pymatgen.io.abinit.qjobs module

Objects and methods to contact the resource manager to get info on the status of the job and useful statistics. Note that this is not a wrapper for the C API but a collection of simple wrappers around the shell commands provided by the resource manager (qsub, qdel and qstat for PBS, sinfo, squeue… for Slurm). The main goal indeed is providing a simplified common interface for different resource managers without having to rely on external libraries.

class BlueGeneJob(queue_id, qname='UnknownQueue')

Bases: pymatgen.io.abinit.qjobs.QueueJob

Not supported

Parameters:

• queue_id – Job identifier.
• qname – Name of the queue (optional).

QTYPE = 'bluegene'

class JobStatus

Bases: int

This object is an integer representing the status of a QueueJob.

Slurm API, see man squeue.

JOB STATE CODES

Jobs typically pass through several states in the course of their execution. The typical states are PENDING, RUNNING, SUSPENDED, COMPLETING, and COMPLETED. An explanation of each state follows.

BF BOOT_FAIL Job terminated due to launch failure, typically due to a hardware failure (e.g.

unable to boot the node or block and the job can not be requeued).

CA CANCELLED Job was explicitly cancelled by the user or system administrator.

The job may or may not have been initiated.

CD COMPLETED Job has terminated all processes on all nodes. CF CONFIGURING Job has been allocated resources, but are waiting for them to become ready for use (e.g. booting). CG COMPLETING Job is in the process of completing. Some processes on some nodes may still be active. F FAILED Job terminated with non-zero exit code or other failure condition. NF NODE_FAIL Job terminated due to failure of one or more allocated nodes. PD PENDING Job is awaiting resource allocation. PR PREEMPTED Job terminated due to preemption. R RUNNING Job currently has an allocation. S SUSPENDED Job has an allocation, but execution has been suspended. TO TIMEOUT Job terminated upon reaching its time limit. SE SPECIAL_EXIT The job was requeued in a special state. This state can be set by users, typically

in EpilogSlurmctld, if the job has terminated with a particular exit value.

classmethod from_string(s)

Return a JobStatus instance from its string representation.

class MoabJob(queue_id, qname='UnknownQueue')

Bases: pymatgen.io.abinit.qjobs.QueueJob

Not supported

Parameters:

• queue_id – Job identifier.
• qname – Name of the queue (optional).

QTYPE = 'moab'

class PbsProJob(queue_id, qname='UnknownQueue')

Bases: pymatgen.io.abinit.qjobs.QueueJob

Handler for PbsPro Jobs.

See also https://github.com/plediii/pbs_util for a similar project.

Parameters:

• queue_id – Job identifier.
• qname – Name of the queue (optional).

PBSSTAT_TO_SLURM = defaultdict(<function PbsProJob.<lambda>>, {'E': <JobStatus: FAILED, at 4715886024>, 'F': <JobStatus: COMPLETED, at 4715885704>, 'Q': <JobStatus: PENDING, at 4715886152>, 'R': <JobStatus: RUNNING, at 4715885896>, 'S': <JobStatus: SUSPENDED, at 4715886344>})

QTYPE = 'pbspro'

estimated_start_time()

get_info(**kwargs)

class QueueJob(queue_id, qname='UnknownQueue')

Bases: object

This object provides methods to contact the resource manager to get info on the status of the job and useful statistics. This is an abstract class.

Parameters:

• queue_id – Job identifier.
• qname – Name of the queue (optional).

QTYPE = None

S_CANCELLED = <JobStatus: CANCELLED, at 4715886984>

S_COMPLETED = <JobStatus: COMPLETED, at 4715885704>

S_FAILED = <JobStatus: FAILED, at 4715886024>

S_NODEFAIL = <JobStatus: NODEFAIL, at 4715885832>

S_PENDING = <JobStatus: PENDING, at 4715886152>

S_PREEMPTED = <JobStatus: PREEMPTED, at 4715885256>

S_RESIZING = <JobStatus: RESIZING, at 4715886472>

S_RUNNING = <JobStatus: RUNNING, at 4715885896>

S_SUSPENDED = <JobStatus: SUSPENDED, at 4715886344>

S_TIMEOUT = <JobStatus: TIMEOUT, at 4715885384>

S_UNKNOWN = <JobStatus: UNKNOWN, at 4717485640>

estimated_start_time()

Return date with estimated start time. None if it cannot be detected

static from_qtype_and_id(qtype, queue_id, qname=None)

Return a new istance of the appropriate subclass.

Parameters:

• qtype – String specifying the Resource manager type.
• queue_id – Job identifier.
• qname – Name of the queue (optional).

get_info(**kwargs)

get_nodes(**kwargs)

get_stats(**kwargs)

has_node_failures

is_completed

is_failed

is_running

likely_code_error()

See http://man7.org/linux/man-pages/man7/signal.7.html

SIGHUP 1 Term Hangup detected on controlling terminal or death of controlling process SIGINT 2 Term Interrupt from keyboard SIGQUIT 3 Core Quit from keyboard SIGILL 4 Core Illegal Instruction SIGABRT 6 Core Abort signal from abort(3) SIGFPE 8 Core Floating point exception SIGKILL 9 Term Kill signal SIGSEGV 11 Core Invalid memory reference SIGPIPE 13 Term Broken pipe: write to pipe with no readers SIGALRM 14 Term Timer signal from alarm(2) SIGTERM 15 Term Termination signal SIGUSR1 30,10,16 Term User-defined signal 1 SIGUSR2 31,12,17 Term User-defined signal 2 SIGCHLD 20,17,18 Ign Child stopped or terminated SIGCONT 19,18,25 Cont Continue if stopped SIGSTOP 17,19,23 Stop Stop process SIGTSTP 18,20,24 Stop Stop typed at terminal SIGTTIN 21,21,26 Stop Terminal input for background process SIGTTOU 22,22,27 Stop Terminal output for background process

The signals SIGKILL and SIGSTOP cannot be caught, blocked, or ignored.

Next the signals not in the POSIX.1-1990 standard but described in SUSv2 and POSIX.1-2001.

Signal Value Action Comment SIGBUS 10,7,10 Core Bus error (bad memory access) SIGPOLL Term Pollable event (Sys V).

Synonym for SIGIO

SIGPROF 27,27,29 Term Profiling timer expired SIGSYS 12,31,12 Core Bad argument to routine (SVr4) SIGTRAP 5 Core Trace/breakpoint trap SIGURG 16,23,21 Ign Urgent condition on socket (4.2BSD) SIGVTALRM 26,26,28 Term Virtual alarm clock (4.2BSD) SIGXCPU 24,24,30 Core CPU time limit exceeded (4.2BSD) SIGXFSZ 25,25,31 Core File size limit exceeded (4.2BSD)

received_signal(sig_name)

set_status_exitcode_signal(status, exitcode, signal)

timeout

unknown_status

class SgeJob(queue_id, qname='UnknownQueue')

Bases: pymatgen.io.abinit.qjobs.QueueJob

Not supported

Parameters:

• queue_id – Job identifier.
• qname – Name of the queue (optional).

QTYPE = 'sge'

class ShellJob(queue_id, qname='UnknownQueue')

Bases: pymatgen.io.abinit.qjobs.QueueJob

Handler for Shell jobs.

Parameters:

• queue_id – Job identifier.
• qname – Name of the queue (optional).

QTYPE = 'shell'

class SlurmJob(queue_id, qname='UnknownQueue')

Bases: pymatgen.io.abinit.qjobs.QueueJob

Handler for Slurm jobs.

Parameters:

• queue_id – Job identifier.
• qname – Name of the queue (optional).

QTYPE = 'slurm'

estimated_start_time()

get_info(**kwargs)

get_stats(**kwargs)

class TorqueJob(queue_id, qname='UnknownQueue')

Bases: pymatgen.io.abinit.qjobs.QueueJob

Not supported

Parameters:

• queue_id – Job identifier.
• qname – Name of the queue (optional).

QTYPE = 'torque'