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Yes, you should bring this to the attention of beagle sysadmins.<br>
<br>
On 6/4/11 1:01 PM, Jonathan S Monette wrote:
<blockquote
cite="mid:BANLkTi=R1LYPZ5jgefYNHbV++MXf=EQYAg@mail.gmail.com"
type="cite">Ok. I have my job submitted and it is currently
waiting in the queue. besides manually resetting this variable
everytime I am on beagle what else can be done? Is this something
that I should bring to the attention of the sys admins for beagle?<br>
<br>
<div class="gmail_quote">On Sat, Jun 4, 2011 at 12:51 PM, Ketan
Maheshwari <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:ketancmaheshwari@gmail.com">ketancmaheshwari@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Alright, so this is the issue. GLOBUS_HOSTNAME is picked up
from HOSTNAME and I do not know where does this none comes in
your case.<br>
<br>
In my case I get hostname: <a moz-do-not-send="true"
href="http://login2.beagle.ci.uchicago.edu" target="_blank">login2.beagle.ci.uchicago.edu</a><br>
<br>
see if you can manually change this env variable and try to
run again.
<div>
<div class="h5"><br>
<br>
<div class="gmail_quote">On Sat, Jun 4, 2011 at 12:49 PM,
Jonathan S Monette <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jonmon@utexas.edu" target="_blank">jonmon@utexas.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>login2.beagle.ci.uchicago.edu.(none)
<div><br>
</div>
</div>
<div>when you ran your test was in on login1 or
login2?
<div>
<div><br>
<br>
<div class="gmail_quote">On Sat, Jun 4, 2011 at
12:47 PM, Ketan Maheshwari <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:ketancmaheshwari@gmail.com"
target="_blank">ketancmaheshwari@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:
0pt 0pt 0pt 0.8ex; border-left: 1px solid
rgb(204, 204, 204); padding-left: 1ex;">What
does <br>
<br>
echo $HOSTNAME give?
<div>
<div><br>
<br>
<div class="gmail_quote">On Sat, Jun 4,
2011 at 12:44 PM, Jonathan S Monette <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jonmon@utexas.edu"
target="_blank">jonmon@utexas.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin: 0pt 0pt 0pt 0.8ex;
border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;">
I am not sure why that (none)
appears. Is this a variable that
the system sets or do I need to set
it?
<div>
<div><br>
<br>
<div class="gmail_quote">On Sat,
Jun 4, 2011 at 12:39 PM, Ketan
Maheshwari <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:ketancmaheshwari@gmail.com"
target="_blank">ketancmaheshwari@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px
solid rgb(204, 204, 204);
padding-left: 1ex;">This
suprises me because, I do
not see that (none) in my
commandline.
<div>
<div><br>
<br>
<div class="gmail_quote">
On Sat, Jun 4, 2011 at
12:38 PM, Jonathan S
Monette <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jonmon@utexas.edu" target="_blank">jonmon@utexas.edu</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin: 0pt
0pt 0pt 0.8ex;
border-left: 1px
solid rgb(204, 204,
204); padding-left:
1ex;">I added
<div>
<div>echo
${OPTIONS}</div>
<div> echo
${COG_OPTS}</div>
<div> echo
${LOCALCLASSPATH}</div>
<div> echo
${EXEC}</div>
<div> echo
${CMDLINE}</div>
<div><br>
</div>
<div>to the
script. It
seems in the
$OPTIONS
variable this
appears.</div>
<div><br>
</div>
<div>-Xmx8192M
-Djava.endorsed.dirs=/home/jonmon/Library/Swift/swift-0.92/bin/../lib/endorsed
-DUID=1881
-DGLOBUS_HOSTNAME=login2.beagle.ci.uchicago.edu.(none)
-DCOG_INSTALL_PATH=/home/jonmon/Library/Swift/swift-0.92/bin/..
-Dswift.home=/home/jonmon/Library/Swift/swift-0.92/bin/..
-Djava.security.egd=<a class="moz-txt-link-freetext" href="file:///dev/urandom">file:///dev/urandom</a></div>
<div><br>
</div>
<div>There is the
line
DGLOBUS_HOSTNAME=login2.beagle.ci.uchicago.edu.(none)
I believe that
is the
parenthesis that
is causing this
to fail. Now
How do I fix it.</div>
<div>
<div><br>
<div
class="gmail_quote">On
Sat, Jun 4,
2011 at 12:36
PM, Jonathan S
Monette <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:jonmon@utexas.edu" target="_blank">jonmon@utexas.edu</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:
0pt 0pt 0pt
0.8ex;
border-left:
1px solid
rgb(204, 204,
204);
padding-left:
1ex;">I may
have found the
error. I
download 0.92
binaries and
changed the
swift command
script. I
added
<div>
<div>
<br>
<br>
<div
class="gmail_quote">On
Sat, Jun 4,
2011 at 12:26
PM, Jonathan S
Monette <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:jonmon@utexas.edu" target="_blank">jonmon@utexas.edu</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:
0pt 0pt 0pt
0.8ex;
border-left:
1px solid
rgb(204, 204,
204);
padding-left:
1ex;">Same
result. Same
error
<div>
<div><br>
<br>
<div
class="gmail_quote">On
Sat, Jun 4,
2011 at 12:24
PM, ketan <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:ketancmaheshwari@gmail.com"
target="_blank">ketancmaheshwari@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:
0pt 0pt 0pt
0.8ex;
border-left:
1px solid
rgb(204, 204,
204);
padding-left:
1ex;">
<div
bgcolor="#ffffff"
text="#000000">
can you try
running the
commandline by
copying from
run.sh and
pasting it at
the prompt.
<div>
<div><br>
<br>
On 6/4/11
12:18 PM,
Jonathan S
Monette wrote:
<blockquote
type="cite">I
do have that
project. I
did projects
--avail and
got back
<div><br>
</div>
<div>
<div>Project
PI
Title</div>
<div>------------------------------------------------------------------------------</div>
<div>CI-CCR000013
Michael Wilde
The
Swift Parallel
Scripting
System</div>
<div><br>
</div>
<div>Here is
my run.sh
file. I
execute with
./run.sh after
I did chmod +x
run.sh</div>
<div><br>
</div>
<div>
<div>#!/bin/bash</div>
<div>swift
-config cf
-tc.file tc
-sites.file
beagle-coaster.xml
catsn.swift
-n=1</div>
</div>
<div><br>
</div>
<div>I do have
sh and cat in
my path. I
can execute
them. Here is
what which sh
and which cat
produced.</div>
<div> <br>
</div>
<div>sh is
/usr/bin/sh</div>
<div>cat is
/bin/cat</div>
<br>
<div
class="gmail_quote">On
Sat, Jun 4,
2011 at 12:10
PM, ketan <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:ketancmaheshwari@gmail.com"
target="_blank">ketancmaheshwari@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:
0pt 0pt 0pt
0.8ex;
border-left:
1px solid
rgb(204, 204,
204);
padding-left:
1ex;">
<div
bgcolor="#ffffff"
text="#000000">
Can you try
"projects
--avail"
command on
beagle to see
if you are
member of a
project.<br>
<br>
Else you will
need to
request
membership.
You can do
this from this
page:<br>
<br>
<a
moz-do-not-send="true"
href="http://pads.ci.uchicago.edu/access/" target="_blank">http://pads.ci.uchicago.edu/access/</a><br>
<br>
In any case,
your error
does not seem
to be because
of the above.
Looks like '('
has sneaked in
because of
some
unexpected
typo in
commandline ..
can you
doublecheck
it.<br>
<br>
Also can you
make sure that
you have all
the files: tc,
beagle-coasters.xml
cf in PATH,
ie. are you
able to access
them w/o ./
<div>
<div><br>
<br>
On 6/4/11
12:03 PM,
Jonathan S
Monette wrote:
</div>
</div>
<blockquote
type="cite">
<div>
<div>I did
change the
work
directory. I
however did
not change the
project name.
I do not know
my project
name so I kept
the same
project that
was in there.
Here is my
modified
beagle-coasters.xml
<div><br>
</div>
</div>
</div>
<div>
<div>
<div>
<div><config></div>
<div>
<pool
handle="pbs"></div>
<div>
<execution
provider="coaster"
jobmanager="local:pbs"/></div>
<div>
<profile
namespace="globus"
key="project">CI-CCR000013</profile></div>
<div><br>
</div>
<div>
<profile
namespace="globus"
key="ppn">24:cray:pack</profile></div>
<div><br>
</div>
<div>
<profile
namespace="globus"
key="workersPerNode">24</profile></div>
<div>
<profile
namespace="globus"
key="maxTime">1000</profile></div>
<div>
<profile
namespace="globus"
key="slots">1</profile></div>
<div>
<profile
namespace="globus"
key="nodeGranularity">1</profile></div>
<div>
<profile
namespace="globus"
key="maxNodes">1</profile></div>
<div><br>
</div>
<div>
<profile
namespace="karajan"
key="jobThrottle">.63</profile></div>
<div>
<profile
namespace="karajan"
key="initialScore">10000</profile></div>
<div><br>
</div>
<div>
<filesystem
provider="local"/></div>
<div>
<workdirectory
>/lustre/beagle/jonmon/Swift/work</workdirectory></div>
<div>
</pool></div>
<div></config></div>
<div><br>
</div>
<br>
</div>
</div>
<div
class="gmail_quote">
<div>
<div>On Sat,
Jun 4, 2011 at
12:00 PM,
Ketan
Maheshwari <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:ketancmaheshwari@gmail.com"
target="_blank">ketancmaheshwari@gmail.com</a>></span>
wrote:<br>
</div>
</div>
<blockquote
class="gmail_quote"
style="margin:
0pt 0pt 0pt
0.8ex;
border-left:
1px solid
rgb(204, 204,
204);
padding-left:
1ex;">
<div>
<div>Jon,<br>
<br>
Thanks for
trying out
catsn on
Beagle. <br>
<br>
I just tried
it myself but
could not
reproduce the
error you are
getting. Have
you made the
changes that
are mentioned
in the README:<br>
==<br>
Change workdir
location in
beagle-coaster.xml<br>
Change the
project entry
in the
beagle-coaster.xml
to your
project name<br>
==<br>
<font
color="#888888"><br>
Ketan</font> </div>
</div>
<div>
<div><br>
<br>
<div
class="gmail_quote">
<div>
<div>On Sat,
Jun 4, 2011 at
11:50 AM,
Jonathan S
Monette <span
dir="ltr"><<a
moz-do-not-send="true" href="mailto:jonmon@utexas.edu" target="_blank">jonmon@utexas.edu</a>></span>
wrote:<br>
</div>
</div>
<blockquote
class="gmail_quote"
style="margin:
0pt 0pt 0pt
0.8ex;
border-left:
1px solid
rgb(204, 204,
204);
padding-left:
1ex;">
<div>
<div>Hello,
<div> I am
trying to run
the catsn test
on beagle
using the
files in
~ketan/catsn.
I have copied
over this
directory over
to my home
directory and
I believe I
set it up
correctly. I
did module
load swift and
the ran run.sh
that was in
this
directory. I
get this
error.</div>
<div><br>
</div>
</div>
</div>
<div>
<div>
<div>
<div>/soft/swift/0.92/bin/swift:
eval: line
152: syntax
error near
unexpected
token `('</div>
</div>
</div>
<div>/soft/swift/0.92/bin/swift:
eval: line
152: `java
-Xmx8192M
-Djava.endorsed.dirs=/soft/swift/0.92/bin/../lib/endorsed
-DUID=1881
-DGLOBUS_HOSTNAME=login2.beagle.ci.uchicago.edu.(none)
-DCOG_INSTALL_PATH=/soft/swift/0.92/bin/..
-Dswift.home=/soft/swift/0.92/bin/..
-Djava.security.egd=<a moz-do-not-send="true">file:///dev/urandom</a>
-classpath
/soft/swift/0.92/bin/../etc:/soft/swift/0.92/bin/../libexec:/soft/swift/0.92/bin/../lib/addressing-1.0.jar:/soft/swift/0.92/bin/../lib/ant.jar:/soft/swift/0.92/bin/../lib/antlr-2.7.5.jar:/soft/swift/0.92/bin/../lib/axis.jar:/soft/swift/0.92/bin/../lib/axis-url.jar:/soft/swift/0.92/bin/../lib/backport-util-concurrent.jar:/soft/swift/0.92/bin/../lib/castor-0.9.6.jar:/soft/swift/0.92/bin/../lib/coaster-bootstrap.jar:/soft/swift/0.92/bin/../lib/cog-abstraction-common-2.4.jar:/soft/swift/0.92/bin/../lib/cog-axis.jar:/soft/swift/0.92/bin/../lib/cog-grapheditor-0.47.jar:/soft/swift/0.92/bin/../lib/cog-jglobus-1.7.0.jar:/soft/swift/0.92/bin/../lib/cog-karajan-0.36-dev.jar:/soft/swift/0.92/bin/../lib/cog-provider-clref-gt4_0_0.jar:/soft/swift/0.92/bin/../lib/cog-provider-coaster-0.3.jar:/soft/swift/0.92/bin/../lib/cog-provider-dcache-0.1.jar:/soft/swift/0.92/bin/../lib/cog-provider-gt2-2.4.jar:/soft/swift/0.92/bin/../lib/cog-provider-gt4_0_0-2.5.jar:/soft/swift/0.92/bin/../lib/cog-pro
vider-local-2.2.jar:/soft/swift/0.92/bin/../lib/cog-provider-localscheduler-0.4.jar:/soft/swift/0.92/bin/../lib/cog-provider-ssh-2.4.jar:/soft/swift/0.92/bin/../lib/cog-provider-webdav-2.1.jar:/soft/swift/0.92/bin/../lib/cog-resources-1.0.jar:/soft/swift/0.92/bin/../lib/cog-swift-svn.jar:/soft/swift/0.92/bin/../lib/cog-trap-1.0.jar:/soft/swift/0.92/bin/../lib/cog-url.jar:/soft/swift/0.92/bin/../lib/cog-util-0.92.jar:/soft/swift/0.92/bin/../lib/commonj.jar:/soft/swift/0.92/bin/../lib/commons-beanutils.jar:/soft/swift/0.92/bin/../lib/commons-collections-3.0.jar:/soft/swift/0.92/bin/../lib/commons-digester.jar:/soft/swift/0.92/bin/../lib/commons-discovery.jar:/soft/swift/0.92/bin/../lib/commons-httpclient.jar:/soft/swift/0.92/bin/../lib/commons-logging-1.1.jar:/soft/swift/0.92/bin/../lib/concurrent.jar:/soft/swift/0.92/bin/../lib/cryptix32.jar:/soft/swift/0.92/bin/../lib/cryptix-asn1.jar:/soft/swift/0.92/bin/../lib/cryptix.jar:/soft/swift/0.92/bin/../lib/globus_delegation_servic
e.jar:/soft/swift/0.92/bin/../lib/globus_delegation_stubs.jar:/soft/swift/0.92/bin/../lib/globus_wsrf_mds_aggregator_stubs.jar:/soft/swift/0.92/bin/../lib/globus_wsrf_rendezvous_service.jar:/soft/swift/0.92/bin/../lib/globus_wsrf_rendezvous_stubs.jar:/soft/swift/0.92/bin/../lib/globus_wsrf_rft_stubs.jar:/soft/swift/0.92/bin/../lib/gram-client.jar:/soft/swift/0.92/bin/../lib/gram-stubs.jar:/soft/swift/0.92/bin/../lib/gram-utils.jar:/soft/swift/0.92/bin/../lib/j2ssh-common-0.2.2.jar:/soft/swift/0.92/bin/../lib/j2ssh-core-0.2.2-patch-b.jar:/soft/swift/0.92/bin/../lib/jakarta-regexp-1.2.jar:/soft/swift/0.92/bin/../lib/jakarta-slide-webdavlib-2.0.jar:/soft/swift/0.92/bin/../lib/jaxrpc.jar:/soft/swift/0.92/bin/../lib/jce-jdk13-131.jar:/soft/swift/0.92/bin/../lib/jgss.jar:/soft/swift/0.92/bin/../lib/jline-0.9.94.jar:/soft/swift/0.92/bin/../lib/jsr173_1.0_api.jar:/soft/swift/0.92/bin/../lib/jug-lgpl-2.0.0.jar:/soft/swift/0.92/bin/../lib/junit.jar:/soft/swift/0.92/bin/../lib/log4j-1.2
.8.jar:/soft/swift/0.92/bin/../lib/naming-common.jar:/soft/swift/0.92/bin/../lib/naming-factory.jar:/soft/swift/0.92/bin/../lib/naming-java.jar:/soft/swift/0.92/bin/../lib/naming-resources.jar:/soft/swift/0.92/bin/../lib/opensaml.jar:/soft/swift/0.92/bin/../lib/puretls.jar:/soft/swift/0.92/bin/../lib/resolver.jar:/soft/swift/0.92/bin/../lib/saaj.jar:/soft/swift/0.92/bin/../lib/stringtemplate.jar:/soft/swift/0.92/bin/../lib/vdldefinitions.jar:/soft/swift/0.92/bin/../lib/wsdl4j.jar:/soft/swift/0.92/bin/../lib/wsrf_core.jar:/soft/swift/0.92/bin/../lib/wsrf_core_stubs.jar:/soft/swift/0.92/bin/../lib/wsrf_mds_index_stubs.jar:/soft/swift/0.92/bin/../lib/wsrf_mds_usefulrp_schema_stubs.jar:/soft/swift/0.92/bin/../lib/wsrf_provider_jce.jar:/soft/swift/0.92/bin/../lib/wsrf_tools.jar:/soft/swift/0.92/bin/../lib/wss4j.jar:/soft/swift/0.92/bin/../lib/xalan.jar:/soft/swift/0.92/bin/../lib/xbean.jar:/soft/swift/0.92/bin/../lib/xbean_xpath.jar:/soft/swift/0.92/bin/../lib/xercesImpl.jar:/soft
/swift/0.92/bin/../lib/xml-apis.jar:/soft/swift/0.92/bin/../lib/xmlsec.jar:/soft/swift/0.92/bin/../lib/xpp3-1.1.3.4d_b4_min.jar:/soft/swift/0.92/bin/../lib/xstream-1.1.1-patched.jar:
org.griphyn.vdl.karajan.Loader
'-config' 'cf'
'-tc.file'
'tc'
'-sites.file'
'beagle-coaster.xml'
'catsn.swift'
'-n=1''</div>
<div>
<div><br>
</div>
<div>I there
something else
I need to load
on beagle to
make swift run
accordingly?</div>
<br>
-- <br>
<p>Any
intelligent
fool can make
things bigger
and more
complex... It
takes a touch
of genius -
and a lot of
courage to
move in the
opposite
direction.</p>
<p>- Albert
Einstein</p>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<div> <br>
<br
clear="all">
<br>
-- <br>
<p>Any
intelligent
fool can make
things bigger
and more
complex... It
takes a touch
of genius -
and a lot of
courage to
move in the
opposite
direction.</p>
<p>- Albert
Einstein</p>
<br>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
<br>
<br
clear="all">
<br>
-- <br>
<p>Any
intelligent
fool can make
things bigger
and more
complex... It
takes a touch
of genius -
and a lot of
courage to
move in the
opposite
direction.</p>
<p>- Albert
Einstein</p>
<br>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br
clear="all">
<br>
-- <br>
<p>Any
intelligent
fool can make
things bigger
and more
complex... It
takes a touch
of genius -
and a lot of
courage to
move in the
opposite
direction.</p>
<p>- Albert
Einstein</p>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br
clear="all">
<br>
-- <br>
<p>Any
intelligent
fool can make
things bigger
and more
complex... It
takes a touch
of genius -
and a lot of
courage to
move in the
opposite
direction.</p>
<p>- Albert
Einstein</p>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br
clear="all">
<br>
-- <br>
<p>Any
intelligent
fool can make
things bigger
and more
complex... It
takes a touch
of genius -
and a lot of
courage to
move in the
opposite
direction.</p>
<p>- Albert
Einstein</p>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<p>Any intelligent fool can make
things bigger and more
complex... It takes a touch of
genius - and a lot of courage
to move in the opposite
direction.</p>
<p>- Albert Einstein</p>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<p>Any intelligent fool can make things bigger
and more complex... It takes a touch of genius
- and a lot of courage to move in the opposite
direction.</p>
<p>- Albert Einstein</p>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<p>Any intelligent fool can make things bigger and more complex...
It takes a touch of genius - and a lot of courage to move in the
opposite direction.</p>
<p>- Albert Einstein</p>
<br>
</blockquote>
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