I've replaced the standard DEFRAG daemon released with Condor with a simpler version that contains a proportional integral (PI) controller.
I hoped this would give us better control over multicore slots. Preliminary results with the proportional part of the controller show that it fails to keep accurate control over the provision of slots. It is subject to hunting due to the long time lags between the onset of drainin and the eventual change in the controlled variable (which is 'running mcore jobs'). The rate of provision was unexpectedly stable at first, considering the simplicity of the algorithm employed, but degraded over time as the controlled variable became more random.
The graph below shows the very preliminary picture, with a temporary period of stable control shown by the green line on the right of the plot. The setpoint is 250.
I have also now included an Integral component to the controller, and I'm in the process of tuning the reset rate on this. I hope to show the results of this test soon.
Tuesday, 17 February 2015
Monday, 17 November 2014
Condor Workernode Heath Script
This is a script that makes some checks on the worker node and "turns it off" if it fails any of them. To implement this, I made use a a Condor feature; startd_cron jobs. I put this in my /etc/condor_config.local file on my worker nodes.
ENABLE_PERSISTENT_CONFIG = TRUE PERSISTENT_CONFIG_DIR = /etc/condor/ral STARTD_ATTRS = $(STARTD_ATTRS) StartJobs, RalNodeOnline STARTD.SETTABLE_ATTRS_ADMINISTRATOR = StartJobs StartJobs = False RalNodeOnline = FalseI use the prefix "Ral" here because I inherited some of this material from Andrew Lahiffe at RAL! Basically, it's just to de-conflict names. I should have used "Liv" right from the start, but I'm not changing it now. Anyway, the first section says to keep a persistent record of configuration settings; it adds new configuration settings called "StartJobs" and “RalNodeOnline”; it's sets them initially to False; and it makes the START configuration setting dependant upon them both being set. Note: the START setting is very important because the node won't start jobs unless it is True. I also need this. It tells the system (startd) to run a cron script every three minutes.
STARTD_CRON_JOBLIST=TESTNODE STARTD_CRON_TESTNODE_EXECUTABLE=/usr/libexec/condor/scripts/testnodeWrapper.sh STARTD_CRON_TESTNODE_PERIOD=300s # Make sure values get over STARTD_CRON_AUTOPUBLISH = If_ChangedThe testnodeWrapper.sh script looks like this:
#!/bin/bash
MESSAGE=OK
/usr/libexec/condor/scripts/testnode.sh > /dev/null 2>&1
STATUS=$?
if [ $STATUS != 0 ]; then
MESSAGE=`grep ^[A-Z0-9_][A-Z0-9_]*=$STATUS\$ /usr/libexec/condor/scripts/testnode.sh | head -n 1 | sed -e "s/=.*//"`
if [[ -z "$MESSAGE" ]]; then
MESSAGE=ERROR
fi
fi
if [[ $MESSAGE =~ ^OK$ ]] ; then
echo "RalNodeOnline = True"
else
echo "RalNodeOnline = False"
fi
echo "RalNodeOnlineMessage = $MESSAGE"
echo `date`, message $MESSAGE >> /tmp/testnode.status
exit 0
This just wraps an existing script which I reuse from out TORQUE/MAUI cluster. The existing script just returns a non-zero code if any error happens. To add a bit of extra info, I also lookup the meaning of the code. The important thing to notice is that it echoes out a line to set the RalNodeOnline setting to false. This is then used in the setting of START. Note: on TORQUE/MAUI, the script ran as “root”; here it runs as “condor”. I had to use sudo for some of the sections which (e.g.) check disks etc. because condor could not get smartctl settings etc.
Right, so I think that's it. When a node fails the test, START goes to False and the node won't run more jobs.
Oh, there's another thing to say. I use two settings to control START. As well as RalNodeOnline, I have the StartJobs setting. I can control this independently, so I can turn a node offline whether or not it has an error. This is useful for stopping the node to (say) rebuild it. It's done on the server, like this.
condor_config_val -verbose -name r21-n01 -startd -set "StartJobs = false" condor_reconfig r21-n01 condor_reconfig -daemon startd r21-n01
Tuesday, 14 October 2014
Tired of full /var ?
This is how I prevent /var from getting full on any of our servers. I wrote these two scripts, spacemonc.py and spacemond.py.
spacemonc.py is a client, and it is installed on each grid system and worker node as a cronjob:
spacemond.py is installed as a service; you'll have to pinch a /etc/init.d script to start and stop it properly (or do it from the command line to start with.) And the code for spacemond.py is pretty small, too:
# crontab -l | grep spacemonc.py 50 18 * * * /root/bin/spacemonc.pyBecause it's going to be an (almost) single threaded server, I use puppet to make it run at a random time on each system (I say "almost" because it actually uses method level locking to hold each thread in a sleep state, so it's actually a queueing server, I think; it won't drop simultaneous incoming connections, but it's unwise to allow too many of them to occur at once.)
cron { "spacemonc":
#ensure => absent,
command => "/root/bin/spacemonc.py",
user => root,
hour => fqdn_rand(24),
minute => fqdn_rand(60),
}
And it's pretty small:
/usr/bin/python
import xmlrpclib
import os
import subprocess
from socket import gethostname
proc = subprocess.Popen(["df | perl -p00e 's/\n\s//g' | grep -v ^cvmfs | grep -v hepraid[0-9][0-9]*_[0-9]"], stdout=subprocess.PIPE, shell=True)
(dfReport, err) = proc.communicate()
s = xmlrpclib.ServerProxy('http://SOMESERVEROROTHER.COM.ph.liv.ac.uk:8000')
status = s.post_report(gethostname(),dfReport)
if (status != 1):
print("Client failed");
The strange piece of perl in the middle is to stop a bad habit in df of breaking lines that have long fields (I hate that; ldapsearch and qstat also do it.) I don't want to know about cvmfs partitions, nor raid storage mounts.
spacemond.py is installed as a service; you'll have to pinch a /etc/init.d script to start and stop it properly (or do it from the command line to start with.) And the code for spacemond.py is pretty small, too:
#!/usr/local/bin/python2.4
import sys
from SimpleXMLRPCServer import SimpleXMLRPCServer
from SimpleXMLRPCServer import SimpleXMLRPCRequestHandler
import time
import smtplib
import logging
if (len(sys.argv) == 2):
limit = int(sys.argv[1])
else:
limit = 90
# Maybe put logging in some time
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(levelname)s %(message)s',
filename="/var/log/spacemon/log",
filemode='a')
# Email details
smtpserver = 'hep.ph.liv.ac.uk'
recipients = ['sjones@hep.ph.liv.ac.uk','sjones@hep.ph.liv.ac.uk']
sender = 'root@SOMESERVEROROTHER.COM.ph.liv.ac.uk'
msgheader = "From: root@SOMESERVEROROTHER.COM.ph.liv.ac.uk\r\nTo: YOURNAME@hep.ph.liv.ac.uk\r\nSubject: spacemon report\r\n\r\n"
# Test the server started
session = smtplib.SMTP(smtpserver)
smtpresult = session.sendmail(sender, recipients, msgheader + "spacemond server started\n")
session.quit()
# Restrict to a particular path.
class RequestHandler(SimpleXMLRPCRequestHandler):
rpc_paths = ('/RPC2',)
# Create server
server = SimpleXMLRPCServer(("SOMESERVEROROTHER.COM", 8000), requestHandler=RequestHandler)
server.logRequests = 0
server.register_introspection_functions()
# Class with a method to process incoming reports
class SpaceMon:
def post_report(address,hostname,report):
full_messages = []
full_messages[:] = [] # Always empty it
lines = report.split('\n')
for l in lines[1:]:
fields = l.split()
if (len(fields) >= 5):
fs = fields[0]
pc = fields[4][:-1]
ipc = int(pc)
if (ipc >= limit ):
full_messages.append("File system " + fs + " on " + hostname + " is getting full at " + pc + " percent.\n")
if (len(full_messages) > 0):
session = smtplib.SMTP(smtpserver)
smtpresult = session.sendmail(sender, recipients, msgheader + ("").join(full_messages))
session.quit()
logging.info(("").join(full_messages))
else:
logging.info("Happy state for " + hostname )
return 1
# Register and serve
server.register_instance(SpaceMon())
server.serve_forever()
And now I get an email if any of my OS partitions is getting too full.
It's surpising how small server software can be when you use a framework like XMLRPC. In the old days, I would have needed 200 lines of parsing code and case statements. Goodbye to all that.
Thursday, 3 July 2014
APEL EMI-3 upgrade
Here are some notes from Manchester upgrade to EMI-3 APEL. The new APEL is much simpler as it is a bunch of python scripts with a couple of key=value configuration files, rather than java scripts with XML files. It doesn't have YAIM to configure it but since it is much easier to install and configure it doesn't really matter anymore. As an added bonus I found that it's also much faster when it publishes and doesn't require any tedious tuning of how many records at the time to publish.
So Manchester starting point to upgrade was
Install a new EMI-3 APEL node
Installed a vanilla VM with
Configure EMI-3 APEL node
I followed the instructions on the official EMI-3 APEL server guide.
There are no tips here I've only changed the obvious fields Like site_name and password plus few others like the top BDII because we have a local one and the location of the hostcertificate because we have a different name.
I didn't install install the publisher cron job at this stage because the machine was not ready yet to publish
Upgrade the CEs parsers to EMI-3 and point them the new node
The CEs as I said are already on EMI-3, only the APEL parsers were still EMI-2 so I disabled the EMI-2 cron job
NOTE: the parser configuration file for me is a bit confusing regarding the batch system name it states
# Batch system hostname. This does not need to be a definitive hostname,
# but it should uniquely identify the batch system.
# Example: pbs.gridpp.rl.ac.uk
lrms_server =
It seems you can use any name. You are of course better off using your batch system server name. We have one for each CE so the configuration file on each contains that. In the database this will identify the records from each machine CE. I'm not sure about what happens with 1 batch system and several CEs. Following literally one should put only the batch system but then there is no distinction between CEs.
Disable the old EMI-2 APEL node and backup its DB
Just removed the old cron job the machine is still running but it isn't doing anything while waiting to be decomissioned.
Run the parsers and fill the new APEL node DB
You will need to publish an entire month prior to when you are installing. For example for us it was publish all the June records, but since I didn't want to republish everything we had in the log files I moved the batch system and blah log files prior to mid May to a backup subdirectory and parsed only the log files for end of May June. May days were needed because some jobs that finished in June early days had started in May and one wants the complete record. The first jobs to finish in June in Manchester started on the 25th of May so you may want to go back a bit with the parsing.
Publish all records for the previous month from the new APEL machine
Finally on the new machine now filled with the June records plus some May I've done a bit of DB clean up as suggested by the APEL team. If you don't do this step the APEL team will do it centrally before stitching the old EMI-2 record and the new ones
So Manchester starting point to upgrade was
- EMI-2 APEL node
- EMI-2 APEL parsers on EMI-3 cream CEs
- We have 1 batch system per CE so I haven't tried a configuration in which there is only 1 batch system and multiple CEs
- In few months we may move to ARC-CE so configuration was done mostly manually
- Install a new EMI-3 APEL node
- Configure it
- Upgrade the CEs parsers to EMI-3 and point them the new node
- Disable the old EMI-2 APEL node and backup its DB
- Run the parsers and fill the new APEL node DB
- Publish all records for the previous month from the new APEL machine
Install a new EMI-3 APEL node
Installed a vanilla VM with
- EMI-3 repositories
- Mysql DB
- Host certificates
- ca-policy-egi-core
- yum install --nogpg emi-release
- yum install apel-ssm apel-client apel-lib
Configure EMI-3 APEL node
I followed the instructions on the official EMI-3 APEL server guide.
There are no tips here I've only changed the obvious fields Like site_name and password plus few others like the top BDII because we have a local one and the location of the hostcertificate because we have a different name.
I didn't install install the publisher cron job at this stage because the machine was not ready yet to publish
Upgrade the CEs parsers to EMI-3 and point them the new node
The CEs as I said are already on EMI-3, only the APEL parsers were still EMI-2 so I disabled the EMI-2 cron job
- rm /etc/cron.d/glite-apel-pbs-parser
- yum install apel-parser
NOTE: the parser configuration file for me is a bit confusing regarding the batch system name it states
# Batch system hostname. This does not need to be a definitive hostname,
# but it should uniquely identify the batch system.
# Example: pbs.gridpp.rl.ac.uk
lrms_server =
It seems you can use any name. You are of course better off using your batch system server name. We have one for each CE so the configuration file on each contains that. In the database this will identify the records from each machine CE. I'm not sure about what happens with 1 batch system and several CEs. Following literally one should put only the batch system but then there is no distinction between CEs.
Disable the old EMI-2 APEL node and backup its DB
Just removed the old cron job the machine is still running but it isn't doing anything while waiting to be decomissioned.
Run the parsers and fill the new APEL node DB
You will need to publish an entire month prior to when you are installing. For example for us it was publish all the June records, but since I didn't want to republish everything we had in the log files I moved the batch system and blah log files prior to mid May to a backup subdirectory and parsed only the log files for end of May June. May days were needed because some jobs that finished in June early days had started in May and one wants the complete record. The first jobs to finish in June in Manchester started on the 25th of May so you may want to go back a bit with the parsing.
Publish all records for the previous month from the new APEL machine
Finally on the new machine now filled with the June records plus some May I've done a bit of DB clean up as suggested by the APEL team. If you don't do this step the APEL team will do it centrally before stitching the old EMI-2 record and the new ones
- Delete from JobRecords where EndTime<"2014-06-01";
- Delete from SuperSummaries where Month="5";
Wednesday, 7 May 2014
Planning for SHA-2
Timeline
The voms servers at CERN will be transferred to new hosts that use the newer SHA-2 certificate standard. The changes are described in this post:
CERN VOMS service will move to new hosts
The picture below lays out the timeline for the change.
![]() | |
| Timeline for Cern Voms Server Changes |
New VOMS Server Hosts
The VOs associated with these changes are alice, atlas, cms, lhcb and ops. Sites supporting any of those will have to make a plan to update.
The new hosts have been set up already and entered against the related VOs in the ops portal. The table below summarises the current set up (ignoring vo.racf.bnl.gov) as advertised in the operations portal (as of 7th May 2014).
| VO | Vomses Port | Old Server | Is admin? | New Server | IsAdmin? |
|---|---|---|---|---|---|
| atlas | 15001 | lcg-voms.cern.ch | No | lcg-voms2.cern.ch | Yes |
| atlas | 15001 | voms.cern.ch | Yes | voms2.cern.ch | Yes |
| alice | 15000 | lcg-voms.cern.ch | No | lcg-voms2.cern.ch | Yes |
| alice | 15000 | voms.cern.ch | Yes | voms2.cern.ch | Yes |
| cms | 15002 | lcg-voms.cern.ch | No | lcg-voms2.cern.ch | Yes |
| cms | 15002 | voms.cern.ch | Yes | voms2.cern.ch | Yes |
| lhcb | 15003 | lcg-voms.cern.ch | No | lcg-voms2.cern.ch | Yes |
| lhcb | 15003 | voms.cern.ch | Yes | voms2.cern.ch | Yes |
| ops | 15009 | lcg-voms.cern.ch | No | lcg-voms2.cern.ch | Yes |
| ops | 15009 | voms.cern.ch | Yes | voms2.cern.ch | Yes |
Notes: The IsAdmin flag tells whether the server could be used to download used to create the DN grid-map file. The port numbers are unaffected by the change.
VOMS Server RPMS
As described in the announcement (see link at the top), a set of rpms have been created, one per WLCG-related VO:- wlcg-voms-alice
- wlcg-voms-atlas
- wlcg-voms-cms
- wlcg-voms-lhcb
- wlcg-voms-ops
The rpms are hosted in the yum repository WLCG repository. To install, e.g.
$ cd /etc/yum.repos.d/
$ wget http://linuxsoft.cern.ch/wlcg/wlcg-sl6.repo
Local Measures at Liverpool
At Liverpool, the configuration of the following servers will need to be changed:- Argus
- Cream CE
- DPM SE
- WN and
...
- UI (eventually)
There will be a gap of some weeks (see the picture) between the deadline for sites to update their services which consume certificates (e.g. Argus, Cream CE, DPM SE, and WN etc.) and the deadline for sites to update their UIs. This is to prevent the use of new-style certificates that cannot be interpreted.
So, to effect this change, Liverpool will apply the RPMS on our consuming service nodes in early May. As soon as the all-sites deadline has passed (2nd June) Liverpool will update its UIs in a similar manner.
If all goes well, Liverpool will remove reference to the old servers after the final deadline, 1st July. The plan in this case is to effect the change using the traditional yaim/site-info.def/vo.d method as these changes will need to be permanently maintained.
Effects on Approved VOs, VomsSnooper etc.
For tracking proposes, the GridPP Approved VOs document will attempt to remain synchronised with the operations portal, but the VomsSnooper process is asynchronous so there may be discrepancies around the deadlines. Sites are advised to watch out for these race conditions.Note: while the servers are being changed (i.e from now until 2nd June for certificate consuming services, and from 2nd June to 1 July (for consuming producing services, e.g. UIs) there can no canonical form of the VOMS records because different sites have their own implementation schedule and may use different settings temporarily, as described in my post above.
Monday, 28 April 2014
Snakey - a mindless way to reboot the cluster
Introduction
I'm fed up with all the book-keeping when I need to reboot or rebuild our cluster.
First I need to set a subset of nodes offline. Then I have to monitor them until some are drained. Then, as soon as any is drained, I have to reboot it by hand, then wait for it to build, then test it and finally put it back online, Then I choose another set (maybe a rack) and go through the same thing over and over until the cluster is done.
So, to cut all that, I've written a pair of perl scripts, called snakey.pl and post_snakey.pl. I run each (at the same time) in a terminal and they do all that work for me, so I can do other things, like Blog Posts. Start snakey.pl first.
Note: all this assumes the use of the test nodes suite written by Rob Fay, at Liverpool.
Part 1 – Snakey
This perl script, called snakey.pl, reads a large list, and puts a selection offline with testnodes. It drains them, and reboots them once drained. For each one that gets booted, another from the list is offlined. In this way, it "snakes" through the selected part of the cluster. Our standard buildtools+puppet+yaim system takes care of the provisioning.
Part 2 – Post Snakey
Another script, post_snakey.pl, tells if the nodes have been rebooted by snakey, and if they pass the testnodes test script. Any that do are put back on , so they come online. The scripts have some safety locks to stop havoc breaking out. They usually just stop if anything weird is seen.
Part 3 – Source Code
#!/usr/bin/perl
use strict;
use Fcntl ':flock';
use Getopt::Long;
my %offlineTimes;
while ( 1 ) {
%offlineTimes = getOfflineTimes();
my @a=keys(%offlineTimes);
my $count = $#a;
if ($count == -1 ) {
print("No work to do\n");
exit(0);
}
foreach my $n (keys(%offlineTimes)) {
my $uptime = -1;
open(B,"ssh -o ConnectTimeout=2 -o BatchMode=yes $n cat /proc/uptime 2>&1|");
while() {
if (/([0-9\.]+)\s+[0-9\.]+/) {
$uptime = $1;
}
}
close(B);
if ($uptime == -1) {
print("Refusing to remove $n because it may not have been rebooted\n");
}
else {
my $offlineTime = $offlineTimes{$n};
my $timeNow = time();
if ($timeNow - $uptime <= $offlineTime ) {
print("Refusing to remove $n. ");
printf("Last reboot - %6.3f days ago. ", $uptime / 24 / 60 /60);
printf("Offlined - %6.3f days ago.\n", ($timeNow - $offlineTime) / 24 / 60 /60);
}
else {
print("$n has been rebooted\n");
open(B,"ssh -o ConnectTimeout=2 -o BatchMode=yes $n ./testnode.sh|");
while() { }
close(B);
my $status = $? >> 8;
if ($status == 0) {
print("$n passes testnode.sh; will remove from exemptions\n");
removeFromExemptions($n);
}
else {
print("$n is not passing testnode.sh - $status\n");
}
}
}
}
sleep 567;
}
#-----------------------------------------
sub getOfflineTimes() {
my %offlineTimes = ();
open(TN,"
while() {
if (/(\S+)\s+\# snakey.pl put this offline (\d+)/) {
$offlineTimes{$1} = $2;
}
}
close(TN);
return %offlineTimes;
}
#-----------------------------------------
sub removeFromExemptions($) {
my $node = shift();
open(TN," my @lines = ;
close( TN );
open(TN,">/root/scripts/testnodes-exemptions.txt") or die("Could not open testnodes.exemptions.txt, $!\n");
flock(TN, LOCK_EX) or die "Could not lock /root/scripts/testnodes-exemptions.txt, $!";
foreach my $line ( @lines ) {
print TN $line unless ( $line =~ m/$node/ );
}
close(TN) or die "Could not write /root/scripts/testnodes-exemptions.txt, $!";
}
I'm fed up with all the book-keeping when I need to reboot or rebuild our cluster.
First I need to set a subset of nodes offline. Then I have to monitor them until some are drained. Then, as soon as any is drained, I have to reboot it by hand, then wait for it to build, then test it and finally put it back online, Then I choose another set (maybe a rack) and go through the same thing over and over until the cluster is done.
So, to cut all that, I've written a pair of perl scripts, called snakey.pl and post_snakey.pl. I run each (at the same time) in a terminal and they do all that work for me, so I can do other things, like Blog Posts. Start snakey.pl first.
Note: all this assumes the use of the test nodes suite written by Rob Fay, at Liverpool.
Part 1 – Snakey
This perl script, called snakey.pl, reads a large list, and puts a selection offline with testnodes. It drains them, and reboots them once drained. For each one that gets booted, another from the list is offlined. In this way, it "snakes" through the selected part of the cluster. Our standard buildtools+puppet+yaim system takes care of the provisioning.
Another script, post_snakey.pl, tells if the nodes have been rebooted by snakey, and if they pass the testnodes test script. Any that do are put back on , so they come online. The scripts have some safety locks to stop havoc breaking out. They usually just stop if anything weird is seen.
Part 3 – Source Code
You've seen all the nice blurb, so
here's the source code. I've had to fix it up because HTML knackers the "<", ">" and "&" chars - I hope I haven't broken it.
Note: not the cleanest code I've ever written, but it gets the job done.
Good luck!
Note: not the cleanest code I've ever written, but it gets the job done.
Good luck!
----- snakey.pl ----------------------
#!/usr/bin/perl
use strict;
use Fcntl ':flock';
use Getopt::Long;
sub initParams();
my %parameter;
initParams();
my @nodesToDo;
open(NODES,"$parameter{'NODES'}") or die("Cannot open file of nodes to reboot, $!\n");
while() {
chomp($_);
push(@nodesToDo,$_);
}
close(NODES);
checkOk(@nodesToDo);
my @selection = selectSome($parameter{'SLICE'});
foreach my $n(@selection) {
print "Putting $n offline\n";
putOffline($n);
}
while( $#selection > -1) {
my $drainedNode = '';
while($drainedNode eq '') {
sleep( 600 );
$drainedNode = checkIfOneHasDrained(@selection);
}
@selection = remove($drainedNode,@selection);
print("Rebooting $drainedNode\n");
my $status = rebootNode($drainedNode);
print("status -- $status\n");
my @nextOne = selectSome(1);
if ($#nextOne == 0) {
my $nextOne = $nextOne[0];
print "Putting $nextOne offline\n";
putOffline($nextOne);
push(@selection,$nextOne);
}
}
#-----------------------------------------
sub putOffline() {
my $node = shift();
open(TN,"/root/scripts/testnodes-exemptions.txt") or die("Could not open testnodes.exemptions.txt, $!\n");
while() {
my $l = $_;
chomp($l);
$l =~ s/#.*//;
$l =~ s/\s*//g;
if ($node =~ /^$l$/) {
print ("Node $node is already in testnodes-exemptions.txt\n");
return;
}
}
close(TN);
open(TN,">>/root/scripts/testnodes-exemptions.txt") or die("Could not open testnodes.exemptions.txt, $!\n");
flock(TN, LOCK_EX) or die "Could not lock /root/scripts/testnodes-exemptions.txt, $!";
print (TN "$node # snakey.pl put this offline " . time() . "\n");
close(TN) or die "Could not write /root/scripts/testnodes-exemptions.txt, $!";
}
#-----------------------------------------
sub remove() {
my $drained = shift();
my @poolOfNodes = @_;
my @newSelection = ();
foreach my $n (@poolOfNodes) {
if ($n !~ /$drained/) {
push(@newSelection,$n);
}
}
die("None removed\n") unless($#newSelection == ($#poolOfNodes -1));
return @newSelection;
}
#-----------------------------------------
sub checkIfOneHasDrained(@) {
my @nodesToCheck = @_;
foreach my $n (@nodesToCheck) {
my $hadReport = 0;
my $state = "";
my $jobCount = 0;
open(PBSNODES,"pbsnodes $n|");
while() {
my $l = $_;
chomp($l);
if ($l =~ /state = (.*)/) {
$state = $1;
$hadReport = 1;
}
if (/jobs = (.*)/) {
my $jobs = $1;
my @jobs = split(/,/,$jobs);
$jobCount = $#jobs + 1;
}
}
close(PBSNODES);
print("Result of check on $n: hadReport - $hadReport, state - $state, jobCount - $jobCount\n");
if (($hadReport) && ($state eq 'offline') && ($jobCount ==0)) {
return $n;
}
}
return "";
}
#-----------------------------------------
sub selectSome($) {
my $max = shift;
my @some = ();
for (my $ii = 0; $ii < $max; $ii++) {
if (defined($nodesToDo[0])) {
push(@some,shift(@nodesToDo));
}
}
return @some;
}
#-----------------------------------------
sub checkOk(){
my @nodes = @_;
foreach my $n (@nodes) {
my $actualNode = 0;
my $state = "";
open(PBSNODES,"pbsnodes $n|") or die("Could not run pbsnodes, $!\n");
while() {
if (/state = (.*)/) {
$state = $1;
$actualNode = 1;
}
}
close(PBSNODES);
if (! $actualNode) {
die("Node $n was not an actual one!\n");
}
if ($state =~ /offline/) {
die ("Node $n was already offline!\n");
}
}
return @nodes;
}
#-----------------------------------------
sub initParams() {
GetOptions ('h|help' => \$parameter{'HELP'},
'n:s' => \$parameter{'NODES'} ,
's:i' => \$parameter{'SLICE'} ,
);
if (defined($parameter{'HELP'})) {
print <
Abstract: A tool to drain and boot a bunch of nodes
-h --help Prints this help page
-n nodes File of nodes to boot
-s slice Size of slice to offline at once
TEXT
exit(0);
}
if (!defined($parameter{'SLICE'})) {
$parameter{'SLICE'} = 5;
}
if (!defined($parameter{'NODES'})) {
die("Please give a file of nodes to reboot\n");
}
if (! -s $parameter{'NODES'} ) {
die("Please give a real file of nodes to reboot\n");
}
}
#-----------------------------------------
sub rebootNode($) {
my $nodeToBoot = shift();
my $nodeToCheck = $nodeToBoot;
my $pbsnodesWorked = 0;
my $hasJobs = 0;
open(PBSNODES,"pbsnodes $nodeToCheck|");
while() {
if (/state =/) {
$pbsnodesWorked = 1;
}
if (/^\s*jobs = /) {
$hasJobs = 1;
}
}
close(PBSNODES);
if (! $pbsnodesWorked) { return 0; }
if ( $hasJobs ) { return 0; }
open(REBOOT,"ssh -o StrictHostKeyChecking=no -o BatchMode=yes -o ConnectTimeout=10 $nodeToBoot reboot|");
while() {
print;
}
return 1;
}
----- post-snakey.pl ----------------------
use strict;
use Fcntl ':flock';
use Getopt::Long;
sub initParams();
my %parameter;
initParams();
my @nodesToDo;
open(NODES,"$parameter{'NODES'}") or die("Cannot open file of nodes to reboot, $!\n");
while(
chomp($_);
push(@nodesToDo,$_);
}
close(NODES);
checkOk(@nodesToDo);
my @selection = selectSome($parameter{'SLICE'});
foreach my $n(@selection) {
print "Putting $n offline\n";
putOffline($n);
}
while( $#selection > -1) {
my $drainedNode = '';
while($drainedNode eq '') {
sleep( 600 );
$drainedNode = checkIfOneHasDrained(@selection);
}
@selection = remove($drainedNode,@selection);
print("Rebooting $drainedNode\n");
my $status = rebootNode($drainedNode);
print("status -- $status\n");
my @nextOne = selectSome(1);
if ($#nextOne == 0) {
my $nextOne = $nextOne[0];
print "Putting $nextOne offline\n";
putOffline($nextOne);
push(@selection,$nextOne);
}
}
#-----------------------------------------
sub putOffline() {
my $node = shift();
open(TN,"/root/scripts/testnodes-exemptions.txt") or die("Could not open testnodes.exemptions.txt, $!\n");
while(
my $l = $_;
chomp($l);
$l =~ s/#.*//;
$l =~ s/\s*//g;
if ($node =~ /^$l$/) {
print ("Node $node is already in testnodes-exemptions.txt\n");
return;
}
}
close(TN);
open(TN,">>/root/scripts/testnodes-exemptions.txt") or die("Could not open testnodes.exemptions.txt, $!\n");
flock(TN, LOCK_EX) or die "Could not lock /root/scripts/testnodes-exemptions.txt, $!";
print (TN "$node # snakey.pl put this offline " . time() . "\n");
close(TN) or die "Could not write /root/scripts/testnodes-exemptions.txt, $!";
}
#-----------------------------------------
sub remove() {
my $drained = shift();
my @poolOfNodes = @_;
my @newSelection = ();
foreach my $n (@poolOfNodes) {
if ($n !~ /$drained/) {
push(@newSelection,$n);
}
}
die("None removed\n") unless($#newSelection == ($#poolOfNodes -1));
return @newSelection;
}
#-----------------------------------------
sub checkIfOneHasDrained(@) {
my @nodesToCheck = @_;
foreach my $n (@nodesToCheck) {
my $hadReport = 0;
my $state = "";
my $jobCount = 0;
open(PBSNODES,"pbsnodes $n|");
while(
my $l = $_;
chomp($l);
if ($l =~ /state = (.*)/) {
$state = $1;
$hadReport = 1;
}
if (/jobs = (.*)/) {
my $jobs = $1;
my @jobs = split(/,/,$jobs);
$jobCount = $#jobs + 1;
}
}
close(PBSNODES);
print("Result of check on $n: hadReport - $hadReport, state - $state, jobCount - $jobCount\n");
if (($hadReport) && ($state eq 'offline') && ($jobCount ==0)) {
return $n;
}
}
return "";
}
#-----------------------------------------
sub selectSome($) {
my $max = shift;
my @some = ();
for (my $ii = 0; $ii < $max; $ii++) {
if (defined($nodesToDo[0])) {
push(@some,shift(@nodesToDo));
}
}
return @some;
}
#-----------------------------------------
sub checkOk(){
my @nodes = @_;
foreach my $n (@nodes) {
my $actualNode = 0;
my $state = "";
open(PBSNODES,"pbsnodes $n|") or die("Could not run pbsnodes, $!\n");
while(
if (/state = (.*)/) {
$state = $1;
$actualNode = 1;
}
}
close(PBSNODES);
if (! $actualNode) {
die("Node $n was not an actual one!\n");
}
if ($state =~ /offline/) {
die ("Node $n was already offline!\n");
}
}
return @nodes;
}
#-----------------------------------------
sub initParams() {
GetOptions ('h|help' => \$parameter{'HELP'},
'n:s' => \$parameter{'NODES'} ,
's:i' => \$parameter{'SLICE'} ,
);
if (defined($parameter{'HELP'})) {
print <
Abstract: A tool to drain and boot a bunch of nodes
-h --help Prints this help page
-n nodes File of nodes to boot
-s slice Size of slice to offline at once
TEXT
exit(0);
}
if (!defined($parameter{'SLICE'})) {
$parameter{'SLICE'} = 5;
}
if (!defined($parameter{'NODES'})) {
die("Please give a file of nodes to reboot\n");
}
if (! -s $parameter{'NODES'} ) {
die("Please give a real file of nodes to reboot\n");
}
}
#-----------------------------------------
sub rebootNode($) {
my $nodeToBoot = shift();
my $nodeToCheck = $nodeToBoot;
my $pbsnodesWorked = 0;
my $hasJobs = 0;
open(PBSNODES,"pbsnodes $nodeToCheck|");
while(
if (/state =/) {
$pbsnodesWorked = 1;
}
if (/^\s*jobs = /) {
$hasJobs = 1;
}
}
close(PBSNODES);
if (! $pbsnodesWorked) { return 0; }
if ( $hasJobs ) { return 0; }
open(REBOOT,"ssh -o StrictHostKeyChecking=no -o BatchMode=yes -o ConnectTimeout=10 $nodeToBoot reboot|");
while(
print;
}
return 1;
}
----- post-snakey.pl ----------------------
#!/usr/bin/perl
use strict;
use Fcntl ':flock';
use Getopt::Long;
my %offlineTimes;
while ( 1 ) {
%offlineTimes = getOfflineTimes();
my @a=keys(%offlineTimes);
my $count = $#a;
if ($count == -1 ) {
print("No work to do\n");
exit(0);
}
foreach my $n (keys(%offlineTimes)) {
my $uptime = -1;
open(B,"ssh -o ConnectTimeout=2 -o BatchMode=yes $n cat /proc/uptime 2>&1|");
while() {
if (/([0-9\.]+)\s+[0-9\.]+/) {
$uptime = $1;
}
}
close(B);
if ($uptime == -1) {
print("Refusing to remove $n because it may not have been rebooted\n");
}
else {
my $offlineTime = $offlineTimes{$n};
my $timeNow = time();
if ($timeNow - $uptime <= $offlineTime ) {
print("Refusing to remove $n. ");
printf("Last reboot - %6.3f days ago. ", $uptime / 24 / 60 /60);
printf("Offlined - %6.3f days ago.\n", ($timeNow - $offlineTime) / 24 / 60 /60);
}
else {
print("$n has been rebooted\n");
open(B,"ssh -o ConnectTimeout=2 -o BatchMode=yes $n ./testnode.sh|");
while() { }
close(B);
my $status = $? >> 8;
if ($status == 0) {
print("$n passes testnode.sh; will remove from exemptions\n");
removeFromExemptions($n);
}
else {
print("$n is not passing testnode.sh - $status\n");
}
}
}
}
sleep 567;
}
#-----------------------------------------
sub getOfflineTimes() {
my %offlineTimes = ();
open(TN,"
if (/(\S+)\s+\# snakey.pl put this offline (\d+)/) {
$offlineTimes{$1} = $2;
}
}
close(TN);
return %offlineTimes;
}
#-----------------------------------------
sub removeFromExemptions($) {
my $node = shift();
open(TN,"
close( TN );
open(TN,">/root/scripts/testnodes-exemptions.txt") or die("Could not open testnodes.exemptions.txt, $!\n");
flock(TN, LOCK_EX) or die "Could not lock /root/scripts/testnodes-exemptions.txt, $!";
foreach my $line ( @lines ) {
print TN $line unless ( $line =~ m/$node/ );
}
close(TN) or die "Could not write /root/scripts/testnodes-exemptions.txt, $!";
}
Tuesday, 15 April 2014
Kernel Problems at Liverpool
Introduction
Liverpool recently updated its cluster to SL6. In doing so, a problem occurred whereby the kernel would experience lockups during normal operations. The signs are unresponsiveness, drop-outs in Ganglia and (later) many "task...blocked for 120 seconds" msgs in /var/log/m.. and dmesg.Description
Kernels in the range 2.6.32-431* exhibited a type of deadlock when run on certain hardware with BIOS dated after 8th March 2010.This problem occured on Supermicto hardware, main boards:
- X8DTT-H
- X9DRT
Notes:
1) No hardware with BIOS dated 8th March 2010 or before showed this defect, even on the same board type.
2) The oldest kernel of the 2.6.32-358 range is solid. This is corroborated by operational experience with the 358 range.
3) All current kernels in the 2.6.32-431 range exhibited the problem on our newest hardware, and a few nodes of the older hardware that had had unusual BIOS updates.
Testing
The lock-ups are hard to reproduce, but after a great deal of trail and error, a ~ 90% effective predictor was found.The procedure is to:
- Build the system completely new in the usual way and
- When yaim gets to "config_user", use a script (stress.sh) to run 36 threads of gzip and one of iozone.
On a susceptible node, this is reasonably certain to make it lock up after a minute. The signs are unresponsiveness and (later) "task...blocked for 120 seconds" msgs in /var/log/m.. and dmesg.
I observed that if the procedure is not followed "exactly", it is unreliable as a predictor. In particular, if you stop Yaim and try again, the predictor is useless.
To test that, I isolated the config_users script from Yaim, and ran it separately along with the stress.sh script. Result: useless - no lock-ups were seen.
Note: This result was rather unexpected because the isolated config_users.sh script works in the same way as the original.
Unsuccessful Theories
A great many theories were tested and rejected or not pursued further (APIC problems, disk problems, BIOS differences,various kernels, examination of kernel logs, much googling etc. etc.) Eventually, a seemingly successful theory was stumbled upon which I describe below.The Successful Theory
All our nodes had unusual vm settings:# grep dirty /etc/sysctl.conf
vm.dirty_background_ratio = 100
vm.dirty_expire_centisecs = 1800000
vm.dirty_ratio = 100
These custom settings facilitate the storage of atlas "short files" in RAM. Basically, they force files to remain off disk for a long time, allowing very fast access.
The modification had been tested almost exhaustively for several years on earlier kernels - but perhaps some change (or latent bug?) in the kernel had invalidated them somehow.
We came up with the idea that the issue originates in the memory operations that occur prior to Yaim/config_users. This would explain why anything but the exact activity created by the procedure might well not trigger the defect. We thought this could tally with the idea of the ATLAS "short file" modifications in sysctl.conf. The theory is that these mods set up the problem during the memory/read/write operations (i.e. the asynchronous OS loading and flushing of the page cache).
To test this, I used the predictor on susceptible nodes , but without applying the ATLAS "short file" patch. Default vm settings were adopted instead.
Result
Very satisfying at last - absolutely no sign on the defect. As the ATLAS "short file" patch is not very beneficial given the current data traffic, we have decided to go back to default "vm.dirty" settings and monitor the situation carefully.Wednesday, 26 February 2014
Central Argus Banning at Liverpool
Introduction
Liverpool uses an ARGUS server, hepgrid9.ph.liv.ac.uk, for user authentication from the CEs and WNs. A requirement came down from above to implement central banning and this is how we went about it. Most of this came from Ewan's TB_SUPPORT email (title: NGI Argus requests for NGI_UK) and from this description here:http://wiki.nikhef.nl/grid/Argus_Global_Banning_Setup_Overview
Central Banning Architecture
The ban policies flow from the central WLCG server through the NGI one and down to the site. This is a feature of ARGUS.
Setup at Liverpool
When we build (or change) our ARGUS server, we use a script (argus.pol.sh) to load our argus policies from a file (argus.pol). The script looks like this now we've added central banning:
#!/bin/bash
/usr/bin/pap-admin rap
/usr/bin/pap-admin apf /root/scripts/argus.pol
pap-admin add-pap ngi argusngi.gridpp.rl.ac.uk "/C=UK/O=eScience/OU=CLRC/L=RAL/CN=argusngi.gridpp.rl.ac.uk"
pap-admin enable-pap ngi
pap-admin set-paps-order ngi default
pap-admin set-polling-interval 3600
/etc/init.d/argus-pdp reloadpolicy
/etc/init.d/argus-pepd clearcache
touch /root/scripts/done_argus.pol.sh
The first few lines just load our standard site policies. The last bit flushes some buffers. The middle bit is the part you need.
Basically, it adds polices from the NGI ARGUS server. We've also reduced the polling interval. When you run the script, you'll connect the local ARGUS server to the NGI one and periodically download the remote (central) banning policies.
Note: Ewan thinks the caching delay is too much - it was 4 hours. So we changed /etc/argus/pdp/pdp.ini, setting "retentionInterval = 21", i.e. 21 minutes.
After running the script, it's best to restart the Java daemons.
Testing
It's best to tell Ewan and Orlin about this as they can send tests over. To check if your site "looks" OK, try this:pap-admin lp --all
And you should see the "remote" policies, e.g.
ngi (argusngi.gridpp.rl.ac.uk:8150):
resource ".*" BLAH BLAH BLAH
Friday, 3 May 2013
A thing of beauty Digital R81
We needed to make space for a couple of new racks and decided to get rid of our 'workbench'. The workbench consisted of an old Digital VAX system which was mostly stripped of it's innards to leave a few sturdy steel frames. Here are some nostalgic pics of the last remaining unit being gutted. Note the gorgeous circuit boards so easily accessible. And yes, that last one is a 500MB harddrive (so I'm told). The motor seems more suited to a washing machine. They don't make 'em like they used to.










Wednesday, 27 February 2013
Wednesday, 20 February 2013
Monday, 24 September 2012
Manchester network improvements in Graphs
As I posted here and here we have upgraded the network infrastructure within the Manchester Tier2. Below are some of the measured benefits of this upgrade so far.
Here is the improvement of the outgoing traffic in the atlas sonar tests between Manchester and BNL after we upgraded the cisco blades and replaced the rack switches with the 10G ones
Here instead is the throughput improvement after I have enabled the 10Gbps interface on the perfsonar machine. The test case is Oxford which also has the 10Gbps interfaces enabled.
and here more general rates with different sites. The 10Gbs is evident with sites that have enabled it.
The perfsonar tests have helped also to debug the poor atlas FTS rates the UK had with FZK (https://ggus.eu/ws/ticket_info.php?ticket=84008) in particular Manchester (and Glasgow) had tried already to investigate last year with iperf within atlas what the problem was without much success due to measures not being taken systematically. This year the problem was finally pinned on FZK firewall and the improvement given by bypassing it is below here.
which reflects also in the improved rates in the atlas sonar tests between Manchester and FZK since also the data servers subnets bypass the firewall now.
Finally here is a increased throughput in data distribution to/from other sites as an atlas T2D. August rates were down due to a combination of problems with the storage but there is a growing trend since the rack switches and the cisco blades were upgraded.
Here is the improvement of the outgoing traffic in the atlas sonar tests between Manchester and BNL after we upgraded the cisco blades and replaced the rack switches with the 10G ones
Here instead is the throughput improvement after I have enabled the 10Gbps interface on the perfsonar machine. The test case is Oxford which also has the 10Gbps interfaces enabled.
and here more general rates with different sites. The 10Gbs is evident with sites that have enabled it.
The perfsonar tests have helped also to debug the poor atlas FTS rates the UK had with FZK (https://ggus.eu/ws/ticket_info.php?ticket=84008) in particular Manchester (and Glasgow) had tried already to investigate last year with iperf within atlas what the problem was without much success due to measures not being taken systematically. This year the problem was finally pinned on FZK firewall and the improvement given by bypassing it is below here.
which reflects also in the improved rates in the atlas sonar tests between Manchester and FZK since also the data servers subnets bypass the firewall now.
Finally here is a increased throughput in data distribution to/from other sites as an atlas T2D. August rates were down due to a combination of problems with the storage but there is a growing trend since the rack switches and the cisco blades were upgraded.
Thursday, 9 August 2012
10GBE Network cards installation in Manchester
This is a collection of recipes I used to install the 10GBE cards. As I said in a previous post we chose to go 10GBASE-T so we bought X520-T2. They use the same chipset as the X520-DA2 so many things are in common.
The new DELL R610 and C6100 were delivered with the cards already installed. Although due to the fact that DA2 and T2 share the same chipset the C6100 were delivered with the wrong connectors so we are now waiting for a replacement. For the old Viglen WNs and storage we bought additional cards that have to be inserted one by one.
I started the installation process from the R610 because a) they had the cards and b) the perfsonar machines are R610. The aim is to use these cards as primaries and kickstart from them. By default pxe booting is not enabled. So one has to get bootutil from the intel site . What one downloads is for some reason a windows executable but once it is unpacked there are directories for other operating systems. The easiest thing to do is what Andrew has done to zip the unpacked directory and use bootutil from the machine without fussing around with USBs or boot disks. Said that it needs the kernel source to compile. You need to make sure you install the same version as the running kernel.
yum install kernel-devel(-running-kernel-version)
unzip APPS.zip
cd APPS/BootUtils/Linux_x86/
chmod 755 ./install
./install
./bootutil64e -BOOTENABLE=pxe -ALL
./bootutil64e -UP=Combo -FILE=../BootIMG.FLB -ALL
The first bootutil command enables pxe the second updates the firmware.
After this you can reboot and enter the bios to rearrange the order of the network devices to boot from. When this is done you can put the 10GBE interface mac address in the dhcp and reinstall from there.
At kickstart time there are some problems with the machine changing the order of the cards you can solve that using ipappend 2 and ksdevice=bootif as suggested in the RH docs in the pxelinux.cfg files. Thanks to Ewan for pointing that out.
Still the machine might not come back up with the interface working. There might be two problems here:
1) X520-T2 interface take longer to wake up than their little 1GBE sisters. It is necessary to insert a delay after the /sbin/ip command in the network scripts. To do this I didn't have to hack anything, I could just set
LINKDELAY=10
in the ifcfg-eth* configuration files and it worked.
2) It is not guarantueed to have the 10GBE interface as eth0. There are many ways to stop this from happening.
One is to make sure HWADRR if ifcfg-eth0 is assigned the mac address value of the card the administrator want and not what the system decides. It can be done at kickstart time but this might mean to have a kickstart file for each machine which we are trying to get away from.
Dan and Chris suggested this might be corrected with udev The recipe they gave me was this
cat /etc/udev/rules.d/70-persistent-net.rules
KERNEL=="eth*", ID=="0000:01:00.0", NAME="eth0"
KERNEL=="eth*", ID=="0000:01:00.1", NAME="eth1"
KERNEL=="eth*", ID=="0000:04:00.0", NAME="eth2"
KERNEL=="eth*", ID=="0000:04:00.1", NAME="eth3"
and uses the pci device ID value which is the same for the same machine types (R610, C6100...). You can get the ID values using lspci | grep Eth. Not essential but if lspci returns something like Unknown device 151c (rev01) in the description it is just the pci database that is not up to date use update-pciid to update the database. There are other recipes around if you don't like this one, but this simplifies a lot the maintenance of the interfaces naming scheme.
The udev recipe doesn't work if HWADDR are set in the ifcfg-eth* files. If they are you need to remove them to make udev work. A quick way to do this in every file is
sed -i -r '/^HWADDR.*$/d' ifcfg-eth*
in the post kickstart and then install the udev file.
10GBE cards might need different TCP tuning in /etc/sysctl.conf for now I took the perfsonar machine one which is similar to something already discussed long time ago.
net.core.rmem_max = 33554432
net.core.wmem_max = 33554432
net.ipv4.tcp_rmem = 4096 87380 16777216
net.ipv4.tcp_wmem = 4096 87380 16777216
net.core.netdev_max_backlog = 30000
net.ipv4.tcp_no_metrics_save = 1
net.ipv4.tcp_congestion_control = htcp
The effects of moving to 10GBE can be seen very well in the perfsonar tests.
The new DELL R610 and C6100 were delivered with the cards already installed. Although due to the fact that DA2 and T2 share the same chipset the C6100 were delivered with the wrong connectors so we are now waiting for a replacement. For the old Viglen WNs and storage we bought additional cards that have to be inserted one by one.
I started the installation process from the R610 because a) they had the cards and b) the perfsonar machines are R610. The aim is to use these cards as primaries and kickstart from them. By default pxe booting is not enabled. So one has to get bootutil from the intel site . What one downloads is for some reason a windows executable but once it is unpacked there are directories for other operating systems. The easiest thing to do is what Andrew has done to zip the unpacked directory and use bootutil from the machine without fussing around with USBs or boot disks. Said that it needs the kernel source to compile. You need to make sure you install the same version as the running kernel.
yum install kernel-devel(-running-kernel-version)
unzip APPS.zip
cd APPS/BootUtils/Linux_x86/
chmod 755 ./install
./install
./bootutil64e -BOOTENABLE=pxe -ALL
./bootutil64e -UP=Combo -FILE=../BootIMG.FLB -ALL
The first bootutil command enables pxe the second updates the firmware.
After this you can reboot and enter the bios to rearrange the order of the network devices to boot from. When this is done you can put the 10GBE interface mac address in the dhcp and reinstall from there.
At kickstart time there are some problems with the machine changing the order of the cards you can solve that using ipappend 2 and ksdevice=bootif as suggested in the RH docs in the pxelinux.cfg files. Thanks to Ewan for pointing that out.
Still the machine might not come back up with the interface working. There might be two problems here:
1) X520-T2 interface take longer to wake up than their little 1GBE sisters. It is necessary to insert a delay after the /sbin/ip command in the network scripts. To do this I didn't have to hack anything, I could just set
LINKDELAY=10
in the ifcfg-eth* configuration files and it worked.
2) It is not guarantueed to have the 10GBE interface as eth0. There are many ways to stop this from happening.
One is to make sure HWADRR if ifcfg-eth0 is assigned the mac address value of the card the administrator want and not what the system decides. It can be done at kickstart time but this might mean to have a kickstart file for each machine which we are trying to get away from.
Dan and Chris suggested this might be corrected with udev The recipe they gave me was this
cat /etc/udev/rules.d/70-persistent-net.rules
KERNEL=="eth*", ID=="0000:01:00.0", NAME="eth0"
KERNEL=="eth*", ID=="0000:01:00.1", NAME="eth1"
KERNEL=="eth*", ID=="0000:04:00.0", NAME="eth2"
KERNEL=="eth*", ID=="0000:04:00.1", NAME="eth3"
and uses the pci device ID value which is the same for the same machine types (R610, C6100...). You can get the ID values using lspci | grep Eth. Not essential but if lspci returns something like Unknown device 151c (rev01) in the description it is just the pci database that is not up to date use update-pciid to update the database. There are other recipes around if you don't like this one, but this simplifies a lot the maintenance of the interfaces naming scheme.
The udev recipe doesn't work if HWADDR are set in the ifcfg-eth* files. If they are you need to remove them to make udev work. A quick way to do this in every file is
sed -i -r '/^HWADDR.*$/d' ifcfg-eth*
in the post kickstart and then install the udev file.
10GBE cards might need different TCP tuning in /etc/sysctl.conf for now I took the perfsonar machine one which is similar to something already discussed long time ago.
net.core.rmem_max = 33554432
net.core.wmem_max = 33554432
net.ipv4.tcp_rmem = 4096 87380 16777216
net.ipv4.tcp_wmem = 4096 87380 16777216
net.core.netdev_max_backlog = 30000
net.ipv4.tcp_no_metrics_save = 1
net.ipv4.tcp_congestion_control = htcp
The effects of moving to 10GBE can be seen very well in the perfsonar tests.
Friday, 20 July 2012
Jobs with memory leaks containment
This week some sites suffered from extreme memory hungry jobs using
up to 16GB of memory and killing the nodes. These were most likely
due to memory leaks. The user cancelled all of them before he was
even contacted but not before he created some annoyance.
We have had some discussion about how to fix this and atlas so far has asked not to limit on memory because their jobs use for brief periods of time more than what is officially requested. And this is true most of their jobs do this infact. According to the logs the production jobs use up to ~3.5GB mem and slightly less than 5GB vmem. See plot below for one random day (other days are similar).
To avoid killing everything but still putting a barrier against the
memory leaks what I'm going to do in Manchester is to limit for mem to 4GB and a limit for vmem to 5GB.
If you are worried about memory leaks you might want to go through a similar check. If you are not monitoring your memory consumption on a per job basis you can parse your logs. For PBS I used this command to produce the plot above
grep atlprd /var/spool/pbs/server_priv/accounting/20120716| awk '{ print $17, $19, $20}'| grep status=0|cut -f3,4 -d'='| sed 's/resources_used.vmem=//'|sort -n|sed 's/kb//g'
numbers are already sorted in numerical order so the last one is the highest (mem,vmem) a job has used that day. atlprd is the atlas production group which you can replace with other groups. Atlas users jobs have up to a point similar usage and then every day you might find a handful crazy numbers like 85GB vmem and 40GB mem. These are the jobs we aim at killing.
I thought the batch system was simplest way because it is only two commands in PBS but after lot of reading and a week of testing it is not possible to over allocate memory without affecting the scheduling and ending up with less jobs on the nodes. This is what I found out:
There are various memory parameters that can be set in PBS:
(p)vmem: virtual memory. PBS doesn't interpret vmem as the almost unlimited address space. If you set this value it will interpret it for scheduling purposes as memory+swap available. It might be different with later versions but that's what happens in torque 2.3.6.
(p)mem: physical memory: that's you RAM.
when there is a p in front it means per process rather than per job
If you set them what happens is as follows:
ALL: if a job arrives without memory settings the batch system will assign these limits as allocated memory for the job not only as a limit the job doesn't have to exceed.
ALL: if a job arrives with memory resources settings that exceed the limits it will be rejected.
(p)vmem,pmem: if a job exceeds the settings at run time it will be killed as these parameters set limits at OS level.
mem: if a job exceeds this limit at run time it will not get killed. This is due to a change in the libraries apparently.
To check how the different parameters affect the jobs you can submit directly to pbs this csh command and play with the parameters
echo 'csh -c limit' | qsub -l vmem=5000000kb,pmem=1GB,mem=2GB,nodes=1:ppn=2
If you want to set these parameters you have to do the following
qmgr
qmgr: set queue long resources_max.vmem = 5gb
qmgr: set queue long resources_max.mem = 4gb
qmgr: set queue long resources_max.pmem = 4gb
These settings will affect the whole queue so if you are worried about other VOs you might want to check what sort of memory usage they have. Although I think only CMS might have a similar usage. I know for sure Lhcb uses less. And as said above this will affect the scheduling.
Update 02/08/2012
RAL and Nikhef use a maui parameter to correct the the over allocation problem
NODEMEMOVERCOMMITFACTOR 1.5
this will cause maui to allocate up to 1.5 times more memory than there is on the nodes. So if a machine has 2GB memory a 1.5 factor allows to allocate 3GB. Same with other memory parameters described above. The factor can of course be tailored to your site.
On the atlas side there is a memory parameter that can be set in panda. It sets a ulimit on vmem on a per process basis in the panda wrapper. It didn't seem to have an effect on the memory seen by the batch system but that might be because forked processes are double counted by PBS which opens a whole different can of worms.
We have had some discussion about how to fix this and atlas so far has asked not to limit on memory because their jobs use for brief periods of time more than what is officially requested. And this is true most of their jobs do this infact. According to the logs the production jobs use up to ~3.5GB mem and slightly less than 5GB vmem. See plot below for one random day (other days are similar).
To avoid killing everything but still putting a barrier against the
memory leaks what I'm going to do in Manchester is to limit for mem to 4GB and a limit for vmem to 5GB. If you are worried about memory leaks you might want to go through a similar check. If you are not monitoring your memory consumption on a per job basis you can parse your logs. For PBS I used this command to produce the plot above
grep atlprd /var/spool/pbs/server_priv/accounting/20120716| awk '{ print $17, $19, $20}'| grep status=0|cut -f3,4 -d'='| sed 's/resources_used.vmem=//'|sort -n|sed 's/kb//g'
numbers are already sorted in numerical order so the last one is the highest (mem,vmem) a job has used that day. atlprd is the atlas production group which you can replace with other groups. Atlas users jobs have up to a point similar usage and then every day you might find a handful crazy numbers like 85GB vmem and 40GB mem. These are the jobs we aim at killing.
I thought the batch system was simplest way because it is only two commands in PBS but after lot of reading and a week of testing it is not possible to over allocate memory without affecting the scheduling and ending up with less jobs on the nodes. This is what I found out:
There are various memory parameters that can be set in PBS:
(p)vmem: virtual memory. PBS doesn't interpret vmem as the almost unlimited address space. If you set this value it will interpret it for scheduling purposes as memory+swap available. It might be different with later versions but that's what happens in torque 2.3.6.
(p)mem: physical memory: that's you RAM.
when there is a p in front it means per process rather than per job
ALL: if a job arrives without memory settings the batch system will assign these limits as allocated memory for the job not only as a limit the job doesn't have to exceed.
ALL: if a job arrives with memory resources settings that exceed the limits it will be rejected.
(p)vmem,pmem: if a job exceeds the settings at run time it will be killed as these parameters set limits at OS level.
mem: if a job exceeds this limit at run time it will not get killed. This is due to a change in the libraries apparently.
To check how the different parameters affect the jobs you can submit directly to pbs this csh command and play with the parameters
echo 'csh -c limit' | qsub -l vmem=5000000kb,pmem=1GB,mem=2GB,nodes=1:ppn=2
If you want to set these parameters you have to do the following
qmgr
qmgr: set queue long resources_max.vmem = 5gb
qmgr: set queue long resources_max.mem = 4gb
qmgr: set queue long resources_max.pmem = 4gb
These settings will affect the whole queue so if you are worried about other VOs you might want to check what sort of memory usage they have. Although I think only CMS might have a similar usage. I know for sure Lhcb uses less. And as said above this will affect the scheduling.
Update 02/08/2012
RAL and Nikhef use a maui parameter to correct the the over allocation problem
NODEMEMOVERCOMMITFACTOR 1.5
this will cause maui to allocate up to 1.5 times more memory than there is on the nodes. So if a machine has 2GB memory a 1.5 factor allows to allocate 3GB. Same with other memory parameters described above. The factor can of course be tailored to your site.
On the atlas side there is a memory parameter that can be set in panda. It sets a ulimit on vmem on a per process basis in the panda wrapper. It didn't seem to have an effect on the memory seen by the batch system but that might be because forked processes are double counted by PBS which opens a whole different can of worms.
Thursday, 5 April 2012
The Big Upgrade in pictures
| New Cisco blades, engines and power supplies |
| DELLs boxes among which new switches |
| Aerial view of the old cabling |
| Frontal view of the mess |
| Cables unplugged from the cisco |
| Cisco old blades with services racks still connected |
| New cat6a cisco cabling aerial view nice and tidy |
| Frontal view of the new cisco blades and cabling nice and tidy |
| Old and new rack switches front view |
| Old and new rack switches rear view |
| Emptying and reorganising the racks |
| Empty racks ready to be filled with new machines |
| Old DELLs cemetery |
The downtime lasted 6 days. Everybody who was involved did a great job and the choice of 10GBASE-T was a good one because the ports auto-negotiation is allowing us to run at 3 different speeds on the same switches: PDU 100Mbps, old WN and storage at 1Gbps, and the connection with the cisco is 10Gbps. We also kept one of the old cisco blades for connections that don't require 10Gbps such as the out-of-band management cables plus two racks of servers that will be upgraded at a later stage are still connected at 1Gbps to the cisco. And we finished perfectly in time for the start of data taking (and Easter). :)
Labels:
infrastructure,
Manchester,
network,
upgrade
Saturday, 31 March 2012
So long and thanks for all the fish
In 2010 we had already decommissioned half of the original mythical 2000 (1800 for us) EM64T CPUs Dell cluster that allowed us to be the 4th of the top 10 countries in EGEE in 2007.
This year we are decommissioning the last 430 machines that served us so well for 6 years and 2 months. So... so long and thanks for all the fish.
Labels:
decomissioning,
dell,
machines,
Manchester,
poweredge,
upgrade
Saturday, 14 January 2012
DPM database file systems synchronization
The synchronisation of the DPM database with the data servers file systems has been a long standing issue. Last week we had a crash that made more imperative to check all the files and I eventually wrote a bash script that makes use of the GridPP DPM admin tools. I don't think this should be the final version but I'm quicker with bash than with python and therefore I started with that. Hopefully later in the year I'll have more time to write a cleaner version in python that can be inserted in the admin tools based on this one. It does the following:
1) Create a list of files that are in the DB but not on disk
2) Create a list of files that are on disk but not in the DB
3) Create a list of SURLs from the list of files in the DB but not on disk to declare lost (this is mostly for atlas but could be used by LFC administrators for other VOs)
4) If not in dry run mode proceed to delete the orphan files and the orphan entries in the DB.
5) Print stats of how many files were in either list.
Although I put few protections this script should be run with care and unless in dry run mode shouldn't be run automatically AT ALL. However in dry run mode it will tell you how many files are lost and it is a good metric to monitor regularly as well as when there is a big crash.
If you want to run it, it has to run on the data servers where there is access to the file system. As it is now it requires a modified version of /opt/lcg/etc/DPMINFO that point to the head node rather than localhost because one of the admin tools used does a direct mysql query. For the same reason it also requires dpminfo user to have mysql select privileges from the data servers. This is the part that really could benefit from a rewriting in python and perhaps a proper API use as the other tool does. I also had to heavily parse the output of the tools which weren't created exactly for this purpose and this could also be avoided in a python script. There are no options but all the variables that could be options to customize the script with your local settings (head node, fs mount point, dry_run) are easily found at the top.
To create the lists it takes really little time no more than 3 minutes on my system but it depends mostly on how busy is your head node.
If you want to do a cleanup instead it is proportional to how many files have been lost and can take several hours since it does one DB operation per file. The time to delete the orphan files also depends on how many and how big they are but should take less than DB cleanup.
The script is here: http://www.sysadmin.hep.ac.uk/svn/fabric-management/dpm/dpm-synchronise-disk-db.sh
1) Create a list of files that are in the DB but not on disk
2) Create a list of files that are on disk but not in the DB
3) Create a list of SURLs from the list of files in the DB but not on disk to declare lost (this is mostly for atlas but could be used by LFC administrators for other VOs)
4) If not in dry run mode proceed to delete the orphan files and the orphan entries in the DB.
5) Print stats of how many files were in either list.
Although I put few protections this script should be run with care and unless in dry run mode shouldn't be run automatically AT ALL. However in dry run mode it will tell you how many files are lost and it is a good metric to monitor regularly as well as when there is a big crash.
If you want to run it, it has to run on the data servers where there is access to the file system. As it is now it requires a modified version of /opt/lcg/etc/DPMINFO that point to the head node rather than localhost because one of the admin tools used does a direct mysql query. For the same reason it also requires dpminfo user to have mysql select privileges from the data servers. This is the part that really could benefit from a rewriting in python and perhaps a proper API use as the other tool does. I also had to heavily parse the output of the tools which weren't created exactly for this purpose and this could also be avoided in a python script. There are no options but all the variables that could be options to customize the script with your local settings (head node, fs mount point, dry_run) are easily found at the top.
To create the lists it takes really little time no more than 3 minutes on my system but it depends mostly on how busy is your head node.
If you want to do a cleanup instead it is proportional to how many files have been lost and can take several hours since it does one DB operation per file. The time to delete the orphan files also depends on how many and how big they are but should take less than DB cleanup.
The script is here: http://www.sysadmin.hep.ac.uk/svn/fabric-management/dpm/dpm-synchronise-disk-db.sh
Labels:
database,
dpm,
file,
Manchester,
optimization,
syncronisation,
system
Wednesday, 30 November 2011
DPM upgrade 1.7.4 -> 1.8.2 (glite 3.2)
Last week I upgraded our DPM installation. It was a major change because I upgraded not only the DPM version but also the hardware and the backend mysql version.
I didn't take any measures this time before and after. I knew that becoming an alpha site in atlas was taking its toll on the old hardware and many of the timeouts were from gridftp but there had been a reappearance of the mysql ones I talked about in previous posts at the level that even restarting the service was hard.
[ ~]# service mysqld restart
Timeout error occurred trying to stop MySQL Daemon.
Stopping MySQL: [FAILED]
Timeout error occurred trying to start MySQL Daemon.
So I decided that the situation had become unsustainable and it was time to move to better hardware and software versions.
* Hardware: 2 cpu, 4GB mem, 2x250 GB raid1 -> 4 cores (HT on = 8 job slots), 24GB mem, 2x2TB raid1
There is no why here it was ok when we had limited access but the recent load was really too much for the old machine even with all the tuning. Suspected bad blocks on disks could be possible but no red leds nor hardware errors were reported by the machine.
* Mysql: 5.0.77 -> 5.5.10
Why mysql 5.5? Because InnoDB is the default engine and they have improved performance and instrumentation. On top of other things that we might actually start to use. A good blog article about the 5 reasons to move is this one: 5 good reasons to upgrade to mysql 5.5.
MySQL 5.5 is not in EPEL yet, but I found this CentOS community site that has the rpms and the instructions to install them.
After the installation I've also optimized the database partially with what I had already done in July, partly running a handy script mysqltuner.pl. This last one helps with variable you might not even know and even if you know them it tells you if they are too small. You need to be patient and let pass few hours before run it again.
* DPM: 1.7.4 -> 1.8.2
Why DPM 1.8.2 from glite 3.2? I would have gone for the UMD release or even the EMI one but then glite 3.2 was moved to production earlier than those and since I waited for this release since at least April I didn't think about it twice when I saw the escape route. It was really good timing too as it happened when I really couldn't postpone an upgrade anymore. You can find more info in the release notes. Among other reasons to upgrade: srmv2.2 in 1.7.4 has a memory leak which wasn't noticeable until the load was contained but for us exploded in October and is the reason I had to restart it every two days in the past few weeks.
Below the steps I took to reinstall the head node
On the old head node
* Set the site in downtime, drain the queues and kill all the remaining jobs.
* Turn off all the dpm and bdii services on the old head node
* Make a dump of the current database for backup
mysqldump -C -Q -u root -p -B dpm_db cns_db > dpm.sql-20111125.gz
* Download dpm-drop-requests-tables.sql supplied by Jean Philippe last July
wget http://www.sysadmin.hep.ac.uk/svn/fabric-management/dpm/dpm-drop-requests-tables.sql
* Drop the requests tables. This step is really useful to avoid painful reload times as I said in this other post about DPM optimization and because it drastically reduces the size of ibdata1 when you reload which has also benefits (my ibdata1 was reduced from 26GB to 1.7GB). Still you need to plan because it might take few hours depending on the system. On my old hardware it took around 7 hours.
mysql -p < dpm-drop-requests-tables.sql
* Dump reduced version of the database
mysqldump -C -Q -u root -p -B dpm_db cns_db > dpm.sql-20111125-v2.gz
* Copy both to a WEB server where they can be downloaded from in a later stage.
* Update the local repository for DPM head node and DPM disk servers. Since it is still glite I just had to rsync the latest mirror to the static area.
On the new head node
* Install the new machines with a DPM head node profile. This was again easy since it is still glite no changes were required in cfengine.
* Most of the following is not standard and I put it in a script. If you have problems with users IDs created by avahi packages you can uninstall them with yum removing all the dependencies and let them be reinstalled by the bdii dependency chain. It should work also uninstalling them with rpm -e --nodeps. This leaves redhat-lsb (which is what the bdii depends on) untouched but I haven't tried this last method. Here are the commands I executed:
# Get the dpm DB file
rm -rf dpm.sql-20111125-v2.gz*
wget http://ks.tier2.hep.manchester.ac.uk/T2/tmp/dpm.sql-20111125-v2.gz
# Install mysql5.5 rpm -Uvh http://repo.webtatic.com/yum/centos/5/latest.rpm
yum -y remove libmysqlclient5 mysql mysql-*
yum -y clean all
yum -y install mysql55 mysql55-server libmysqlclient5 --enablerepo=webtatic
service mysql stop
rm -rf /var/lib/mysql/*
# Get the local my.cnf
cfagent -vq
service mysqld start
# Install the DPM rpmsyum -y remove cups avahi avahi-compat-libdns_sd avahi-glib
yum -y install glite-SE_dpm_mysql lcg-CA
# Modify sql scripts for mysql5.5
cd
/opt/lcg/share/DPM/ for a in create_dp*.sql; do sed -i.old 's/TYPE/ENGINE/g' $a;done
grep ENGINE *
# Run YAIM and upload old DB
cd
/opt/glite/yaim/bin/yaim -c -s /opt/glite/yaim/etc/site-info.def -n glite-SE_dpm_mysql
mysql -u root -p -C < /root/dpm.sql-20111125-v2.gz
# NECESSARY FOR THE FINAL UPDATES
/opt/glite/yaim/bin/yaim -c -s /opt/glite/yaim/etc/site-info.def -n glite-SE_dpm_mysql
* You will need to install the dpm-contrib-admintool rm because it is not in the glite repository it might be in the EMI one. Last time I heard it made it to ETICS. If you can't find it there's still the sysadmin repo version and related notes on the GridPP wiki (Sam or Wahid welcome to leave an update on this one).
* To upgrade the disk servers I just updated the repository, upgraded the rpms and rerun yaim.
I didn't take any measures this time before and after. I knew that becoming an alpha site in atlas was taking its toll on the old hardware and many of the timeouts were from gridftp but there had been a reappearance of the mysql ones I talked about in previous posts at the level that even restarting the service was hard.
[ ~]# service mysqld restart
Timeout error occurred trying to stop MySQL Daemon.
Stopping MySQL: [FAILED]
Timeout error occurred trying to start MySQL Daemon.
So I decided that the situation had become unsustainable and it was time to move to better hardware and software versions.
* Hardware: 2 cpu, 4GB mem, 2x250 GB raid1 -> 4 cores (HT on = 8 job slots), 24GB mem, 2x2TB raid1
There is no why here it was ok when we had limited access but the recent load was really too much for the old machine even with all the tuning. Suspected bad blocks on disks could be possible but no red leds nor hardware errors were reported by the machine.
* Mysql: 5.0.77 -> 5.5.10
Why mysql 5.5? Because InnoDB is the default engine and they have improved performance and instrumentation. On top of other things that we might actually start to use. A good blog article about the 5 reasons to move is this one: 5 good reasons to upgrade to mysql 5.5.
MySQL 5.5 is not in EPEL yet, but I found this CentOS community site that has the rpms and the instructions to install them.
After the installation I've also optimized the database partially with what I had already done in July, partly running a handy script mysqltuner.pl. This last one helps with variable you might not even know and even if you know them it tells you if they are too small. You need to be patient and let pass few hours before run it again.
* DPM: 1.7.4 -> 1.8.2
Why DPM 1.8.2 from glite 3.2? I would have gone for the UMD release or even the EMI one but then glite 3.2 was moved to production earlier than those and since I waited for this release since at least April I didn't think about it twice when I saw the escape route. It was really good timing too as it happened when I really couldn't postpone an upgrade anymore. You can find more info in the release notes. Among other reasons to upgrade: srmv2.2 in 1.7.4 has a memory leak which wasn't noticeable until the load was contained but for us exploded in October and is the reason I had to restart it every two days in the past few weeks.
Below the steps I took to reinstall the head node
On the old head node
* Set the site in downtime, drain the queues and kill all the remaining jobs.
* Turn off all the dpm and bdii services on the old head node
* Make a dump of the current database for backup
mysqldump -C -Q -u root -p -B dpm_db cns_db > dpm.sql-20111125.gz
* Download dpm-drop-requests-tables.sql supplied by Jean Philippe last July
wget http://www.sysadmin.hep.ac.uk/svn/fabric-management/dpm/dpm-drop-requests-tables.sql
* Drop the requests tables. This step is really useful to avoid painful reload times as I said in this other post about DPM optimization and because it drastically reduces the size of ibdata1 when you reload which has also benefits (my ibdata1 was reduced from 26GB to 1.7GB). Still you need to plan because it might take few hours depending on the system. On my old hardware it took around 7 hours.
mysql -p < dpm-drop-requests-tables.sql
* Dump reduced version of the database
mysqldump -C -Q -u root -p -B dpm_db cns_db > dpm.sql-20111125-v2.gz
* Copy both to a WEB server where they can be downloaded from in a later stage.
* Update the local repository for DPM head node and DPM disk servers. Since it is still glite I just had to rsync the latest mirror to the static area.
On the new head node
* Install the new machines with a DPM head node profile. This was again easy since it is still glite no changes were required in cfengine.
* Most of the following is not standard and I put it in a script. If you have problems with users IDs created by avahi packages you can uninstall them with yum removing all the dependencies and let them be reinstalled by the bdii dependency chain. It should work also uninstalling them with rpm -e --nodeps. This leaves redhat-lsb (which is what the bdii depends on) untouched but I haven't tried this last method. Here are the commands I executed:
# Get the dpm DB file
rm -rf dpm.sql-20111125-v2.gz*
wget http://ks.tier2.hep.manchester.ac.uk/T2/tmp/dpm.sql-20111125-v2.gz
# Install mysql5.5 rpm -Uvh http://repo.webtatic.com/yum/centos/5/latest.rpm
yum -y remove libmysqlclient5 mysql mysql-*
yum -y clean all
yum -y install mysql55 mysql55-server libmysqlclient5 --enablerepo=webtatic
service mysql stop
rm -rf /var/lib/mysql/*
# Get the local my.cnf
cfagent -vq
service mysqld start
# Install the DPM rpmsyum -y remove cups avahi avahi-compat-libdns_sd avahi-glib
yum -y install glite-SE_dpm_mysql lcg-CA
# Modify sql scripts for mysql5.5
cd
/opt/lcg/share/DPM/ for a in create_dp*.sql; do sed -i.old 's/TYPE/ENGINE/g' $a;done
grep ENGINE *
# Run YAIM and upload old DB
cd
/opt/glite/yaim/bin/yaim -c -s /opt/glite/yaim/etc/site-info.def -n glite-SE_dpm_mysql
mysql -u root -p -C < /root/dpm.sql-20111125-v2.gz
# NECESSARY FOR THE FINAL UPDATES
/opt/glite/yaim/bin/yaim -c -s /opt/glite/yaim/etc/site-info.def -n glite-SE_dpm_mysql
* You will need to install the dpm-contrib-admintool rm because it is not in the glite repository it might be in the EMI one. Last time I heard it made it to ETICS. If you can't find it there's still the sysadmin repo version and related notes on the GridPP wiki (Sam or Wahid welcome to leave an update on this one).
* To upgrade the disk servers I just updated the repository, upgraded the rpms and rerun yaim.
Wednesday, 28 September 2011
Friday, 9 September 2011
cvmfs upgrade to 2.0.3
Last week I upgraded the cvmfs on all the WN to cvmfs-2.0.3. The upgrade for us required two steps.
1) change of repository: since Manchester was the first to use the new atlas setup we were pointing to CERN repository. The new setup has now become standard so I just had to remove the override variable CVMFS_SERVER_URL from atlas.cern.ch.local. The file is distributed by cfengine so I just changed it in cvs.
2) rpms upgrade: I had some initial difficulties because I was following the instructions for atlas T3 - which normally work also for T2 - that suggested to install cvmfs-auto-setup rpm. This rpm runs service cvmfs restartautofs and in the instructions it was suggested also to rerun it manually. This on busy machines causes the repositories to disappear and requires a service cvmfs restartclean which wipes the cache off and is not really recommended in production. In reality none of this is really necessary and a simple
yum -y update cvmfs cvmfs-init-scripts
is sufficient. I could add the rpms version in cfengine and that was enough. The change from one version to another happens at the first unmount. Forcing this with a restartautofs is counterproductive (thanks to Ian for pointing this out).
Next week there should be a bug fix version that will take care of slow mount and some slow client tools routines on busy machines.
http://savannah.cern.ch/bugs/?86349
But since the upgrade procedure is so easy and the corrupted files problem
http://savannah.cern.ch/support/?122564
is fixed in cvmfs >2.0.2 I decided to upgrade anyway on Wednesday to avoid further errors in atlas and possibly lhcb.
NOTE: Of course I tested each step on few nodes to check everything worked before rolling out with cfengine on all nodes. Always a good practice not to follow recipes blindly!
1) change of repository: since Manchester was the first to use the new atlas setup we were pointing to CERN repository. The new setup has now become standard so I just had to remove the override variable CVMFS_SERVER_URL from atlas.cern.ch.local. The file is distributed by cfengine so I just changed it in cvs.
2) rpms upgrade: I had some initial difficulties because I was following the instructions for atlas T3 - which normally work also for T2 - that suggested to install cvmfs-auto-setup rpm. This rpm runs service cvmfs restartautofs and in the instructions it was suggested also to rerun it manually. This on busy machines causes the repositories to disappear and requires a service cvmfs restartclean which wipes the cache off and is not really recommended in production. In reality none of this is really necessary and a simple
yum -y update cvmfs cvmfs-init-scripts
is sufficient. I could add the rpms version in cfengine and that was enough. The change from one version to another happens at the first unmount. Forcing this with a restartautofs is counterproductive (thanks to Ian for pointing this out).
Next week there should be a bug fix version that will take care of slow mount and some slow client tools routines on busy machines.
http://savannah.cern.ch/bugs/?86349
But since the upgrade procedure is so easy and the corrupted files problem
http://savannah.cern.ch/support/?122564
is fixed in cvmfs >2.0.2 I decided to upgrade anyway on Wednesday to avoid further errors in atlas and possibly lhcb.
NOTE: Of course I tested each step on few nodes to check everything worked before rolling out with cfengine on all nodes. Always a good practice not to follow recipes blindly!
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