 from pilot.util.proxy import get_proxy
 
 logger = logging.getLogger(__name__)
@@ -134,7 +137,7 @@ def verify_arcproxy(envsetup: str, limit: int, proxy_id: str = "pilot", test: bo
         if not hasattr(verify_arcproxy, "cache"):
             verify_arcproxy.cache = {}
 
-        if proxy_id in verify_arcproxy.cache:  # if exist, then calculate result from current cache
+        if proxy_id in verify_arcproxy.cache:  # if exists, then calculate result from current cache
             validity_end_cert = verify_arcproxy.cache[proxy_id][0]
             validity_end = verify_arcproxy.cache[proxy_id][1]
             if validity_end < 0:  # previous validity check failed, do not try to re-check
@@ -162,7 +165,7 @@ def verify_arcproxy(envsetup: str, limit: int, proxy_id: str = "pilot", test: bo
     _exit_code, _, _ = execute(cmd, shell=True)  # , usecontainer=True, copytool=True)
 
     cmd = f"{envsetup}arcproxy -i validityEnd -i validityLeft -i vomsACvalidityEnd -i vomsACvalidityLeft"
-    _exit_code, stdout, stderr = execute(cmd, shell=True)  # , usecontainer=True, copytool=True)
+    _exit_code, stdout, stderr = execute_nothreads(cmd, shell=True)  # , usecontainer=True, copytool=True)
     if stdout is not None:
         if 'command not found' in stdout:
             logger.warning(f"arcproxy is not available on this queue,"
@@ -243,7 +246,7 @@ def verify_vomsproxy(envsetup: str, limit: int) -> tuple[int, str]:
     if os.environ.get('X509_USER_PROXY', '') != '':
         cmd = f"{envsetup}voms-proxy-info -actimeleft --timeleft --file $X509_USER_PROXY"
         logger.info(f'executing command: {cmd}')
-        _exit_code, stdout, stderr = execute(cmd, shell=True)
+        _exit_code, stdout, stderr = execute_nothreads(cmd, shell=True)
         if stdout is not None:
             if "command not found" in stdout:
                 logger.info("skipping voms proxy check since command is not available")

pilot/user/atlas/utilities.py

@@ -32,7 +32,10 @@
     NoSuchFile
 )
 from pilot.info.jobdata import JobData
-from pilot.util.container import execute
+from pilot.util.container import (
+    execute,
+    execute_nothreads
+)
 from pilot.util.filehandling import (
     read_json,
     copy,
@@ -830,7 +833,7 @@ def filter_output(stdout):
 
     # CPU arch script has now been copied, time to execute it
     # (reset irrelevant stderr)
-    ec, stdout, stderr = execute(cmd)
+    ec, stdout, stderr = execute_nothreads(cmd)
     if ec == 0 and ('RHEL9 and clone support is relatively new' in stderr or
                     'RHEL8 and clones are not supported for users' in stderr):
         stderr = ''

pilot/util/auxiliary.py

@@ -17,7 +17,7 @@
 # under the License.
 #
 # Authors:
-# - Paul Nilsson, [email protected], 2017-23
+# - Paul Nilsson, [email protected], 2017-24
 
 """Auxiliary functions."""
 
@@ -33,6 +33,7 @@
 from numbers import Number
 from time import sleep
 from typing import Any
+from uuid import uuid4
 
 from pilot.util.constants import (
     SUCCESS,
@@ -44,7 +45,10 @@
 )
 from pilot.common.errorcodes import ErrorCodes
 from pilot.util.container import execute
-from pilot.util.filehandling import dump
+from pilot.util.filehandling import (
+    dump,
+    grep
+)
 
 zero_depth_bases = (str, bytes, Number, range, bytearray)
 iteritems = 'items'
@@ -444,7 +448,7 @@ def get_memory_usage(pid: int) -> (int, str, str):
     return execute(f'ps aux -q {pid}', timeout=60)
 
 
-def extract_memory_usage_value(output: str) -> int:
+def extract_memory_usage_value(output: str) -> str:
     """
     Extract the memory usage value from the ps output (in kB).
 
@@ -482,34 +486,38 @@ def cut_output(txt: str, cutat: int = 1024, separator: str = '\n[...]\n') -> str
     return txt
 
 
-def has_instruction_set(instruction_set: str) -> bool:
+def has_instruction_sets(instruction_sets: list) -> str:
     """
     Determine whether a given CPU instruction set is available.
 
     The function will use grep to search in /proc/cpuinfo (both in upper and lower case).
+    Example: instruction_sets = ['AVX', 'AVX2', 'SSE4_2', 'XXX'] -> "AVX|AVX2|SSE4_2"
 
-    :param instruction_set: instruction set (e.g. AVX2) (str)
-    :return: True if given instruction set is available, False otherwise (bool).
+    :param instruction_sets: instruction set (e.g. AVX2) (list)
+    :return: string of pipe-separated instruction sets (str).
     """
-    status = False
-    cmd = fr"grep -o \'{instruction_set.lower()}[^ ]*\|{instruction_set.upper()}[^ ]*\' /proc/cpuinfo"
-    exit_code, stdout, stderr = execute(cmd)
-    if not exit_code and not stderr:
-        if instruction_set.lower() in stdout.split() or instruction_set.upper() in stdout.split():
-            status = True
+    ret = ""
 
-    return status
+    for instr in instruction_sets:
+        pattern = re.compile(fr'{instr.lower()}[^ ]*', re.IGNORECASE)
+        out = grep(patterns=[pattern], file_name="/proc/cpuinfo")
 
+        for stdout in out:
+            if instr.upper() not in ret and (instr.lower() in stdout.split() or instr.upper() in stdout.split()):
+                ret += f'|{instr.upper()}' if ret else instr.upper()
 
-def has_instruction_sets(instruction_sets: str) -> bool:
+    return ret
+
+
+def has_instruction_sets_old(instruction_sets: list) -> str:
     """
     Determine whether a given list of CPU instruction sets is available.
 
     The function will use grep to search in /proc/cpuinfo (both in upper and lower case).
     Example: instruction_sets = ['AVX', 'AVX2', 'SSE4_2', 'XXX'] -> "AVX|AVX2|SSE4_2"
 
-    :param instruction_sets: instruction set (e.g. AVX2) (str)
-    :return: True if given instruction set is available, False otherwise (bool).
+    :param instruction_sets: instruction set (e.g. AVX2) (list)
+    :return: string of pipe-separated instruction sets (str).
     """
     ret = ""
     pattern = ""
@@ -709,8 +717,8 @@ def get_host_name():
         else:
             try:
                 host = socket.gethostname()
-            except socket.herror as exc:
-                logger.warning(f'failed to get host name: {exc}')
+            except socket.herror as e:
+                logger.warning(f'failed to get host name: {e}')
                 host = 'localhost'
         return host.split('.')[0]
 
@@ -821,3 +829,12 @@ def is_kubernetes_resource() -> bool:
         return True
     else:
         return False
+
+
+def uuidgen_t() -> str:
+    """
+    Generate a UUID string in the same format as "uuidgen -t".
+
+    :return: A UUID in the format "00000000-0000-0000-0000-000000000000" (str).
+    """
+    return str(uuid4())

pilot/util/constants.py

@@ -27,8 +27,8 @@
 # Pilot version
 RELEASE = '3'   # released number should be fixed at 3 for Pilot 3
 VERSION = '9'   # version number is '1' for first release, '0' until then, increased for bigger updates
-REVISION = '0'  # revision number should be reset to '0' for every new version release, increased for small updates
-BUILD = '17'     # build number should be reset to '1' for every new development cycle
+REVISION = '1'  # revision number should be reset to '0' for every new version release, increased for small updates
+BUILD = '13'     # build number should be reset to '1' for every new development cycle
 
 SUCCESS = 0
 FAILURE = 1

pilot/util/container.py

@@ -21,6 +21,7 @@
 
 """Functions for executing commands."""
 
+import errno
 import os
 import subprocess
 import logging
@@ -113,12 +114,17 @@ def read_output(stream, queue):
         while True:
             try:
                 line = stream.readline()
-            except AttributeError:
-                # Handle the case where stream is None
-                break
-
-            if not line:
+                if not line:
+                    break
+            except (AttributeError, ValueError):
+                # Handle the case where stream is None (AttributeError) or closed (ValueError)
                 break
+            except OSError as e:
+                if e.errno == errno.EBADF:
+                    # Handle the case where the file descriptor is bad
+                    break
+                else:
+                    raise
 
             queue.put(line)
 
@@ -146,8 +152,11 @@ def read_output(stream, queue):
         exit_code = process.poll()
 
     # Wait for the threads to finish reading
-    stdout_thread.join()
-    stderr_thread.join()
+    try:
+        stdout_thread.join()
+        stderr_thread.join()
+    except Exception as e:
+        logger.warning(f'exception caught in execute: {e}')
 
     # Read the remaining output from the queues
     while not stdout_queue.empty():
@@ -263,12 +272,15 @@ def read_output(pipe, output_list):
     return exit_code, stdout, stderr
 
 
-def execute_old(executable: Any, **kwargs: dict) -> Any:
+def execute_nothreads(executable: Any, **kwargs: dict) -> Any:
     """
     Execute the command with its options in the provided executable list using subprocess time-out handler.
 
     The function also determines whether the command should be executed within a container.
 
+    This variant of execute() is not using threads to read stdout and stderr. This is required for some use-cases like
+    executing arcproxy where the stdout is time-ordered.
+
     :param executable: command to be executed (str or list)
     :param kwargs: kwargs (dict)
     :return: exit code (int), stdout (str) and stderr (str) (or process if requested via returnproc argument).

pilot/util/filehandling.py

@@ -252,6 +252,32 @@ def grep(patterns: list, file_name: str) -> list:
     """
     Search for the patterns in the given list in a file.
 
+    Example:
+      grep(["St9bad_alloc", "FATAL"], "athena_stdout.txt")
+      -> [list containing the lines below]
+        CaloTrkMuIdAlg2.sysExecute()             ERROR St9bad_alloc
+        AthAlgSeq.sysExecute()                   FATAL  Standard std::exception is caught
+
+    :param patterns: list of regexp patterns (list)
+    :param file_name: file name (str)
+    :return: list of matched lines in file (list).
+    """
+    matched_lines = []
+    compiled_patterns = [re.compile(pattern) for pattern in patterns]
+
+    with open(file_name, 'r', encoding='utf-8') as _file:
+        matched_lines = [
+            line for line in _file
+            if any(compiled_pattern.search(line) for compiled_pattern in compiled_patterns)
+        ]
+
+    return matched_lines
+
+
+def grep_old(patterns: list, file_name: str) -> list:
+    """
+    Search for the patterns in the given list in a file.
+
     Example:
       grep(["St9bad_alloc", "FATAL"], "athena_stdout.txt")
       -> [list containing the lines below]

pilot/util/monitoring.py

@@ -30,7 +30,7 @@
 from signal import SIGKILL
 
 from pilot.common.errorcodes import ErrorCodes
-from pilot.common.exception import PilotException, MiddlewareImportFailure
+from pilot.common.exception import PilotException, MiddlewareImportFailure  #, FileHandlingFailure
 from pilot.util.auxiliary import set_pilot_state  #, show_memory_usage
 from pilot.util.config import config
 from pilot.util.constants import PILOT_PRE_PAYLOAD
@@ -40,7 +40,8 @@
     remove_files,
     get_local_file_size,
     read_file,
-    zip_files
+    zip_files,
+    #write_file
 )
 from pilot.util.loopingjob import looping_job
 from pilot.util.math import (
@@ -135,7 +136,7 @@ def job_monitor_tasks(job: JobData, mt: MonitoringTime, args: object) -> tuple[i
         if exit_code != 0:
             return exit_code, diagnostics
 
-        # display OOM process info
+        # display OOM process info (once)
         display_oom_info(job.pid)
 
     # should the pilot abort the payload?
@@ -204,20 +205,31 @@ def display_oom_info(payload_pid):
 
     :param payload_pid: payload pid (int).
     """
-
+    #fname = f"/proc/{payload_pid}/oom_score_adj"
     payload_score = get_score(payload_pid) if payload_pid else 'UNKNOWN'
     pilot_score = get_score(os.getpid())
-    logger.info(f'oom_score(pilot) = {pilot_score}, oom_score(payload) = {payload_score}')
+    if isinstance(pilot_score, str) and pilot_score == 'UNKNOWN':
+        logger.warning(f'could not get oom_score for pilot process: {pilot_score}')
+    else:
+        #relative_payload_score = "1"
+
+        # write the payload oom_score to the oom_score_adj file
+        #try:
+        #    write_file(path=fname, contents=relative_payload_score)
+        #except Exception as e:  # FileHandlingFailure
+        #    logger.warning(f'could not write oom_score to file: {e}')
 
+        #logger.info(f'oom_score(pilot) = {pilot_score}, oom_score(payload) = {payload_score} (attempted writing relative score 1 to {fname})')
+        logger.info(f'oom_score(pilot) = {pilot_score}, oom_score(payload) = {payload_score}')
 
-def get_score(pid):
+
+def get_score(pid) -> str:
     """
     Get the OOM process score.
 
-    :param pid: process id (int).
-    :return: score (string).
+    :param pid: process id (int)
+    :return: score (str).
     """
-
     try:
         score = '%s' % read_file('/proc/%d/oom_score' % pid)
     except Exception as error: