INF-110

GPFS Installation
 Overview
• Plan the installation
Before installing any software, it is important to plan the GPFS installation by choosing
the hardware, deciding which kind of disk connectivity to use (direct attached or
network attached disks), selecting the network capabilities (which depends a lot on
the disk connectivity), and, maybe the most important, verifying that your
application can take advantage of GPFS.

• Install the packages

At this point, the GPFS architecture has been defined and the machines have Linux
installed . It is time now to install the packages on all the nodes that will be part of
the GPFS cluster.

• Create the GPFS cluster

Once the GPFS packages are installed on the nodes, you need to create the GPFS
cluster. To create the GPFS cluster, we need a file that contains all of the node host
names or IP addresses. Then we have to use the mmcrcluster command to
create the cluster. This command will create cluster data information on all nodes
chosen to be part of the GPFS cluster. In case a new node needs to be added to an
already existing GPFS cluster, the mmaddcluster command can be used.

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 Overview (continued)
• Start GPFS
After the nodeset is created, you should start it before defining the disk. Use the
mmstartup command to start the GPFS daemons.

• Disk definition
All disks used by GPFS in a nodeset have to be described in a file, and then this file
has to be passed to the mmcrnsd command. This command gives a name to each
described disk and ensures that all the nodes included in the nodeset are able to
gain access to the disks with their new name.

• Creating the file system

Once the cluster, the nodeset(s), and the disks have been defined, then it is time to
create the file system. With GPFS, the mmcrfs command is used for that purpose.
There are many options that can be activated at this time, like file system auto-
mounting, file system block size, data or metadata replication, and so on.

• Mounting the file system

At last, you have to mount the file system after it is being created. Once the file system
had been mounted, it can be used by the nodes for read and write operations. If
you set auto-mounting option, your GPFS file system will be automatically mounted
when the nodes reboot.

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 Setup GPFS Environments
• Add a path to the GPFS binary directory to your $PATH environment
in all nodes. Type:
mkdir -p /cfmroot/etc/profile.d

• Create /cfmroot/etc/profile.d/mmfs.sh, which contains:

PATH=$PATH:/usr/lpp/mmfs/bin
MANPATH=$MANPATH:/usr/lpp/mmfs/man

• Type:
chmod 755 /cfmroot/etc/profile.d/mmfs.sh
cfmupdatenode -a
cp /cfmroot/etc/profile.d/mmfs.sh /etc/profile.d
. /etc/profile.d/mmfs.sh

• This way, you will distribute /etc/profile.d/mmfs.sh to all

nodes, including its attributes.

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 Install GPFS
• The GPFS install and update files are located on the management
node in the /lab/gpfs directory.

• Extract updates.
mkdir -p /tmp/gpfs/updates
cp –r /lab/gpfs/* /tmp/gpfs
cd /tmp/gpfs/updates
tar zxvf *update.tar.gz

• Install GPFS and updates on management node.

cd /tmp/gpfs;rpm -ivh gpfs*rpm
cd /tmp/gpfs/updates;rpm -Uvh gpfs*rpm

• Copy packages on compute nodes.

dsh -a mkdir –p /tmp/gpfs/updates
cd /tmp/gpfs
dcp -a *rpm /tmp/gpfs
dcp –a updates/*rpm /tmp/gpfs/updates

• Install GPFS on compute nodes.

dsh -a 'cd /tmp/gpfs;rpm -ivh gpfs*rpm‘

• Install GPFS updates.

dsh -a 'cd /tmp/gpfs/updates;rpm -Uvh gpfs*rpm‘
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 Prepare kernel
• Since GPFS code works at the kernel level (as kernel extensions), it
highly depends on the kernel level to run properly. Therefore, you
have to build your GPFS open source portability module before
building a GPFS cluster, and a kernel source file is required for that.
You may check the list of kernel versions that may be supported at the
following site:

• http://www-1.ibm.com/servers/eserver/clusters/software/gpfs_faq.html

• Lab Note: There are a few patches that should be applied. Read the
FAQ in the future. In this Lab we will not be apply the patches to save
time.

• Create Link to kernel source

cd /usr/src
ln –s linux-2.4 linux

• Clean up tree
cd /usr/src/linux
make mrproper

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 Prepare kernel (continued)
• Check the content of the VERSION, PATCHLEVEL, SUBLEVEL, and
EXTRAVERSION variables in the /usr/src/linux/Makefile file
to match the release version of your kernel.

uname -r to check your version, e.g. 2.4.21-27.ELsmp

• Edit Makefile

VERSION = 2
PATCHLEVEL = 4
SUBLEVEL = 21
EXTRAVERSION = -27.ELsmp

• Copy kernel configuration file

cp configs/kernel-2.4.21-i686-smp.config .config

• Type:
make oldconfig
make dep

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 Build the GPFS open source portability layer
• You have to build the GPFS open source portability layer manually on one
node (in our case, the management node), then copy them through all nodes.

• Below are the steps to build GPFS open source portability layer. Also, check
the /usr/lpp/mmfs/src/README file for more up to date information on
building the GPFS Open Source portability layer:

export SHARKCLONEROOT=/usr/lpp/mmfs/src
cd /usr/lpp/mmfs/src/config
cp site.mcr.proto site.mcr

Edit the /usr/lpp/mmfs/src/config/site.mcr file. There are some sections that need to be
checked (bold):

• /* $Id: site.mcr.proto,v 1.442.2.5 2004/06/07 15:45:28 gjertsen Exp $ */

• ........
• /* Linux distribution (select/uncomment only one) */
• /* LINUX_DISTRIBUTION = REDHAT_LINUX */
• LINUX_DISTRIBUTION = REDHAT_AS_LINUX
• ........
• /* #define LINUX_DISTRIBUTION_LEVEL 80 */
• ........
• /* Linux kernel versions supported for each architecture */
• #define LINUX_KERNEL_VERSION 2042127

cd ..
make World
make InstallImages
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 Distribute the GPFS portability layer
• Copy the above binaries to the /cfmroot/usr/lpp/mmfs/bin
directory and distribute them to all nodes using the cfmupdatenode
command or your own scripts :

mkdir -p /cfmroot/usr/lpp/mmfs/bin
cd /usr/lpp/mmfs/bin
cp mmfslinux lxtrace tracedev dumpconv /cfmroot/usr/lpp/mmfs/bin
cfmupdatenode -a

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 Creating the GPFS nodes descriptor file
• ssh to node1. All GPFS commands should be run from nodes that will be
running GPFS. The management node will NOT be running GPFS.

ssh node1

• When creating your GPFS cluster, you need to provide a file containing a list of
node descriptors, one per line for each node to be included in the cluster,
including the storage nodes. Each descriptor must be specified in the form:

NodeName:NodeDesignations

• where:

NodeName The host name or IP address of

the node for GPFS daemon to
daemon communication.

NodeDesignations An optional, - separated list of

node roles. Roles include:

manager|client
quorum|nonquorum
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 Creating the GPFS nodes descriptor file
• Create a file /tmp/gpfs.allnodes with a list of your nodes and
their roles. Ensure there is at least one node with quorum and
manager roles defined. For example:

node1:manager-quorum
node2:manager-quorum
Node3:quorum
node4:

• The above file signifies that we have four nodes in our GPFS cluster.

Node1 has configuration manager and quorum roles.

Node2 has configuration manager and quorum roles.
Node3 has the quorum role.
Node4 is using the defaults of non-quorum and client roles.

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 Defining the GPFS cluster
• Run the mmcrcluster command to define the GPFS cluster.

• Defined your node1 as the primary, node2 as the secondary (for GPFS data),
ssh as remote shell command and scp as remote file copy commands.

• For example:
mmcrcluster -p node1 -s node2 -n /tmp/gpfs.allnodes -r /usr/bin/ssh -R
/usr/bin/scp

Tue Aug 10 14:00:46 CDT 2004: mmcrcluster: Processing node

node1.cluster.net
Tue Aug 10 14:00:48 CDT 2004: mmcrcluster: Processing node
node2.cluster.net
Tue Aug 10 14:00:49 CDT 2004: mmcrcluster: Processing node
node3.cluster.net
Tue Aug 10 14:00:50 CDT 2004: mmcrcluster: Processing node
node4.cluster.net
Tue Aug 10 14:00:55 CDT 2004: mmcrcluster: Initializing needed RSCT
subsystems.
mmcrcluster: Command successfully completed

• After creating the cluster definitions, you can see the definitions using the
mmlscluster command. Type:
mmlscluster
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 Starting GPFS
• After creating the GPFS cluster, you can start the GPFS services on
every node in the cluster by issuing the mmstartup command with
the -a parameter. The -a parameter will start GPFS on all nodes in the
cluster.

• Type:

mmstartup –a

Note: To shutdown GPFS type: mmshutdown -a (do not type it now)

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 Prepare Disks (Skip)
• For Fiber disks, create arrays, LUNs, and mappings
• Use CSM and GPFS Redbook as a guide
• Use GPFS documentation
• Use DS4xxx (FAStT) documentation
• Lab Note: We were unable to obtain DS4xxx controllers and disk.
• For each disk to be used for GPFS on each node use fdisk to remove
any partitions. NOTE: We will be using disk /dev/hdc in nodes1-
nodes4.

For Example:

ssh node1
fdisk /dev/hdc

Use ? for a list of commands to display and remove partitions.

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 Disk definitions
• A GPFS cluster with NSD network attached servers means that all
access to the disks and replication will be through one or two storage
attached servers (also known as storage node). If your cluster has an
internal network segment, this segment will be used for this purpose.

• If a disk is defined with one storage attached server only, and the
server fails, the disks would become unavailable to GPFS. If the disk
is defined with two NSD network attached servers, then GPFS
automatically transfers the I/O requests to the backup server.

• Lab Note: We were unable to provide Fiber storage. You will be

unable to define two paths to the storage.

• Lab Note: The four nodes in your cluster (e.g. node1 - node4) each
contain a single 40GB drive (/dev/hdc). You will use this as your
GPFS storage.

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 Creating Network Shared Disks (NSDs)
• You will need to create a descriptor file before creating your NSDs.
This file should contain information about each disk that will be a NSD,
and should have the following syntax:

DeviceName:PrimaryNSDServer:SecondaryNSDServer:DiskUsage:FailureGroup

DeviceName The real device name of the external storage partition (such as /dev/hdc).

PrimaryServer The host name of the server that the disk is attached to; Remember you must
always use the node names defined in the cluster definitions.

SecondaryServer The server where the secondary disk attachment is connected.

DiskUsage The kind of information should be stored in this disk. The valid values
are data, metadata, and dataAndMetadata (default).
FailureGroup An integer value (0 to 4000) that identifies the failure group to which this disk
belongs. All disks with a common point of failure must belong to the same
failure group. The value -1 indicates that the disk has no common point of failure
with any other disk in the file system. GPFS uses the failure group information
to assure that no two replicas of data or metadata are placed in the same group
and thereby become unavailable due to a single failure. When this field is not
specified, GPFS assigns a failure group (higher than 4000) automatically to
each disk.
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 Creating Network Shared Disks (NSDs)
• Create a new file /tmp/descfile

E.g.

/dev/hdc:node1::dataAndMetadata:-1
/dev/hdc:node2::dataAndMetadata:-1
/dev/hdc:node3::dataAndMetadata:-1
/dev/hdc:node4::dataAndMetadata:-1

• Now create the Network Shared Disks by using the mmcrnsd

command:
mmcrnsd -F /tmp/descfile -v no

• After successfully creating the NSD for GPFS cluster, mmcrnsd will
comment the original disk device and put the GPFS assigned global
name for that disk device at the following line. cat /tmp/descfile to see
the changes.
cat /tmp/descfile

• You can see the new device names by using the mmlsnsd command.
mmlsnsd

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 Creating the GPFS file system
• Once you have your NSDs ready, you can create the GPFS file
system. In order to create the file system, you will use the mmcrfs
command, where you must define the following attributes in this order:
– The mount point.
– The name of the device for the file system.
– The descriptor file (-F).

• Type:
mmcrfs /gpfs1 /dev/gpfs1 -F /tmp/descfile -A yes -B 256K -n 4 -v no

• Validate with mmlsdisk

mmlsdisk gpfs1

• Mount filesystems, exit node1 and type from the mgmt1 node:
dsh -a mount –a

• Validate with df. You should have a single 156GB filesystem spanning
4 disks in 4 nodes available to all nodes.
dsh -a df

• Please review the CSM and GPFS Redbook and GPFS

documentation for a list of administrative functions.

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 Removing GPFS (Skip)
• Often it is desired to completely remove GPFS and start over. The
most common cause is SSH and DNS setup issues that cause
distributed GPFS commands to fail. Cleanup can be difficult.

• Remove GPFS from management node.

rpm -e gpfs.base gpfs.docs gpfs.gpl gpfs.msg.en_US

rm -rf /var/mmfs

• Remove GPFS from all nodes.

dsh -a ‘rpm -e gpfs.base gpfs.docs gpfs.gpl gpfs.msg.en_US’

dsh -a rm -rf /var/mmfs

• Do not remove any SRC or RSCT components.

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 Authentication
• HPC clusters require a global authentication solution
enabling all nodes view all users with the same properties.

• Many authentication solutions exist. The most common

are:
– NIS
– LDAP
– File synchronization

• File synchronization is most popular with HPC clusters

and is the most scalable solution for very large clusters. It
is also easy to setup.

• Create a cluster use on your management node:

useradd (username), For example:

useradd bob

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 Authentication (continued)
• Backup existing /etc/passwd and /etc/group files first. If for any
reason /etc/passwd gets corrupted you will be unable to login even
as root. A reboot to single user mode will be required to recover the
backup.
dsh -a cp /etc/passwd /etc/passwd.SAVE
dsh -a cp /etc/group /etc/group.SAVE

• Push the /etc/passwd and /etc/group files to all nodes

• Verify
dsh -a grep (username) /etc/passwd, For example:
dsh -a grep bob /etc/passwd (check the output)

• Each time a new user is added, a node is added, or a node is

reinstalled run cfmupdatenode -a again.

• Generate SSH keys for each cluster user. (root is NOT a cluster
user). rsh clusters may need to create a .rhosts file per user.

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 File Systems
• Like authentication, HPC clusters also require a global file system solution
enabling all nodes to view the same files with the same properties.

• There are many solutions available. The most common are:

NFS
GPFS

GPFS is usually not required for user, application, and library directories. GPFS is
best suited for data directories.

• In this LAB we will create 2 global name spaces.

NFS: /home for user application
NFS: /usr/local for system applications and libraries.

• To setup NFS you must first export the /home and /usr/local file systems
from your management node. Append the follow lines to your
/etc/exports file:

/home *(rw,no_root_squash,sync)
/usr/local *(rw,no_root_squash,sync)

• Restart NFS.
service nfs restart
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 File Systems (continued)
• Verify
dsh -a ls -l /home | grep (user name you added, e.g. bob)

For example:
dsh -a ls -l /home | grep bob

• This verification checks that both the file systems and authentication
are working properly. Your dsh output should have listed the
/home/username directory for your cluster user AND the user should
have owned the directory, e.g.

node1: drwx------ 5 bob bob 4096 Mar 24 05:01 bob

node2: drwx------ 5 bob bob 4096 Mar 24 05:01 bob
node3: drwx------ 5 bob bob 4096 Mar 24 05:01 bob
node4: drwx------ 5 bob bob 4096 Mar 24 05:01 bob

• Also verify the /usr/local was mounted.

dsh -a df | grep /usr/local

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 MPICH-IP
• MPICH is a freely available, portable implementation of MPI, the Standard for
message-passing libraries the runs over IP.

• MPICH URL http://www-unix.mcs.anl.gov/mpi/mpich

• Install MPICH for GNU compiler.

mkdir –p /tmp/mpi
cp /lab/hpc/mpich*tar.gz /tmp/mpi
cp /lab/hpc/mpimaker /tmp/mpi
export MPICHROOT=/usr/local/mpich
cd /tmp/mpi
./mpimaker mpich-1.2.7 up gnu ssh

• A successful build should return:

mpimaker: 1.2.5.2 up gnu ssh build start
mpimaker: 1.2.5.2 up gnu ssh make
mpimaker: 1.2.5.2 up gnu ssh build successful

MPICH installed in /usr/local/mpich/1.2.5.2/ip/up/gnu/ssh

• Please check config.cmd make.log install.log configure.log in

/usr/local/mpich/1.2.5.2/ip/up/gnu/ssh for errors. config.cmd
was the command used to build MPICH

• If the build failed check the files config.cmd make.log install.log

24 configure.log in /tmp/hpc/mpich-1.2.5.2.
 mpiiotest
• mpiiotest is a simple utility to test parallel file systems

• su to the the user you created earlier

su – (user name you added, e.g. bob) For example:

su – bob

• Copy the mpiiotest to the user’s home directory

mkdir ~/bench/
cp /lab/hpc/mpiiotest.tgz ~/bench/
cd ~/bench/
tar zxvf mpiiotest.gz

• Build mpiiotest
export MPICH=/usr/local/mpich/1.2.7/ip/i686/up/gnu/ssh
export PATH=$MPICH/bin:$PATH
cd ~/bench/
make clean
make

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 mpiiotest (continued)
• Setup the users environment:
ssh node1
cd ~/bench
export MPICH=/usr/local/mpich/1.2.7/ip/i686/up/gnu/ssh
export PATH=$MPICH/bin:$PATH

• Create a file "machinefile" with 1 entries per node, e.g.:

node1
node2
node3
node4

• Open another xterm on your workstation machine as root and type:

xhost +

• Type the following as root on your management node:

dsh -a chmod 777 /gpfs1

• Type on one line:

mpirun -machinefile machinefile -np 4 mpiiotest --filename /gpfs1/test
--filesize 10240 --blocksize 64 --display mgmt1:0 -g 1000x30

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 mpiiotest (continued)
• First mpiiotest creates the file in parallel. Each red band represents the status
of the current process write progress. When the bar is red the file has been
written.

• Next mpiiotest reads the created file. Each blue band represents the status of
the current process read progress. When the bar is blue the file has been red.

• Exit back to the mgmt1 node.

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 mpiiotest (continued)
• The performance of any filesystem is affected by the blocksize used
by that filesystem vs the blocksize that the application is using. Since
the GPFS filesystem was setup with a 256K blocksize, the optimal
blocksize for this test should be 256K. Test this by trying a couple of
different blocksizes, recording the total read and write performance for
each run.

• Type on one line:

mpirun -machinefile machinefile -np 4 mpiiotest --filename
/gpfs1/test --filesize 10240 --blocksize 128 --display
mgmt1:0 -g 1000x30

mpirun -machinefile machinefile -np 4 mpiiotest --filename

/gpfs1/test --filesize 10240 --blocksize 256 --display
mgmt1:0 -g 1000x30

mpirun -machinefile machinefile -np 4 mpiiotest --filename

/gpfs1/test --filesize 10240 --blocksize 512 --display
mgmt1:0 -g 1000x30

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 Modify GPFS Block Size
• If time permits modify the blocksize of the GPFS filesystem and rerun
the mpiiotest benchmark with the same three blocksizes used above.

• Follow the steps above to remove GPFS (page 20)

• Follow the steps above to reinstall GPFS (page 6)

• Follow the steps above to reconfigure GPFS (pages 10-19). On page

19 modify the mmcrfs command to read as follows:
mmcrfs /gpfs1 /dev/gpfs1 -F /tmp/descfile -A yes -B 64K -n 4 -v no

• Type the following as root on your management node:

dsh -a chmod 777 /gpfs1

• Follow the steps above to rerun the mpiiotest benchmark with the
three blocksizes (pages 27-30)

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