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Page History
...
Analysis-Server
...
Installation
...
Guide
...
This
...
page
...
provides
...
an
...
introduction
...
to
...
Analysis
...
Server,
...
with
...
installation
...
and
...
troubleshooting
...
information.
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{
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Introduction
The Analysis Server performs on-the-fly
...
statistical
...
calculations
...
for
...
the
...
caIntegartor
...
application.
...
It
...
can
...
be
...
hosted
...
on
...
the
...
same
...
machine
...
that
...
runs
...
the
...
any
...
application
...
(ex.
...
Rembrandt
...
or
...
ISPY)
...
or
...
it
...
can
...
be
...
run
...
on
...
any
...
number
...
of
...
remote
...
compute
...
machines.
...
In
...
the
...
remote
...
configuration,
...
each
...
compute
...
machine
...
communicates
...
with
...
the
...
appropriate
...
application
...
via
...
the
...
JBossMQ
...
Java
...
Messaging
...
Service
...
(JMS)
...
provided
...
by
...
JBoss.
...
It
...
is
...
important
...
to
...
note
...
that
...
each
...
compute
...
machine
...
does
...
not
...
require
...
its
...
own
...
JBoss
...
instance.
...
The
...
Analysis
...
Server
...
relies
...
on
...
the
...
JMS
...
queues
...
defined
...
in
...
the
...
JBoss
...
instance
...
running
...
the
...
caIntegator
...
application,
...
such
...
as
...
Rembrandt.
...
Analysis-commons
...
is
...
a
...
module
...
which
...
defines
...
classes
...
for
...
communicating
...
with
...
the
...
analysis
...
server.
...
caIntegrator
...
Applications
...
like
...
Rembrandt
...
,
...
I-SPY
...
etc
...
use
...
the
...
request
...
and
...
response
...
classes
...
defined
...
in
...
the
...
analysis
...
commons
...
module
...
for
...
communication
...
with
...
the
...
analysis
...
server.
...
Requirements
The following assumptions are in place:
You have Java and Ant installed, as listed below
| Wiki Markup |
|---|
{table-plus} || Required Software Name \\ Version \\ URL to Download || Description || | JDK 1.5.X (currently using 1.5.14) \\ [http://java.sun.com/javase/downloads/index_jdk5.jsp] | The J2SE Develop¬ment Kit (JDK) supports creat¬ing J2SE applications. | | JBOSS Application Server (4.0.X) \\ [http://labs.jboss.com/jbossas/downloads/] | JBoss Application server is the Java application Server | | Apache Ant, 1.7.0 \\ [http://ant.apache.org/bindownload.cgi] | Apache Ant is a Java-based build tool. | {table-plus} |
...
R
...
and
...
Rserve
...
have
...
been
...
installed.
...
Please
...
see
...
the
...
Rserve
...
homepage
...
at:
...
http://stats.math.uni-augsburg.de/Rserve/
...
And
...
the
...
Rserve
...
installation
...
instructions:
...
http://stats.math.uni-augsburg.de/Rserve/doc.shtml
...
It
...
is
...
recommended
...
that
...
you
...
read
...
the
...
Rserve
...
installation
...
instructions
...
before
...
installing
...
R.
...
Specifically,
...
the
...
Rserve
...
instructions
...
recommend
...
building
...
the
...
R
...
distribution
...
from
...
source
...
using
...
the
...
(color:red)
...
--enable-R-shlib
...
flag
...
(color).
...
The
...
R
...
source
...
distribution
...
can
...
be
...
obtained
...
from
...
R
...
project
...
site:
...
...
(click
...
the
...
link
...
under
...
download)
...
Setting
...
the
...
Environment
...
Variables:
| Note |
|---|
| } The purpose of setting operating system environment variables is so that the Java SDK and Ant build tool are available to run from anywhere in the system. {note} h3. Linux To set the environment variables in Linux, follow these steps: || Step || Action || | 1 | As the root user, enter the following in the /etc/profile file. \\ A PATH variable should already be created in this file, so be sure to define the JAVA_HOME and ANT_HOME export before the PATH export. \\ Replace <installation_directory> with the directory where you have installed the Java SDK and Ant. \\ (The location example in the Apache Ant installation (p. 5) is /usr/java.) \\ export JAVA_HOME=*{*{*}_)<installation_directory>(_{*}*)* |
Linux
To set the environment variables in Linux, follow these steps:
Step | Action |
|---|---|
1 | As the root user, enter the following in the /etc/profile file. |
...
|
...
ANT_HOME= |
...
( |
...
)<installation_directory>( |
...
) |
...
/apache-ant-1.7.0 |
...
|
...
PATH=$JAVA_HOME/bin:$ANT_HOME/bin:$PATH |
...
2 | Log out and log back in so that the system recognizes your changes. |
Verifying the Environment Variables in Linux
To verify that environment variables have been set correctly, follow these steps:
Step | Action |
|---|---|
1 | From the command line, enter: |
2 | To verify your Java SDK installation, enter java -version from a command prompt. |
...
. |
Connection to CVS Repository
1) Connect to CVS repository
2) Here are the parameters
a) Host: cbiocvs2.nci.nih.gov
...
b)
...
Repository
...
path:
...
/share/content/cvsroot
...
c)
...
User:
...
anonymous
...
d)
...
Password:
...
anonymous
...
e)
...
Connection
...
type:
...
pserver
...
Downloading
...
and
...
Deploying
...
the
...
Codebase
...
Step
...
1
...
Check
...
out
...
caintergrator-analysis
...
commons
...
from
...
HEAD
...
or
...
provided
...
CVS
...
tag.
...
Built
...
it
...
using
...
ant
...
script.
...
(Please
...
follow
...
the
...
steps)
...
a)
...
Open
...
a
...
COMMAND
...
prompt.
...
cd
...
into
...
caintergrator-analysis
...
commons
...
folder.
...
b)
...
then
...
type
...
ant
...
build_dependency
...
.
...
It
...
will
...
start
...
the
...
build
...
and
...
get
...
the
...
message
...
BUILD
...
SUCCESSFUL
...
.
...
c)
...
Do
...
a
...
CVS
...
check
...
out
...
of
...
the
...
caintegrator-analysis-server
...
Step:2
...
Download
...
the
...
latest
...
client
...
jar
...
file
...
(use
...
the
...
exceptions
...
version)
...
from:
...
http://stats.math.uni-augsburg.de/Rserve/down.shtml
...
after
...
agreeing
...
to
...
their
...
licensing
...
terms
...
and
...
conditions.
...
Copy
...
the
...
downloaded
...
file
...
into
...
the
...
lib
...
directory
...
under
...
the
...
analysis
...
server
...
install
...
directory
...
and
...
rename
...
it
...
to
...
Rserve.jar
...
.
...
Step
...
:3
...
1)
...
Build
...
it
...
using
...
ant
...
script
...
from
...
command
...
prompt.
...
a)
...
cd
...
into
...
caintergrator-analysis
...
commons
...
folder.
...
b)
...
then
...
type
...
ant
...
build_tar
...
.
...
It
...
will
...
start
...
the
...
build
...
and
...
you
...
will
...
get
...
the
...
message
...
BUILD
...
SUCCESSFUL.
...
Step
...
4
...
Setup
...
JMS
...
Configuration
...
Files:
...
1)
...
Copy
...
the
...
file
...
"caintegrator-jbossmq-destinations-service.xml"
...
from
...
\artifacts
...
to
...
the
...
directory
...
where
...
you
...
installed
...
JBoss.
...
/jboss-4.0.4.GA/server/default/deploy/jms
...
folder
...
2)
...
Copy
...
the
...
application
...
specific
...
file
...
for
...
example
...
"rembrandt-jbossmq-destinations-service.xml"
...
(for
...
REMBRANDT)
...
from
...
\artifacts
...
to
...
the
...
directory
...
where
...
you
...
installed
...
JBoss.
...
/jboss-4.0.4.GA/server/default/deploy/
...
jms folder
Step 5
Deploy the Analysis Server.
| Warning |
|---|
The purpose of setting operating system environment variables is so that the Java SDK and Ant build tool are available to run from anywhere in the system. |
Step 5.1
Copy the caintegrator-analysis-server.tar
...
file
...
created
...
to
...
the
...
directory
...
/local/content/caintegrator
...
.
...
Step
...
5.2
...
Type
...
the
...
command:
...
tar
...
-xvf
...
caintegrator-analysis-server.tar
...
Step 6
Go to the newly created directory /local/content/caintegrator/bin
...
.
...
Type
...
the
...
commands:
...
chmod u+x *.sh
dos2unix *.sh
Step 7
Start Rserve by typing:
./startRserve.sh
Rserve should now be running. The last line printed on the console should be:
"Rserv started in daemon mode."
Step 8
Go to the directory /home/caintegrator (you can do this by just typing cd).
Start the analysis server by executing the command:
./S92Rserver start
Additional post-deployment test case instructions
1) Open the file/local/content/caintegrator/log/analysisServer.log
...
and
...
you
...
should
...
see
...
something
...
similar
...
to:
...
a)
...
[translationalResearch:main
...
]
...
INFO
...
gov.nih.nci.caintegrator.analysis.server.RThread
...
-
...
Done
...
initializing
...
Rserver
...
connection
...
elapsedTime=5100
...
b)
...
[translationalResearch:main
...
]
...
INFO
...
gov.nih.nci.caintegrator.analysis.server.RThread
...
-
...
RThread
...
name=Thread-0
...
successfully
...
initialized
...
R
...
connection.
...
5046
...
2)
...
There
...
may
...
be
...
a
...
warning:
...
a)
...
[translationalResearch:main
...
]
...
WARN
...
gov.nih.nci.caintegrator.analysis.server.AnalysisServer
...
-
...
could
...
not
...
establish
...
connection
...
with...
...
But
...
this
...
is
...
of
...
no
...
concern.
...
It
...
is
...
because
...
there
...
will
...
be
...
no
...
JMS
...
MQs
...
available
...
until
...
JMS
...
message
...
Queues
...
have
...
been
...
established,
...
running
...
and
...
listed
...
in
...
the
...
JNDI
...
lookup
...
found
...
at
...
the
...
location
...
specified
...
in
...
the
...
property:
...
3)
...
After
...
you
...
deploy
...
the
...
application
...
you
...
should
...
return
...
to
...
this
...
log
...
file
...
and
...
see
...
the
...
following:
...
a)
...
[translationalResearch:main
...
]
...
INFO
...
gov.nih.nci.caintegrator.analysis.server.AnalysisServer
...
-
...
Now
...
listening
...
for
...
requests...
...
Troubleshooting
...
:
...
- "could
...
- not
...
- establish
...
- connection
...
- with
...
- provider.."
...
- when
...
- starting
...
- the
...
- Analysis
...
- Server.
...
This
...
error
...
can
...
occur
...
when
...
the
...
Java
...
Messaging
...
Service
...
(JMS)
...
provider
...
is
...
not
...
running
...
or
...
has
...
not
...
fully
...
initialized.
...
Make
...
sure
...
that
...
the
...
JMS
...
provider
...
that
...
is
...
configured
...
in
...
the
...
analysis
...
server
...
build
...
file
...
is
...
running.
...
If
...
it
...
is
...
running
...
but
...
has
...
not
...
fully
...
initialized
...
the
...
analysis
...
server
...
will
...
automatically
...
connect
...
when
...
it
...
is
...
fully
...
initialized.
...
- Analysis
...
- Server
...
- appears
...
- to
...
- be
...
- running
...
- but
...
- no
...
- results
...
- are
...
- returned.
...
Using
...
the
...
jmx-console
...
(see
...
the
...
JBoss
...
documentation)
...
application
...
go
...
to
...
the
...
jboss.mq.destination
...
section
...
and
...
inspect
...
the
...
AnalysisResponseQueue.
...
Make
...
sure
...
that
...
the
...
receivers
...
count
...
equals
...
1.
...
If
...
it
...
is
...
greater
...
than
...
1
...
then
...
there
...
is
...
another
...
listener
...
on
...
the
...
queue
...
which
...
is
...
stealing
...
the
...
results
...
from
...
application.
...
Next
...
inspect
...
the
...
AnalysisRequestQueue.
...
Make
...
sure
...
that
...
the
...
receivers
...
count
...
is
...
equal
...
to
...
the
...
number
...
of
...
analysis
...
server
...
machines.
...
For
...
example
...
if
...
you
...
have
...
configured
...
four
...
analysis
...
server
...
machines
...
then
...
the
...
receivers
...
count
...
should
...
equal
...
four.
...
If
...
the
...
receiver
...
counts
...
are
...
not
...
as
...
expected
...
then
...
the
...
problem
...
may
...
stem
...
from
...
network/firewall
...
issues
...
or
...
from
...
a
...
conflicting
...
instance
...
of
...
the
...
application.
...
- If
...
- you
...
- are
...
- using
...
- a
...
- version
...
- of
...
- JBoss
...
- other
...
- than
...
- 4.0.2,
...
- you
...
- should
...
- replace
...
- the
...
- following
...
- jar
...
- files:
...
concurrent.jar
...
jbossmq-client.jar
...
jboss-common-client.jar
...
jboss-system-client.jar
...
jnp-client.jar
...
in
...
the
...
lib
...
directory
...
under
...
the
...
analysis
...
server
...
install
...
directory,
...
with
...
the
...
corresponding
...
jar
...
files
...
from
...
the
...
JBoss
...
distribution.
...
Steps
...
to
...
add
...
a
...
Data
...
File
...
Step
...
1
...
Click
...
on
...
this
...
link
...
https://gforge.nci.nih.gov/frs/?group_id=406
...
and
...
you
...
will
...
find
...
data
...
files
...
for
...
particular
...
application
...
For
...
example:
...
Rembrandt:
...
Rembrandt_mas5.dataMatrix_275_10-15-07.Rda
...
Rembrandt_UnifiedGene.dataMatrix_275_10-15-07.Rda
...
Ispy:
...
newDataFile.zip
...
Step
...
2
...
Copy
...
the
...
data
...
file
...
to
...
the
...
directory
...
local/content/caintegrator/Rdatafiles/
...
Step
...
3
...
Restart
...
the
...
analysis
...
server
...
Log
...
in
...
to
...
the
...
analysis
...
machine
...
Stop
...
the
...
analysis
...
server
...
by
...
executing
...
the
...
command
...
:
./S92Rserver
...
stop
Start the analysis server by executing the command:
./S92Rserver start
Using the Analysis Server for Development Purposes:
On caIntegrator project, for development, the developers share a common analysis server and have a dedicate JMS node for their local Jboss.
This allows us to independently develop and test queries against the analysis server.
You can setup something similar for development using our files
1) Copy StartStopNodes_develop to /home/caIntegrator and started and stopped similar to S92Rserver
./StartStopNodes_develop stop
And
./StartStopNodes_develop start
2) Copy runDeveloperNodes.sh to /local/content/caintegrator/bin/
...
And
...
modify
...
it
...
by
...
adding
...
a
...
new
...
line
...
for
...
each
...
developer
...
using
...
this
...
file
...
as
...
an
...
example
...
3)
...
Copy
...
&
...
rename
...
analysisServerDeveloper1.properties
...
to
...
local/content/caintegrator/bin/
...
And
...
modify
...
the
...
ip
...
address
...
of
...
the
...
developer
...
in
...
this
...
file
...
plus
...
the
...
file
...
name
...
should
...
match
...
the
...
setting
...
in
...
the
...
runDeveloperNodes.sh
...
file
...
Next
...
use
...
localhost:1099
...
on
...
your
...
server
...
to
...
connect
...
to
...
the
...
analysis
...
server.
...
You
...
do
...
not
...
need
...
to
...
start
...
and
...
stop
...
the
...
analysis
...
server
...
for
...
each
...
developer
...
unless
...
your
...
going
...
to
...
upload
...
a
...
new
...
R-binary
...
file.
...
You
...
can
...
substitute
...
actual
...
developer
...
name
...
to
...
identify
...
each
...
node.
