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From K Yoshimoto <kenn...@sdsc.edu>
Subject Re: airavata-server.sh fails to start?
Date Tue, 14 Oct 2014 23:19:44 GMT

Thanks, Lahiru.  I'll change to execute mode and use that for
startup for now.

Kenneth

On Tue, Oct 14, 2014 at 07:14:27PM -0400, Lahiru Gunathilake wrote:
> Hi Kenneth,
> 
> I was able to reproduce the issue with Ubuntu. My sugession works fine but
> I will look in to this and fix it to work with all cases.
> 
> Thanks for pointing this out.
> 
> Again: I think ./airavata-server.sh will work.
> 
> Regards
> Lahiru
> 
> On Tue, Oct 14, 2014 at 7:11 PM, Lahiru Gunathilake <glahiru@gmail.com>
> wrote:
> 
> > Hi Kennath,
> >
> > I am not sure why it is but if you give execute permission you can try. I
> > remember having the same issue with some projects I used when I use ubuntu
> > bash.
> >
> > Ex:
> >
> >  sh ./zkServer.sh start
> >
> > JMX enabled by default
> >
> > ./zkServer.sh: 81: /usr/local/zookeeper/zookeeper-3.4.6/bin/zkEnv.sh:
> > Syntax error: "(" unexpected (expecting "fi")
> >
> > sgg@sgg-OptiPlex-990:/usr/local/zookeeper/zookeeper-3.4.6/bin$
> >
> > sgg@sgg-OptiPlex-990:/usr/local/zookeeper/zookeeper-3.4.6/bin$
> >
> > sgg@sgg-OptiPlex-990:/usr/local/zookeeper/zookeeper-3.4.6/bin$ sh
> > zkServer.sh star
> >
> > JMX enabled by default
> >
> > zkServer.sh: 81: /usr/local/zookeeper/zookeeper-3.4.6/bin/zkEnv.sh: Syntax
> > error: "(" unexpected (expecting "fi")
> >
> > sgg@sgg-OptiPlex-990:/usr/local/zookeeper/zookeeper-3.4.6/bin$
> > ./zkServer.sh start
> >
> > JMX enabled by default
> >
> > Using config: /usr/local/zookeeper/zookeeper-3.4.6/bin/../conf/zoo.cfg
> >
> > Starting zookeeper ... STARTED
> >
> > On Tue, Oct 14, 2014 at 7:08 PM, K Yoshimoto <kenneth@sdsc.edu> wrote:
> >
> >>
> >> As unpacked from the distribition, it does not have execute mode
> >> set:
> >>
> >> ./airavata-server.sh
> >> bash: ./airavata-server.sh: Permission denied
> >>
> >>
> >> On Tue, Oct 14, 2014 at 07:05:31PM -0400, Lahiru Gunathilake wrote:
> >> > Hi Kennath,
> >> >
> >> > Can you please try ./airavata-server.sh ?
> >> >
> >> > Regards
> >> > Lahiru
> >> >
> >> > On Tue, Oct 14, 2014 at 6:55 PM, K Yoshimoto <kenneth@sdsc.edu> wrote:
> >> >
> >> > >
> >> > > sh ./airavata-server.sh
> >> > >
> >> > > On Tue, Oct 14, 2014 at 04:20:13PM -0400, Saminda Wijeratne wrote:
> >> > > > Just curious, are you starting the server like,
> >> > > >
> >> > > > $ sh airavata-server.sh
> >> > > >
> >> > > > or
> >> > > >
> >> > > > $ ./airavata-server.sh
> >> > > >
> >> > > >
> >> > > >
> >> > > > On Tue, Oct 14, 2014 at 1:55 PM, K Yoshimoto <kenneth@sdsc.edu>
> >> wrote:
> >> > > >
> >> > > > >
> >> > > > > Yes, something is probably sitting on the port.  But should
I
> >> > > > > comment out the syntax error part of airavata-server.sh
for
> >> > > > > startup?
> >> > > > >
> >> > > > > On Tue, Oct 14, 2014 at 01:44:55PM -0400, Marlon Pierce
wrote:
> >> > > > > > I'm guessing you have some old processes that you may
need to
> >> > > manually
> >> > > > > > kill (ps -elf|grep java to find).
> >> > > > > >
> >> > > > > > Marlon
> >> > > > > >
> >> > > > > > On 10/14/14, 1:38 PM, K Yoshimoto wrote:
> >> > > > > > >It gets further, then stops with an address-in-use,
maybe
> >> unrelated
> >> > > > > issue.
> >> > > > > > >
> >> > > > > > >
> >> > > > > > >...
> >> > > > > > >[INFO] Finished starting ZK: State:CONNECTED Timeout:6000
> >> > > > > > >sessionid:0x1490fb31c030003 local:/127.0.0.1:42013
> >> > > > > > >remoteserver:localhost/127.0.0.1:2181 lastZxid:13
xid:8 sent:8
> >> > > recv:9
> >> > > > > > >queuedpkts:0 pendingresp:0 queuedevents:0
> >> > > > > > >[ERROR] Cannot connect to a RabbitMQ Server:
> >> > > > > > >java.net.ConnectException: Connection refused
> >> > > > > > >         at java.net.PlainSocketImpl.socketConnect(Native
> >> Method)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
> >> > > > > > >         at
> >> > > java.net.SocksSocketImpl.connect(SocksSocketImpl.java:385)
> >> > > > > > >         at java.net.Socket.connect(Socket.java:546)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> com.rabbitmq.client.ConnectionFactory.createFrameHandler(ConnectionFactory.java:445)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> com.rabbitmq.client.ConnectionFactory.newConnection(ConnectionFactory.java:504)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> com.rabbitmq.client.ConnectionFactory.newConnection(ConnectionFactory.java:533)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> org.apache.airavata.gfac.monitor.impl.push.amqp.SimpleJobFinishConsumer.listen(SimpleJobFinishConsumer.java:50)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> org.apache.airavata.gfac.monitor.impl.pull.qstat.HPCPullMonitor.<init>(HPCPullMonitor.java:96)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> org.apache.airavata.gfac.monitor.handlers.GridPullMonitorHandler.initProperties(GridPullMonitorHandler.java:71)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.startDaemonHandlers(BetterGfacImpl.java:181)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> org.apache.airavata.gfac.server.GfacServerHandler.<init>(GfacServerHandler.java:108)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> org.apache.airavata.gfac.server.GfacServer.start(GfacServer.java:102)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:289)
> >> > > > > > >         at
> >> > > > > > >
> >> > > > >
> >> > >
> >> org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:141)
> >> > > > > > >         at
> >> > > > > org.apache.airavata.server.ServerMain.main(ServerMain.java:130)
> >> > > > > > >[INFO] ------------- Push monitoring for HPC jobs
is disabled
> >> > > > > -------------
> >> > > > > > >[INFO] Registering listener:
> >> > > > > > >org.apache.airavata.gfac.core.monitor.AiravataJobStatusUpdator
> >> > > > > > >[INFO] Registering listener:
> >> > > > > > >org.apache.airavata.gfac.core.monitor.AiravataTaskStatusUpdator
> >> > > > > > >[INFO] Registering listener:
> >> > > > > >
> >> > >
> >> >org.apache.airavata.gfac.core.monitor.AiravataWorkflowNodeStatusUpdator
> >> > > > > > >[INFO] Registering listener:
> >> > > > > >
> >> > >
> >> >org.apache.airavata.api.server.listener.AiravataExperimentStatusUpdator
> >> > > > > > >[INFO] Registering listener:
> >> > > > > > >org.apache.airavata.gfac.core.monitor.GfacInternalStatusUpdator
> >> > > > > > >[INFO] Registering listener:
> >> > > > > > >org.apache.airavata.workflow.engine.util.ProxyMonitorPublisher
> >> > > > > > >[INFO] Starting Gfac Server on Port 8950
> >> > > > > > >[INFO] Listening to Gfac Clients ....
> >> > > > > > >Tue Oct 14 10:29:07 PDT 2014 : Could not listen
on port 1527
> >> on host
> >> > > > > > >0.0.0.0:
> >> > > > > > >  java.net.BindException: Address already in use
> >> > > > > > >[INFO] Database already created for App Catalog!
> >> > > > > > >[INFO] Starting Airavata Workflow Server on Port
8931
> >> > > > > > >[INFO] Listening to Workflow API Clients ....
> >> > > > > > >
> >> > > > > > >
> >> > > > > > >
> >> > > > > > >On Tue, Oct 14, 2014 at 01:21:42PM -0400, Saminda
Wijeratne
> >> wrote:
> >> > > > > > >>If you comment-out or remove the section relating
to
> >> > > "f_split=(${f//_/
> >> > > > > > >>});", does the script works for you afterwards
as expected to
> >> > > start the
> >> > > > > > >>server?
> >> > > > > > >>
> >> > > > > > >>On Tue, Oct 14, 2014 at 1:06 PM, K Yoshimoto
<
> >> kenneth@sdsc.edu>
> >> > > wrote:
> >> > > > > > >>
> >> > > > > > >>>I'm running Ubuntu 12.04LTS.
> >> > > > > > >>>
> >> > > > > > >>>On Tue, Oct 14, 2014 at 11:11:36AM -0400,
Chathuri Wimalasena
> >> > > wrote:
> >> > > > > > >>>>Hi Kenneth,
> >> > > > > > >>>>
> >> > > > > > >>>>I was able to build and run airavata
server in ubuntu 12.10
> >> > > without
> >> > > > > any
> >> > > > > > >>>>issues.
> >> > > > > > >>>>
> >> > > > > > >>>>Thanks..
> >> > > > > > >>>>Chathuri
> >> > > > > > >>>>
> >> > > > > > >>>>On Mon, Oct 13, 2014 at 9:05 AM, Marlon
Pierce <
> >> marpierc@iu.edu>
> >> > > > > wrote:
> >> > > > > > >>>>
> >> > > > > > >>>>>Hi Kenneth--
> >> > > > > > >>>>>
> >> > > > > > >>>>>What OS are you using?
> >> > > > > > >>>>>
> >> > > > > > >>>>>Marlon
> >> > > > > > >>>>>
> >> > > > > > >>>>>
> >> > > > > > >>>>>On 10/11/14, 2:23 PM, K Yoshimoto
wrote:
> >> > > > > > >>>>>
> >> > > > > > >>>>>>It looks like this line:
> >> > > > > > >>>>>>
> >> > > > > > >>>>>>                  f_split=(${f//_/
});
> >> > > > > > >>>>>>
> >> > > > > > >>>>>>
> >> > > > > > >>>>>>apache-airavata-server-0.14-SNAPSHOT/bin$
sh
> >> airavata-server.sh
> >> > > > > >
> >> >>>>>>...._....................._..............._...._............
> >> > > > > > >>>>>>.........._.........
> >> > > > > > >>>>>>.../ \..._.__...__._..___|
|__...___...../
> >> > > > > > >>>\..(_)_.__.__.___...____._|.|_
> >> > > > > > >>>>>>.__._..
> >> > > > > > >>>>>>../ _ \.| '_ \./ _` |/ __|
'_ \./ _ \.../ _ \.| | '__/ _`
> >> \
> >> > > \./ /
> >> > > > > _` |
> >> > > > > > >>>>>>__/ _` |.
> >> > > > > > >>>>>>./ ___ \| |_) | (_| | (__|
|.| |  __/../ ___ \| | |.| (_|
> >> |\ V
> >> > > /
> >> > > > > (_|
> >> > > > > > >>>| ||
> >> > > > > > >>>>>>(_| |.
> >> > > > > > >>>>>>/_/...\_\
> >> > > > > .__/.\__,_|\___|_|.|_|\___|./_/...\_\_|_|..\__,_|.\_/.\__,_|
> >> > > > > > >>>>>>\__\__,_|.
> >> > > > > >
> >> >>>>>>........|_|.................................................
> >> > > > > > >>>>>>....................
> >> > > > > >
> >> >>>>>>............................................................
> >> > > > > > >>>>>>....................
> >> > > > > >
> >> >>>>>>................,+????++~..~~++..+????????+??++.++~...~+=???
> >> > > > > > >>>>>>+++.................
> >> > > > > >
> >> >>>>>>..............:???????....:::...~??????????????.~..::...=???
> >> > > > > > >>>>>>?????...............
> >> > > > > >
> >> >>>>>>............????????..~~..?????..??????????????.?????..~~~.~
> >> > > > > > >>>>>>???????.............
> >> > > > > >
> >> >>>>>>...........?????????I,~I~~??????.+????????????.~??????~=~..?
> >> > > > > > >>>>>>????????~...........
> >> > > > > >
> >> >>>>>>.........?????++??????..????????:.??????????I..????????..???
> >> > > > > > >>>>>>?????+????..........
> >> > > > > >
> >> >>>>>>........??.....???????....???????...???????+..+??????+.I.???
> >> > > > > > >>>>>>?????.....?,........
> >> > > > > >
> >> >>>>>>........????==????????..??..?????..=???????=..?????,.=+?.???
> >> > > > > > >>>>>>??????===??=........
> >> > > > > >
> >> >>>>>>......=??????????+????..+??=.???=.~??????????,.???=,???,.???
> >> > > > > > >>>>>>?=+??????????.......
> >> > > > > >
> >> >>>>>>....??????????+...+I++..???,=...:??????????????.....+??..++
> >> > > > > > >>>>>>I?+..,??????????.....
> >> > > > > >
> >> >>>>>>....???????=??..........??..+??.:=:.???????......??..??=....
> >> > > > > > >>>>>>......?=???????=....
> >> > > > > >
> >> >>>>>>....??????..?...........+?..???.....???????......???.??.....
> >> > > > > > >>>>>>......~=.??????=....
> >> > > > > >
> >> >>>>>>....~???~.~..............?..???.~=..,??????...7..???.?.:....
> >> > > > > > >>>>>>..........~????:....
> >> > > > > > >>>>>>...7....7 ...............?..????.
...??????...
> >> > > > > .????.?.?.............I
> >> > > > > > >>>>>>..:.:....
> >> > > > > >
> >> >>>>>>.....+7=,.+?................????:,I...?????..=.?????.?......
> >> > > > > > >>>>>>.......??~.=7+......
> >> > > > > >
> >> >>>>>>..........????..............??????~...~??..~~??????..?......
> >> > > > > > >>>>>>.....+???,..........
> >> > > > > >
> >> >>>>>>...........???............=.+???????,.?+:.?????????..+......
> >> > > > > > >>>>>>.....???+...........
> >> > > > > >
> >> >>>>>>............??............?,.??????.,??..??????????.,.......
> >> > > > > > >>>>>>.....???............
> >> > > > > >
> >> >>>>>>...........??,.............=.,????.?+....????????I.I........
> >> > > > > > >>>>>>......=?............
> >> > > > > >
> >> >>>>>>..........I?..................+??.:?~.....=??????...........
> >> > > > > > >>>>>>.......??...........
> >> > > > > >
> >> >>>>>>..........??...?...............??.:?=......??????...........
> >> > > > > > >>>>>>...?...??...........
> >> > > > > >
> >> >>>>>>............++?..............?.????...?....??????.+.........
> >> > > > > > >>>>>>.....++I............
> >> > > > > >
> >> >>>>>>.............................?.??????~....???????.?.........
> >> > > > > > >>>>>>....................
> >> > > > > >
> >> >>>>>>............................~~.??????......??????...........
> >> > > > > > >>>>>>....................
> >> > > > > >
> >> >>>>>>.............................=???????......???????+.........
> >> > > > > > >>>>>>....................
> >> > > > > >
> >> >>>>>>..........................=I??++?+++?......?+++++++?+.......
> >> > > > > > >>>>>>....................
> >> > > > > > >>>>>>..........................,..77..77.........
 ..
> >> > > > > > >>>>>>...7..........................
> >> > > > > >
> >> >>>>>>............................................................
> >> > > > > > >>>>>>....................
> >> > > > > > >>>>>>airavata-server.sh: 86: airavata-server.sh:
Syntax error:
> >> "("
> >> > > > > > >>>unexpected
> >> > > > > > >>>>>>(expecting "done")
> >> > > > > > >>>>>>
> >> > > > > > >>>>>>bash --version
> >> > > > > > >>>>>>GNU bash, version 4.2.25(1)-release
(x86_64-pc-linux-gnu)
> >> > > > > > >>>>>>Copyright (C) 2011 Free Software
Foundation, Inc.
> >> > > > > > >>>>>>License GPLv3+: GNU GPL version
3 or later <
> >> > > > > > >>>http://gnu.org/licenses/gpl.
> >> > > > > > >>>>>>html>
> >> > > > > > >>>>>>
> >> > > > > > >>>>>>This is free software; you
are free to change and
> >> redistribute
> >> > > it.
> >> > > > > > >>>>>>There is NO WARRANTY, to the
extent permitted by law.
> >> > > > > > >>>>>>
> >> > > > > > >>>>>>
> >> > > > > > >>>>>>On Sat, Oct 11, 2014 at 01:47:45PM
-0400, Raminder Singh
> >> wrote:
> >> > > > > > >>>>>>
> >> > > > > > >>>>>>>I build everything from
head this morning and did not run
> >> > > into any
> >> > > > > > >>>>>>>problem. I am using Airavata
distribution in
> >> > > > > > >>>modules/distribution/server/
> >> > > > > > >>>>>>>target/apache-airavata-server-0.14-SNAPSHOT-bin.tar.gz.
> >> Only
> >> > > > > > >>>exception
> >> > > > > > >>>>>>>i am getting is related
to RabbitMQ server but this is a
> >> > > optional
> >> > > > > > >>>service.
> >> > > > > > >>>>>>>   2014-10-11 13:44:45,800
[main] ERROR
> >> > > org.apache.airavata.gfac.
> >> > > > > > >>>>>>>monitor.impl.push.amqp.SimpleJobFinishConsumer
 - Cannot
> >> > > connect
> >> > > > > to a
> >> > > > > > >>>>>>>RabbitMQ Server:
> >> > > > > > >>>>>>>java.net.ConnectException:
Connection refused
> >> > > > > > >>>>>>>
> >> > > > > > >>>>>>>Please share more details
about the failure.
> >> > > > > > >>>>>>>
> >> > > > > > >>>>>>>Thanks
> >> > > > > > >>>>>>>Raminder
> >> > > > > > >>>>>>>
> >> > > > > > >>>>>>>On Oct 10, 2014, at 7:01
PM, K Yoshimoto <
> >> kenneth@sdsc.edu>
> >> > > > > wrote:
> >> > > > > > >>>>>>>
> >> > > > > > >>>>>>>  I'm getting an error
when trying to startup an airavata
> >> > > server:
> >> > > > > > >>>>>>>>airavata-server.sh:
86: airavata-server.sh: Syntax
> >> error: "("
> >> > > > > > >>>>>>>>unexpected (expecting
"done")
> >> > > > > > >>>>>>>>
> >> > > > > > >>>>>>>>
> >> > > > > > >>>>>>>>
> >> > > > >
> >> > >
> >> >
> >> >
> >> >
> >> > --
> >> > Research Assistant
> >> > Science Gateways Group
> >> > Indiana University
> >>
> >
> >
> >
> > --
> > Research Assistant
> > Science Gateways Group
> > Indiana University
> >
> 
> 
> 
> -- 
> Research Assistant
> Science Gateways Group
> Indiana University

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