Commit 373f6892 authored by Nikolay Simakov's avatar Nikolay Simakov
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---
title: "Slurm Simulator Toolkit"
output:
pdf_document:
latex_engine: xelatex
monofont: "DejaVu Sans Mono"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Python Command Line Utilities
## cp_slurm_conf_dir.py - Slurm etc Directory Copying and Paths Update
cp_slurm_conf_dir.py copy Slurm configuration from one location to new and updates pathways withing that configuration to new location.
Can be used to initiate new simulation from previous configuration.
Slurm configuration has several parameters which specified as absolute file-system path, cp_slurm_conf_dir.py allows copying of the slurm configuration with modification of such parameters to new file-system location.
**Usage:**
```{bash,eval=FALSE}
cp_slurm_conf_dir.py [-h] -s SLURM_BIN [-o] [-v] old_etc new_slurm_topdir
```
**Positional Arguments:**
old_etc
: etc directory for copied Slurm configuration
new_slurm_topdir
: new location of slurm topdir
**Optional Arguments**
-h, --help
: show help message and exit
-s SLURM_BIN_, --slurm-bin SLURM_BIN
: top directory of slurm binaries installation
-o, --overwrite
: overwrite existing files
-v, --verbose
: turn on verbose logging
^.*\.Rproj$
^\.Rproj\.user$
Package: RSlurmSimTools
Type: Package
Title: R Toolkit for Slurm Simulator
Version: 1.0
Date: 2017-05-01
Author: Nikolay Simakov
Maintainer: Nikolay Simakov <your@email.com>
Description: R utilities for job traces preparation and results analysis for Slurm Simulator
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.8),rPython,stringr,lubridate
LinkingTo: Rcpp
SystemRequirements: python (>=2.7.10)
RoxygenNote: 6.0.1
useDynLib(RSlurmSimTools)
exportPattern("^[[:alpha:]]+")
importFrom(Rcpp, evalCpp)
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
write_trace_cpp <- function(filename, jobs) {
invisible(.Call('RSlurmSimTools_write_trace_cpp', PACKAGE = 'RSlurmSimTools', filename, jobs))
}
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Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 4
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageRoxygenize: rd,collate,namespace
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Hostlist library
#
# Copyright (C) 2008 Kent Engström <kent@nsc.liu.se>,
# Thomas Bellman <bellman@nsc.liu.se> and
# Pär Andersson <paran@nsc.liu.se>,
# National Supercomputer Centre
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA.
"""Handle hostlist expressions.
This module provides operations to expand and collect hostlist
expressions.
The hostlist expression syntax is the same as in several programs
developed at LLNL (https://computing.llnl.gov/linux/). However in
corner cases the behaviour of this module have not been compared for
compatibility with pdsh/dshbak/SLURM et al.
"""
__version__ = "1.16"
import re
import itertools
# Exception used for error reporting to the caller
class BadHostlist(Exception): pass
# Configuration to guard against ridiculously long expanded lists
MAX_SIZE = 100000
# Hostlist expansion
def expand_hostlist(hostlist, allow_duplicates=False, sort=False):
"""Expand a hostlist expression string to a Python list.
Example: expand_hostlist("n[9-11],d[01-02]") ==>
['n9', 'n10', 'n11', 'd01', 'd02']
Unless allow_duplicates is true, duplicates will be purged
from the results. If sort is true, the output will be sorted.
"""
results = []
bracket_level = 0
part = ""
for c in hostlist + ",":
if c == "," and bracket_level == 0:
# Comma at top level, split!
if part: results.extend(expand_part(part))
part = ""
#bad_part = False
else:
part += c
if c == "[": bracket_level += 1
elif c == "]": bracket_level -= 1
if bracket_level > 1:
raise BadHostlist("nested brackets")
elif bracket_level < 0:
raise BadHostlist("unbalanced brackets")
if bracket_level > 0:
raise BadHostlist("unbalanced brackets")
if not allow_duplicates:
results = remove_duplicates(results)
if sort:
results = numerically_sorted(results)
return results
def expand_hostlists_to_list(hostlists, allow_duplicates=False, sort=False):
return [expand_hostlist(hostlist, allow_duplicates, sort) for hostlist in hostlists]
def expand_part(s):
"""Expand a part (e.g. "x[1-2]y[1-3][1-3]") (no outer level commas)."""
# Base case: the empty part expand to the singleton list of ""
if s == "":
return [""]
# Split into:
# 1) prefix string (may be empty)
# 2) rangelist in brackets (may be missing)
# 3) the rest
m = re.match(r'([^,\[]*)(\[[^\]]*\])?(.*)', s)
(prefix, rangelist, rest) = m.group(1,2,3)
# Expand the rest first (here is where we recurse!)
rest_expanded = expand_part(rest)
# Expand our own part
if not rangelist:
# If there is no rangelist, our own contribution is the prefix only
us_expanded = [prefix]
else:
# Otherwise expand the rangelist (adding the prefix before)
us_expanded = expand_rangelist(prefix, rangelist[1:-1])
# Combine our list with the list from the expansion of the rest
# (but guard against too large results first)
if len(us_expanded) * len(rest_expanded) > MAX_SIZE:
raise BadHostlist("results too large")
return [us_part + rest_part
for us_part in us_expanded
for rest_part in rest_expanded]
def expand_rangelist(prefix, rangelist):
""" Expand a rangelist (e.g. "1-10,14"), putting a prefix before."""
# Split at commas and expand each range separately
results = []
for range_ in rangelist.split(","):
results.extend(expand_range(prefix, range_))
return results
def expand_range(prefix, range_):
""" Expand a range (e.g. 1-10 or 14), putting a prefix before."""
# Check for a single number first
m = re.match(r'^[0-9]+$', range_)
if m:
return ["%s%s" % (prefix, range_)]
# Otherwise split low-high
m = re.match(r'^([0-9]+)-([0-9]+)$', range_)
if not m:
raise BadHostlist("bad range")
(s_low, s_high) = m.group(1,2)
low = int(s_low)
high = int(s_high)
width = len(s_low)
if high < low:
raise BadHostlist("start > stop")
elif high - low > MAX_SIZE:
raise BadHostlist("range too large")
results = []
for i in range(low, high+1):
results.append("%s%0*d" % (prefix, width, i))
return results
def remove_duplicates(l):
"""Remove duplicates from a list (but keep the order)."""
seen = set()
results = []
for e in l:
if e not in seen:
results.append(e)
seen.add(e)
return results
# Hostlist collection
def collect_hostlist(hosts, silently_discard_bad = False):
"""Collect a hostlist string from a Python list of hosts.
We start grouping from the rightmost numerical part.
Duplicates are removed.
A bad hostname raises an exception (unless silently_discard_bad
is true causing the bad hostname to be silently discarded instead).
"""
# Split hostlist into a list of (host, "") for the iterative part.
# (Also check for bad node names now)
# The idea is to move already collected numerical parts from the
# left side (seen by each loop) to the right side (just copied).
left_right = []
for host in hosts:
# We remove leading and trailing whitespace first, and skip empty lines
host = host.strip()
if host == "": continue
# We cannot accept a host containing any of the three special
# characters in the hostlist syntax (comma and flat brackets)
if re.search(r'[][,]', host):
if silently_discard_bad:
continue
else:
raise BadHostlist("forbidden character")
left_right.append((host, ""))
# Call the iterative function until it says it's done
looping = True
while looping:
left_right, looping = collect_hostlist_1(left_right)
return ",".join([left + right for left, right in left_right])
def collect_hostlist_1(left_right):
"""Collect a hostlist string from a list of hosts (left+right).
The input is a list of tuples (left, right). The left part
is analyzed, while the right part is just passed along
(it can contain already collected range expressions).
"""
# Scan the list of hosts (left+right) and build two things:
# *) a set of all hosts seen (used later)
# *) a list where each host entry is preprocessed for correct sorting
sortlist = []
remaining = set()
for left, right in left_right:
host = left + right
remaining.add(host)
# Match the left part into parts
m = re.match(r'^(.*?)([0-9]+)?([^0-9]*)$', left)
(prefix, num_str, suffix) = m.group(1,2,3)
# Add the right part unprocessed to the suffix.
# This ensures than an already computed range expression
# in the right part is not analyzed again.
suffix = suffix + right
if num_str is None:
# A left part with no numeric part at all gets special treatment!
# The regexp matches with the whole string as the suffix,
# with nothing in the prefix or numeric parts.
# We do not want that, so we move it to the prefix and put
# None as a special marker where the suffix should be.
assert prefix == ""
sortlist.append(((host, None), None, None, host))
else:
# A left part with at least an numeric part
# (we care about the rightmost numeric part)
num_int = int(num_str)
num_width = len(num_str) # This width includes leading zeroes
sortlist.append(((prefix, suffix), num_int, num_width, host))
# Sort lexicographically, first on prefix, then on suffix, then on
# num_int (numerically), then...
# This determines the order of the final result.
sortlist.sort()
# We are ready to collect the result parts as a list of new (left,
# right) tuples.
results = []
needs_another_loop = False
# Now group entries with the same prefix+suffix combination (the
# key is the first element in the sortlist) to loop over them and
# then to loop over the list of hosts sharing the same
# prefix+suffix combination.
for ((prefix, suffix), group) in itertools.groupby(sortlist,
key=lambda x:x[0]):
if suffix is None:
# Special case: a host with no numeric part
results.append(("", prefix)) # Move everything to the right part
remaining.remove(prefix)
else:
# The general case. We prepare to collect a list of
# ranges expressed as (low, high, width) for later
# formatting.
range_list = []
for ((_, _), num_int, num_width, host) in group:
if host not in remaining:
# Below, we will loop internally to enumate a whole range
# at a time. We then remove the covered hosts from the set.
# Therefore, skip the host here if it is gone from the set.
continue
assert num_int is not None
# Scan for a range starting at the current host
low = num_int
while True:
host = "%s%0*d%s" % (prefix, num_width, num_int, suffix)
if host in remaining:
remaining.remove(host)
num_int += 1
else:
break
high = num_int - 1
assert high >= low
range_list.append((low, high, num_width))
# We have a list of ranges to format. We make sure
# we move our handled numerical part to the right to
# stop it from being processed again.
needs_another_loop = True
if len(range_list) == 1 and range_list[0][0] == range_list[0][1]:
# Special case to make sure that n1 is not shown as n[1] etc
results.append((prefix,
"%0*d%s" %
(range_list[0][2], range_list[0][0], suffix)))
else:
# General case where high > low
results.append((prefix, "[" + \
",".join([format_range(l, h, w)
for l, h, w in range_list]) + \
"]" + suffix))
# At this point, the set of remaining hosts should be empty and we
# are ready to return the result, together with the flag that says
# if we need to loop again (we do if we have added something to a
# left part).
assert not remaining
return results, needs_another_loop
def format_range(low, high, width):
"""Format a range from low to high inclusively, with a certain width."""
if low == high:
return "%0*d" % (width, low)
else:
return "%0*d-%0*d" % (width, low, width, high)
# Sort a list of hosts numerically
def numerically_sorted(l):
"""Sort a list of hosts numerically.
E.g. sorted order should be n1, n2, n10; not n1, n10, n2.
"""
return sorted(l, key=numeric_sort_key)
nsk_re = re.compile("([0-9]+)|([^0-9]+)")
def numeric_sort_key(x):
return [handle_int_nonint(i_ni) for i_ni in nsk_re.findall(x)]
def handle_int_nonint(int_nonint_tuple):
if int_nonint_tuple[0]:
return int(int_nonint_tuple[0])
else:
return int_nonint_tuple[1]
# Parse SLURM_TASKS_PER_NODE into a list of task numbers
#
# Description from the SLURM sbatch man page:
# Number of tasks to be initiated on each node. Values
# are comma separated and in the same order as
# SLURM_NODELIST. If two or more consecutive nodes are
# to have the same task count, that count is followed by
# "(x#)" where "#" is the repetition count. For example,
# "SLURM_TASKS_PER_NODE=2(x3),1" indicates that the first
# three nodes will each execute three tasks and the
# fourth node will execute one task.
def parse_slurm_tasks_per_node(s):
res = []
for part in s.split(","):
m = re.match(r'^([0-9]+)(\(x([0-9]+)\))?$', part)
if m:
tasks = int(m.group(1))
repetitions = m.group(3)
if repetitions is None:
repetitions = 1
else:
repetitions = int(repetitions)
if repetitions > MAX_SIZE:
raise BadHostlist("task list repetitions too large")
for _ in range(repetitions):
res.append(tasks)
else:
raise BadHostlist("bad task list syntax")
return res
#
# Keep this part to tell users where the command line interface went
#
#if __name__ == '__main__':
# import os, sys
# sys.stderr.write("The command line utility has been moved to a separate 'hostlist' program.\n")
# sys.exit(os.EX_USAGE)
\name{RSlurmSimTools-package}
\alias{RSlurmSimTools-package}
\alias{RSlurmSimTools}
\docType{package}
\title{
A short title line describing what the package does
}
\description{
A more detailed description of what the package does. A length
of about one to five lines is recommended.
}
\details{
This section should provide a more detailed overview of how to use the
package, including the most important functions.
}
\author{
Your Name, email optional.
Maintainer: Your Name <your@email.com>
}
\references{
This optional section can contain literature or other references for
background information.
}
\keyword{ package }
\seealso{
Optional links to other man pages
}
\examples{
\dontrun{
## Optional simple examples of the most important functions
## These can be in \dontrun{} and \donttest{} blocks.
}
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/trace_job_util.R
\name{get_utilization}
\alias{get_utilization}
\title{get_utilization - calculate resource utilization}
\usage{
get_utilization(sacct0, total_proc, dt = 60L)
}
\arguments{
\item{sacct0}{data frame with jobs execution history}
\item{total_proc}{total number of cores in the resource}
\item{dt}{time aggregation size, seconds. \emph{Default}: 60L}
}
\value{
data frame with resource utilization over time
}
\description{
Calculate resource utilization
}
\examples{
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/trace_job_util.R
\name{read_simstat_backfill}
\alias{read_simstat_backfill}
\title{read_simstat_backfill - read backfill execution stats}
\usage{
read_simstat_backfill(filename)
}
\arguments{
\item{filename}{name of file to read}
}
\value{
data frame with resource utilization over time
}
\description{
Cread stats of backfill execution during simulated Slurm Run
}
\examples{
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/trace_job_util.R
\name{sim_job}
\alias{sim_job}
\title{sim_job - Generates R-list with Resource Requested by Job}
\usage{
sim_job(job_id = NA, submit = "2001-01-01 00:00:00", wclimit = 0L,
duration = 0L, tasks = 0L, tasks_per_node = 0L, username = "user1",
qosname = "normal", partition = "normal", account = "account1",
req_mem = NA, req_mem_per_cpu = 0L, features = "", gres = "",
shared = 1L, cpus_per_task = 1L, dependency = "", cancelled = NA, ...)
}
\arguments{
\item{job_id}{Job ID. If it is not set then will use increamented \code{last_job_id values}. \emph{\emph{Default}}: NA}
\item{submit}{Date-Time to sumbit job. \emph{Default}: "2001-01-01 00:00:00"}
\item{wclimit}{Requested time in minutes. \emph{Default}: 0L}
\item{duration}{Simulated actual job walltime in seconds. \emph{Default}: 0L}
\item{tasks}{Requested number of tasks. \emph{Default}: 0L}