VMware Virtual Machine (atlas-vm)

WARNING: This page is obsolete.

June 2010: Support for this product is phased out in favor of CernVM. If you need it, please contact us.

See a movie of atlas-vm and what it can do : click on this URL.

Important Note:

• We encourage users to use CernVM which has nicer features. atlas-VM continues to be supported since we are using them for testing software on Scientific Linux.

atlas-vm is a VMware virtual machine (VM) that contains only the basics to run the ATLAS software. There are no graphics/productivity tools or KDE; only Gnome, compilers, etc ... that is, the essentials.

There is also a new virtual machine CernVM which you may also want to look into. This is a real light weight machine and has many nice features. (Please use the support channels in the CernVM link if you have questions / problems.) The rest of this page details the atlas-vm virtual machine which is supported by ATLAS Canada.

Summary of available versions

Unless otherwise indicated, the VMs listed below are

• System: Scientific Linux - i686 (not SLC), with afs, gnome desktop ,development tools, legacy tools and miscellaneous items on an LVM partition, and have (or will install after download)
• ATLASLocalRootBase
• ManageTier3SW
• gLite
• Pacman
• PandaClient
• DQ2Client
• Ganga
• ROOT

installed on them (versions can be easily updated, please read on.) The Athena Kit installed on them may differ as shown in this table (these different versions are for user's convenience; you can install your preferred Athena version in any of these VMs).

(atlasvm versions prior to 2.00 have been phased out - 18 Jan 2010.)

Installation Instructions

You first need to download the free VMware Player or VMware Server or for Mac users, purchase VMware Fusion. (You may need the latest versions if you have an old VMware product installed; see the atlas-vm configuration details in the sections below.)

Note that, if using Player or Server, you need version 2.x or newer; also you cannot install the player if the server is already installed on your computer.

Windows users: installing the VM requires you to use "ftp" (NOT "sftp", so Putty won't work...) and "gtar"; if you have Cygwin installed, this is a convenient way to get those commands. If anyone knows of an easier way, we'd love to hear about it!

The VM image is available from ATLAS Canada's ftp server:

ftp ftp.atlas-canada.ca  # login as anonymous
cd vm
cd 3.00 # or the version you want
get atlasvm-3.00-md5sum=e6c63e4b0be76824e9ffb041a6326c221.tar.gz  # for example

There is an md5 checksum appended to the filename; check this after downloading, unpack and delete the tarball.

md5sum atlasvm-3.00-md5sum=e6c63e4b0be76824e9ffb041a6326c221.tar.gz
gtar zxf atlasvm-3.00-md5sum=e6c63e4b0be76824e9ffb041a6326c221.tar.gz
rm atlasvm-3.00-md5sum=e6c63e4b0be76824e9ffb041a6326c221.tar.gz

Then start the VM (click on the .vmx file to launch the VMware Player/Server on Linux/Windows or on the VM icon to launch Fusion on a Mac) and let it boot. If it asks if the VM is moved or copied, say it was copied. Also, if it says the network configuration is incorrect, you can let it reconfigure for you or do it in the next step.

Initial Setup - root

There are 2 accounts already setup - root and atlasadmin - and both have expired passwords "changeme". You will be asked to change the passwords as soon as you login.

Login as root and open a new terminal window. Run the following commands to fix the network, update the software and to create your user account.

# do not reboot until after the account is created
fixNetwork.sh
# once network is up, update the software from the ATLAS Canada CVS repository
atlas-vmUpdate.sh
# next create your own user account
createMyAccount.sh

If the network still fails, delete and recreate your network using the UI before doing the next steps.

If you are near TRIUMF, you may want to use that proxy server instead of CERN's for /opt/atlas. This can be easily done by editing /etc/rc.d/rc.local and changing the line /root/bin/mountAtlasCvmfs-CERN.sh to /root/bin/mountAtlasCvmfs-TRIUMF.sh. (You can also switch between the two proxy servers by running either one of the two scripts.)

Next reboot, you should not need to login as root again.

You can run atlas-vmUpdate.sh periodically to fix problems which have been diagnosed and resolved by ATLAS Canada User Support. However, do not make this a cron job !

Initial Setup - atlasadmin

Login as atlasadmin (you will be asked to change your password) and do

atlasLocalRootBaseUpdate.sh

This will take approximately 40 minutes when run for the first time while it installs gLite, Ganga, pandaClient, ROOT, etc. atlasvm 3.00 will grow in size by about 1.3 GB after these software are installed.

You can do this periodically (eg. a cron job) to update software; you are recommended to do this daily or at least weekly. Software, as tested by user support, on this page will be automatically installed whenever you run the above script.

logout.

Initial Setup - user

Login to your user account which you created earlier. The password should be "changeme" which you will be asked to change.

Next,

• create the keys for password-less ssh access to the CERN CVS repository; instructions are here. (There is already a file ~/.ssh/config in your new account.)
• copy your grid certificates to ~/.globus

The system is now ready for use. You can also ssh into the atlasvm from another machine; to get the IP address, type
/sbin/ifconfig eth0 | grep "inet addr"
(If you are running in a NAT [default], you can ssh in from your host machine; however if you change atlasvm to run in a bridge mode - ie. your ISP will provide an IP address - you can login from anywhere.)

If you checkout software from the CERN CVS repository and get kerberos timeout errors, you may want to use the CVS ssh passwordless access instead. You can change this in your ~/cmthome/requirements file (just uncomment the relevant lines). From atlas-vm 1.03 and newer, you can source ~/cmthome/setup.sh -tag=<...>,sshcvs instead.

Also, if you type setupATLAS, you will see a menu of how to run the installed software.

...Type localSetupDQ2Client to use DQ2 Client
...Type localSetupGanga to use Ganga
...Type localSetupGLite to use GLite
...Type localSetupPacman to use Pacman
...Type localSetupPandaClient to use Panda Client
...Type localSetupROOT to setup (standalone) ROOT
...Type saveSnapshot [--help] to save your settings
...Type showVersions to show versions of installed software
...Type createRequirements [--help] to create requirements/setup files

You can create your requirements file as follows: createRequirements --kitDir=Kits_SL4-i686 if Athena kits were installed. Note that if you use the proxy-server, you should just source the setup script in /opt/atlas/software for the appropriate release - you should not create a requirements file. Do not run createRequirements on /opt/atlas. (You may find it slow the first time you use /opt/atlas; this is because files are downloaded and cached so subsequent use will be faster. Also, we are considering setting up nearer servers so that speeds will increase.)

Note that PATHENA_GRID_SETUP_SH will be already defined in your environment when you setup PandaClient; you should not have to set this before running Panda (pathena) jobs.

If you are not a Canadian user, you may want to change the following line in ~/.gangarc (create by $ATLAS_LOCAL_ROOT_BASE/user/generateGangarc.sh --voms=atlas:/atlas/ca) :

  init_opts = -voms atlas:/atlas/ca
    to 
  init_opts = -voms atlas

Hardware configuration and what is installed

The VM was created on a Mac using VMware Fusion. You may need to download the latest version of VMware Player/Server/Fusion to use this, please see the VMware site.

The software installed are described above and were installed as described in this link. Note that these are in the directories /atlas/ATLASLocalRootBase and there are _README files explaining how they were installed.

In addition,

• The VM has also been tested to be ATLAS-ready.
• There is a /data/<user> space for user datafiles.

The VM disks are all logical volumes (LVM) to accommodate expansion. Since the VM disks are sparse images (the host machine's disk usage increases only by the amount used by the VM), some of them have been defined to be huge physical volumes (in case they are used on a desktop). However, only a fraction of them are used in the logical volumes. The usage is summarized below for atlasvm 2.00:

# which filesystems are available and current disk usage
[root@atlas-vm ~]# df -h
Filesystem            Size  Used Avail Use% Mounted on
/dev/mapper/VolGroup00-LogVol00
                      7.7G  2.7G  4.7G  37% /
/dev/sda1              99M   20M   74M  22% /boot
none                  252M     0  252M   0% /dev/shm
/dev/mapper/VG--home-home
                      9.9G  350M  9.1G   4% /home
/dev/mapper/VG--atlas-atlas
                       30G   77M   28G   1% /atlas
/dev/mapper/VG--data-data
                       20G   77M   19G   1% /data
/dev/mapper/VG--scratch-scratch
                      9.9G   56M  9.3G   1% /scratch
.host:/                17T   17T     0 100% /mnt/hgfs
AFS                   8.6G     0  8.6G   0% /afs

# which logical volumes are available
[root@atlas-vm ~]# lvscan
  ACTIVE            '/dev/VG-scratch/scratch' [10.00 GB] inherit
  ACTIVE            '/dev/VG-data/data' [20.00 GB] inherit
  ACTIVE            '/dev/VG-atlas/atlas' [30.00 GB] inherit
  ACTIVE            '/dev/VG-home/home' [10.00 GB] inherit
  ACTIVE            '/dev/VolGroup00/LogVol00' [7.81 GB] inherit
  ACTIVE            '/dev/VolGroup00/LogVol01' [1.97 GB] inherit

# which physical volumes are available and how much of them have been allocated or are free)
[root@atlas-vm ~]# pvscan
  PV /dev/sde1   VG VG-scratch   lvm2 [499.99 GB / 489.99 GB free]
  PV /dev/sdd1   VG VG-data      lvm2 [499.99 GB / 479.99 GB free]
  PV /dev/sdc1   VG VG-atlas     lvm2 [499.99 GB / 469.99 GB free]
  PV /dev/sdb1   VG VG-home      lvm2 [499.99 GB / 489.99 GB free]
  PV /dev/sda2   VG VolGroup00   lvm2 [11.88 GB / 2.09 GB free]
  Total: 5 [1.96 TB] / in use: 5 [1.96 TB] / in no VG: 0 [0   ]

When you need to increase the partition size, you can do something like the following example (assuming your host machine has enough space!)

# example, to expand /atlas by 20G ... 
lvextend -L +20G /dev/VG-atlas/atlas
 ext2online /dev/VG-atlas/atlas

Note also that, if you can afford it, you should increase the physical memory used by the VM.

Updating

You should be able to install or update any software by following the instructions for the ManageTier3SW package; login as atlasadmin and type the appropriate commands as detailed in the ManageTier3SW page.

You can also install/remove any Athena base release kit, Tier0 or Production cache with the instructions listed on the ManageTier3SW page. Do check first that you have enough disk space on the VM (caches are a ~O(200 MB) while base releases are ~O(7 GB)). It will take approximately 1 hour to download and install a base release kit.

There is also a script to automate installations (login as atlasadmin and run atlasLocalRootBaseUpdate.sh); this will install only these up-to-date software packages which have been tested by ATLAS Canada User Support. You can run this as a cron job if you wish and you are recommended to do this at least weekly, if not daily.

Tips and Tricks

• TRIUMF users: please see this link for using the ATLAS software mounts at TRIUMF.
• VMware Fusion (Macintosh OS X) tips.
• VMware Player - (Linux, Windows) - To gain access to file systems on the host machine, configure NFS, increase memory, etc. More information is here.
• VMFolder Share between your VM and host.
• Stripping atlasvm

Trouble-shooting

Installation of VMware software

This is beyond the scope of this Twiki page but there are excellent resources available on the VMware site. Note in particular the VMware Communities, for example, for Desktop Products which is searchable.

Expired crl when voms-proxy-init

If your voms-proxy-init fails with messages about expired CRLs:

globus_gsi_callback_module: Invalid CRL: The available CRL has expired

then

• for atlasvm 1.xx:
  login as root and run
  /opt/glite/libexec/fetch-crl.sh
• for atlasvm 2.xx:
  login as atlasadmin and run
  $ATLAS_LOCAL_ROOT_BASE/utilities/fetchCRL.sh

Normally this runs as a cron job every 6 hours but, with a laptop, it may not had an opportunity to run (although anacron is installed and configured to run this after 65 minutes of starting up the VM.)

Full screen mode

If your VM does not look right when using in the full screen mode, login as root and type /usr/bin/vmware-config-tools.pl. You may need to reboot next.

/opt/atlas is empty

Login as root and run mountAtlasCvmfs-CERN.sh (or mountAtlasCvmfs-<nearest server>.sh, if available). This will unmount and mount the partition.

/opt/atlas/software/setup*.sh gives errors

Login as root and run mountAtlasCvmfs-CERN.sh (or mountAtlasCvmfs-<nearest server>.sh, if available). This will unmount and mount the partition and refresh the cache.

Kerberos authentication takes a long time to complete

Login as root and run atlas-vmUpdate.sh.

Java issues (eg. needed for Atlantis)

Java is not installed by default in atlasvm; it is easy for users to install - please login as root and type yum install java-1.6.0.

Contact

To report problems or bugs, you can contact atlas-user-support@triumf.ca or post in the Canadian e-Groups forum.

-- AsokaDeSilva - 16 May 2008