Custom HPC software & tools from Wirawan. Primarily tailored toward ODU HPC sytems.
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#!/usr/bin/env python
# 20160826
# Wirawan Purwanto
# A tool that dumps every possibly imaginable info I want to get from
# a SGE-managed cluster.
This is a tool that dumps every possible imaginable info I want to get from
a SGE-managed cluster.
This tool runs at user-level, so can only gather information that an
ordinary user can mine from the cluster.
Currently the info available for dumping are:
- cpufreq
- lscpu
- lspci
- free memory (the `free` command)
- uname
- dmesg
- mount
- df
Typical workflow
As a starter, use routine `Gather_all` to gather all information bits
from the compute nodes. This is an expensive gather operation; it may
take a while to complete.
There is a tool called `test_accessible_hosts` to read the list of
nodes from `qhost` SGE command, then checks the availability of every
node by performing ssh into each one.
Analysis: CPU variety
To summarize the kinds of CPUs available on the compute nodes, as well
as listing the nodes that have them, use `summarize_cpu` and
This tool requires that the output of `gather_cpuinfo` has been saved
to `cluster-info/$HOSTNAME/cpuinfo.txt` files`, where $HOSTNAME stands
for the host basename (without domain qualifier) for every compute
The routine that does them all is `analyze_cpu_composition`.
import os
import re
import subprocess
import sys
def pipe_out(args, split=False, shell=False):
"""Executes a shell command, piping out the stdout to python for parsing.
This is my customary shortcut for backtick operator.
The result is either a single string (if split==False) or a list of strings
with EOLs removed (if split==True)."""
retval = subprocess.Popen(args, stdout=subprocess.PIPE, shell=shell).communicate()[0]
if not split:
return retval
return retval.splitlines()
class pipe_in(object):
"""Executes a shell command, piping in the stdin from python for driving.
This is the reverse of pipe_out.
Commands are given through file-like write() or writelines() methods."""
def __init__(self, args, shell=False):
self.px = subprocess.Popen(args, stdin=subprocess.PIPE, shell=shell)
self.args = args
def write(self, line):
def writelines(self, lines):
for line in lines:
def flush(self):
def close(self):
def errchk(cmd, args, retcode):
"""Checking for error after the invocation of an external command."""
if retcode == 0: return
print >>sys.stderr, "Error executing ", cmd, " ".join(args)
if retcode < 0:
err = "Command %s was terminated by signal %d" % (cmd, -retcode)
err = "Command %s returned %d" % (cmd, retcode)
raise RuntimeError, err
class sh(object):
def run(prg, args):
retcode =,) + tuple(args))
errchk(prg, args, retcode)
return 0
_g = globals()
_g.setdefault("NODE_LIST", [])
#_g.setdefault("NODE_BAD_LIST", set())
_g.setdefault("NODE_BAD_LIST", [])
_g.setdefault("NODE_GOOD_LIST", [])
_g.setdefault("ROOT_DIR", "cluster-info")
def get_node_list():
"""Reads node list from SGE configuration."""
node_list = pipe_out(("qconf", "-sel"), split=True)
return node_list
def node_list():
global NODE_LIST
if not NODE_LIST:
NODE_LIST = get_node_list()
return NODE_LIST
def rhost_pipe_out(host, cmdline, split=False):
cmdline_full = ["ssh", "-o", "PreferredAuthentications=publickey", host] \
+ (list(cmdline) if not isinstance(cmdline, basestring) else cmdline.split())
rslt = pipe_out(cmdline_full, split=split)
return rslt
def rhost_run(host, cmdline):
cmdline_full = ["ssh", "-o", "PreferredAuthentications=publickey", host] \
+ (list(cmdline) if not isinstance(cmdline, basestring) else cmdline.split())
rslt =[0], cmdline_full[1:])
return rslt
def rhosts_pipe_out(cmdline, filename, hosts=None, rootdir=None):
"""Executes cmdline on each remote host (the list is given in and
global ROOT_DIR
from os.path import dirname, join, isdir
path_join = join
Verb = 100
if hosts is None:
hosts = node_list()
if rootdir is None:
rootdir = ROOT_DIR
for H in hosts:
host_base = H.split(".")[0]
outfname = path_join(rootdir, host_base, filename)
outdir = dirname(outfname)
if not isdir(outdir):
if Verb >= 1:
print(" exec: %s %s" % (H, cmdline))
out = rhost_pipe_out(H, cmdline, split=False)
with open(outfname, "w") as F:
def test_accessible_hosts(hosts=None):
"""Tests ssh connectivity for all the hosts and return a two-tuple
containing lists of good and inaccessible hosts, respectively."""
from os.path import dirname, join, isdir
path_join = join
Verb = 100
if hosts is None:
hosts = node_list()
good_hosts = []
bad_hosts = []
for H in hosts:
host_base = H.split(".")[0]
msg_send = "Success login from host " + host_base
msg_recv = rhost_pipe_out(H, ("echo", msg_send))
if msg_send == msg_recv.rstrip():
return good_hosts, bad_hosts
def cpuinfo_extract_processor_names(fn, ht=False):
"""Extracts the names of processors from /proc/cpuinfo.
Returns it as a list of processor names.
WARNING: Hyperthreading is detected with a lame methodology,
and only half of the number of cores are reported (i.e. only
physical cores)"""
A = []
siblings_on_socket = None
cores_on_socket = None
with open(fn, "r") as F:
for L in F:
if L.startswith("model name"):
modelname = L.split(":", 1)[1].strip()
elif L.startswith("siblings"):
siblings_on_socket = int(L.split(":", 1)[1].strip())
elif L.startswith("cpu cores"):
cores_on_socket = int(L.split(":", 1)[1].strip())
#print "siblings: ", siblings_on_socket
#print "cores: ", cores_on_socket
# FIXME: Quick-and-dirty solution for hyperthreading;
# see Red Hat site above; not 100% reliable if there are several
# kinds of CPU models, which I don't think I'll ever encountered.
if (not ht) \
and siblings_on_socket is not None \
and cores_on_socket is not None \
and siblings_on_socket != cores_on_socket:
assert cores_on_socket*2 == siblings_on_socket
# ^^otherwise it's not Hyperthreading, the code has to be fixed!
A = A[0:len(A)/2] ### HACK!!!
print("Warning: hyperthreading detected in %s" % fn)
return A
def agg_count_names(namelist):
"""Aggregates the names in namelist to names->count mapping, as a dict.
Useful, e.g. for counting number of unique elements in a list.
A = {}
for C in namelist:
A[C] = A[C] + 1
except KeyError:
A[C] = 1
return A
# Below are the main gather tools
def gather_cpuinfo(hosts=None):
"""Gather tool: for cpuinfo"""
rhosts_pipe_out(("cat", "/proc/cpuinfo"), "cpuinfo.txt", hosts=hosts)
def gather_lscpu(hosts=None):
"""Gather tool: for lscpu"""
rhosts_pipe_out(("lscpu"), "lscpu.txt", hosts=hosts)
def gather_lspci(hosts=None):
"""Gather tool: for lspci"""
rhosts_pipe_out(("lspci"), "lspci.txt", hosts=hosts)
def gather_free(hosts=None):
"""Gather tool: for free"""
rhosts_pipe_out(("free"), "free.txt", hosts=hosts)
def gather_uname_a(hosts=None):
"""Gather tool: for free"""
rhosts_pipe_out(("uname", "-a"), "uname-a.txt", hosts=hosts)
def gather_dmesg(hosts=None):
"""Gather tool: for dmesg"""
rhosts_pipe_out(("dmesg",), "dmesg.txt", hosts=hosts)
def gather_mount(hosts=None):
"""Gather tool: for mount points"""
rhosts_pipe_out(("mount",), "mount.txt", hosts=hosts)
def gather_df(hosts=None):
"""Gather tool: for disk free"""
rhosts_pipe_out(("df",), "df.txt", hosts=hosts)
#def dict_str_sorted(d):
# return "{" + ", ".
def summarize_cpu(hosts=None):
from pprint import pformat
global ROOT_DIR
hosts_base = [ H.split(".")[0] for H in hosts ]
getfile = lambda H, bn: os.path.join(ROOT_DIR, H, bn)
cpu_info = []
px_hosts_by_type = {}
for H in hosts_base:
px_names = cpuinfo_extract_processor_names(getfile(H, "cpuinfo.txt"))
px_group = agg_count_names(px_names)
#print("%s : %s" % (H, px_group))
px_group_key = pformat(px_group) # use pretty representation
px_hosts_by_type[px_group_key]["hosts"] += [ H ]
except KeyError:
px_hosts_by_type[px_group_key] = {
"cpu_count": px_group,
"hosts": [ H ]
return px_hosts_by_type
def print_summarize_cpu(summary):
host_types = sorted(summary.keys())
nproc_grand_total = 0
nnode_grand_total = 0
for T in host_types:
rec = summary[T]
nproc_per_node = sum(rec["cpu_count"].values())
print("%s:: %d hosts, %d procs/node, total %d procs" \
% (T,
len(rec["hosts"]) * nproc_per_node,
print(" " + " ".join(sorted(rec["hosts"])))
nproc_grand_total += len(rec["hosts"]) * nproc_per_node
nnode_grand_total += len(rec["hosts"])
print("Grand total %d procs" % nproc_grand_total)
print("Grand total %d nodes" % nnode_grand_total)
def tally_summarize_cpu(summary):
"""Tallies up the total number of processors
def analyze_cpu_composition():
"""Performs analysis of the CPU composition of an SGE cluster.
Automatically queries the up (available) nodes and gathers the cpuinfo,
if it is necessary.
global ROOT_DIR
getfile = lambda H, bn: os.path.join(ROOT_DIR, H.split('.')[0], bn)
if len(NODE_GOOD_LIST) == 0:
print("Warning: need to test node accesibility...")
NODE_GOOD_LIST, NODE_BAD_LIST = test_accessible_hosts()
if not os.path.exists(getfile(NODE_GOOD_LIST[0], "cpuinfo.txt")):
print("Warning: need to gather cpuinfo...")
# Most likely you haven't run gather_cpuinfo then...
summ = summarize_cpu(NODE_GOOD_LIST)
def Gather_all():
"""Master gathering routine, to gather everything all at once.
It will take some time to gather every bit of information.
print("Testing node accesibility...")
NODE_GOOD_LIST, NODE_BAD_LIST = test_accesible_hosts()
print("\nGathering cpuinfo...")
print("\nGathering lscpu...")
print("\nGathering lspci...")
print("\nGathering free mem...")
print("\nGathering uname...")
print("\nGathering dmesg...")
print("\nGathering mount...")
print("\nGathering df...")