Couldnt connect to host http://localhost:8080/ XNAT 1.7.2

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piero.chia...@gmail.com

chưa đọc,
11:14:39 11 thg 2, 201711/2/17
đến xnat_discussion
Hi xnat experts,
I try to lunch a pipeline but 've this message:

/media/NAS/qNATitab/data/qnat/pipeline/bin/schedule /media/NAS/qNATitab/data/qnat/pipeline/bin/XnatPipelineLauncher -pipeline /media/NAS/qNATitab/data/qnat/pipeline/catalog/xnat-pipelines/QAP/qap_anat_processing.xml -id qNAT_E00001 -host http://192.168.30.228:8080 -u 9356b705-aa6a-4aba-a3d8-8dfe2854aa34 -pwd ******** -dataType xnat:mrSessionData -recordWorkflow false -label sub01_MR1 -supressNotification -project "test01" -parameterFile /media/NAS/qNATitab/data/qnat/build/test01/20170211_150430/sub01_MR1/sub01_MR1_params_20170211.xml -notify p.chiacc...@unich.it -notify in...@ser-ve.it -parameter mailhost='xxxxxxx' -parameter userfullname='xxxxxxxxx' -parameter builddir='/media/NAS/qNATitab/data/qnat/build/test01/20170211_150430' -parameter xnatserver='qNAT' -parameter adminemail='in...@ser-ve.it' -parameter useremail='p.chiacc...@unich.it'
Param Value Pair id=qNAT_E00001
Param Value Pair host=http://192.168.30.228:8080/
Param Value Pair u=9356b705-aa6a-4aba-a3d8-8dfe2854aa34
Param Value Pair pwd=********
Param Value Pair label=sub01_MR1
Param Value Pair project=test01
Param Value Pair mailhost=XXXXXXX
Param Value Pair userfullname=P.Chiacchiaretta
Param Value Pair builddir=/media/NAS/qNATitab/data/qnat/build/test01/20170211_150430
Param Value Pair xnatserver=xNAT
Param Value Pair adminemail=xxxxxx
Param Value Pair useremail=xxxxxxxxxt
User Shell is sh
Param Value Pair id=qNAT_E00001
Param Value Pair host=http://192.168.30.228:8080/
Param Value Pair u=9356b705-aa6a-4aba-a3d8-8dfe2854aa34
Param Value Pair pwd=********
Param Value Pair label=sub01_MR1
Param Value Pair project=test01
Param Value Pair mailhost=XXXXXX
Param Value Pair userfullname=xxxxxxxx
Param Value Pair builddir=/media/NAS/qNATitab/data/qnat/build/test01/20170211_150430
Param Value Pair xnatserver=xNAT
Param Value Pair adminemail=xxxx
Param Value Pair useremail=xxxxxxx
Native host spec   -shell y -V  -q qNAT01.q
 Job 19 is on HOLD. Assigning jobId to workflow
null JOB_LOG_FILE null is null
org.nrg.xnattools.exception.SessionManagerNotInitedException
at org.nrg.xnattools.SessionManager.createJSESSION(SessionManager.java:92)
at org.nrg.xnattools.SessionManager.getJSESSION(SessionManager.java:136)
at org.nrg.xnattools.xml.XMLSearch.getIdentifiers(XMLSearch.java:129)
at org.nrg.xnattools.xml.XMLSearch.searchAll(XMLSearch.java:79)
at org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold(XNATPipelineLauncher.java:381)
at org.nrg.pipeline.client.XNATPipelineLauncher.assignGridJobIdToWorkflow(XNATPipelineLauncher.java:97)
at org.nrg.pipeline.client.PipelineJobSubmitter.run(PipelineJobSubmitter.java:248)
at org.nrg.pipeline.client.PipelineJobSubmitter.main(PipelineJobSubmitter.java:391)
Couldnt connect to host http://localhost:8080/
FATAL main org.nrg.pipeline.client.XNATPipelineLauncher - Couldn't search for queued workflows
org.nrg.xnattools.exception.SessionManagerNotInitedException
at org.nrg.xnattools.SessionManager.createJSESSION(SessionManager.java:92)
at org.nrg.xnattools.SessionManager.getJSESSION(SessionManager.java:136)
at org.nrg.xnattools.xml.XMLSearch.getIdentifiers(XMLSearch.java:129)
at org.nrg.xnattools.xml.XMLSearch.searchAll(XMLSearch.java:79)
at org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold(XNATPipelineLauncher.java:381)
at org.nrg.pipeline.client.XNATPipelineLauncher.assignGridJobIdToWorkflow(XNATPipelineLauncher.java:97)
at org.nrg.pipeline.client.PipelineJobSubmitter.run(PipelineJobSubmitter.java:248)
at org.nrg.pipeline.client.PipelineJobSubmitter.main(PipelineJobSubmitter.java:391)
1 [main] FATAL org.nrg.pipeline.client.XNATPipelineLauncher  - Couldn't search for queued workflows
org.nrg.xnattools.exception.SessionManagerNotInitedException
at org.nrg.xnattools.SessionManager.createJSESSION(SessionManager.java:92)
at org.nrg.xnattools.SessionManager.getJSESSION(SessionManager.java:136)
at org.nrg.xnattools.xml.XMLSearch.getIdentifiers(XMLSearch.java:129)
at org.nrg.xnattools.xml.XMLSearch.searchAll(XMLSearch.java:79)
at org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold(XNATPipelineLauncher.java:381)
at org.nrg.pipeline.client.XNATPipelineLauncher.assignGridJobIdToWorkflow(XNATPipelineLauncher.java:97)
at org.nrg.pipeline.client.PipelineJobSubmitter.run(PipelineJobSubmitter.java:248)
at org.nrg.pipeline.client.PipelineJobSubmitter.main(PipelineJobSubmitter.java:391)
org.nrg.xnattools.exception.SessionManagerNotInitedException
at org.nrg.xnattools.SessionManager.createJSESSION(SessionManager.java:92)
at org.nrg.xnattools.SessionManager.getJSESSION(SessionManager.java:136)
at org.nrg.xnattools.xml.WorkflowStore.store(WorkflowStore.java:60)
at org.nrg.xnattools.xml.WorkflowStore.store(WorkflowStore.java:96)
at org.nrg.pipeline.client.XNATPipelineLauncher.assignGridJobIdToWorkflow(XNATPipelineLauncher.java:112)
at org.nrg.pipeline.client.PipelineJobSubmitter.run(PipelineJobSubmitter.java:248)
at org.nrg.pipeline.client.PipelineJobSubmitter.main(PipelineJobSubmitter.java:391)
Unable to store workflow with http://localhost:8080/
org.nrg.xnattools.exception.SessionManagerNotInitedException
at org.nrg.xnattools.SessionManager.createJSESSION(SessionManager.java:92)
at org.nrg.xnattools.SessionManager.getJSESSION(SessionManager.java:136)
at org.nrg.xnattools.xml.WorkflowStore.store(WorkflowStore.java:60)
at org.nrg.xnattools.xml.WorkflowStore.store(WorkflowStore.java:96)
at org.nrg.pipeline.client.XNATPipelineLauncher.assignGridJobIdToWorkflow(XNATPipelineLauncher.java:112)
at org.nrg.pipeline.client.PipelineJobSubmitter.run(PipelineJobSubmitter.java:248)
at org.nrg.pipeline.client.PipelineJobSubmitter.main(PipelineJobSubmitter.java:391)
Unable to store workflow with http://localhost:8080/
FATAL main org.nrg.pipeline.client.XNATPipelineLauncher - Unable to store workflow entry. Host http://192.168.30.228:8080/ may not be accessible?
org.nrg.xnattools.exception.SessionManagerNotInitedException
at org.nrg.xnattools.SessionManager.createJSESSION(SessionManager.java:92)
at org.nrg.xnattools.SessionManager.getJSESSION(SessionManager.java:136)
at org.nrg.xnattools.xml.WorkflowStore.store(WorkflowStore.java:60)
at org.nrg.xnattools.xml.WorkflowStore.store(WorkflowStore.java:96)
at org.nrg.pipeline.client.XNATPipelineLauncher.assignGridJobIdToWorkflow(XNATPipelineLauncher.java:112)
at org.nrg.pipeline.client.PipelineJobSubmitter.run(PipelineJobSubmitter.java:248)
at org.nrg.pipeline.client.PipelineJobSubmitter.main(PipelineJobSubmitter.java:391)
305 [main] FATAL org.nrg.pipeline.client.XNATPipelineLauncher  - Unable to store workflow entry. Host http://192.168.30.228:8080/ may not be accessible?
org.nrg.xnattools.exception.SessionManagerNotInitedException
at org.nrg.xnattools.SessionManager.createJSESSION(SessionManager.java:92)
at org.nrg.xnattools.SessionManager.getJSESSION(SessionManager.java:136)
at org.nrg.xnattools.xml.WorkflowStore.store(WorkflowStore.java:60)
at org.nrg.xnattools.xml.WorkflowStore.store(WorkflowStore.java:96)
at org.nrg.pipeline.client.XNATPipelineLauncher.assignGridJobIdToWorkflow(XNATPipelineLauncher.java:112)
at org.nrg.pipeline.client.PipelineJobSubmitter.run(PipelineJobSubmitter.java:248)
at org.nrg.pipeline.client.PipelineJobSubmitter.main(PipelineJobSubmitter.java:391)
Releasing the hold on  Job 19
Scheduling Command: /media/NAS/qNATitab/data/qnat/pipeline/bin/XnatPipelineLauncher -pipeline  /media/NAS/qNATitab/data/qnat/pipeline/catalog/xnat-pipelines/QAP/qap_anat_processing.xml  -id  qNAT_E00001  -host  http://192.168.30.228:8080  -u  9356b705-aa6a-4aba-a3d8-8dfe2854aa34  -pwd  '20170211_150430'  qNAT_E00001_wrk.xml  -dataType  xnat:mrSessionData  -recordWorkflow  false  -label  sub01_MR1  -supressNotification  -project  test01  -parameterFile  /media/NAS/qNATitab/data/qnat/build/test01/20170211_150430/sub01_MR1/sub01_MR1_params_20170211.xml  -notify  p.chiacc...@unich.it  -notify  xxxxxxxxt  -parameter  mailhost=xxxxxxx  -parameter  userfullname=xxxxxxx  -parameter  builddir=/media/NAS/qNATitab/data/qnat/build/test01/20170211_150430  -parameter  xnatserver=xNAT  -parameter  adminemail=in...@ser-ve.it  -parameter  useremail=p.chiacc...@unich.it  -config  /media/NAS/qNATitab/data/qnat/pipeline/pipeline.config  -catalogPath  /media/NAS/qNATitab/data/qnat/pipeline/catalog




thanks

John Flavin

chưa đọc,
09:32:36 13 thg 2, 201713/2/17
đến xnat_discussion
How did you set up your pipeline engine? Did you run the pipeline setup script? The reason I ask is that the server http://localhost:8080/ is a default value that the pipeline engine uses if you have not told it a different address for your server.

Flavin

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piero.chia...@gmail.com

chưa đọc,
10:34:08 13 thg 2, 201713/2/17
đến xnat_discussion
So i download the xnat-pipeline-1.7.2.zip 

then i modified the gradle.properties:

xnatUrl=http://master:8080

siteName=qNAT

adminEmail=in...@ser-ve.it

smtpServer=smtp.server.it

destination=/media/NAS/qNATitab/data/qnat/pipeline



and launch the ./gradlew

the fstab configuration file is :

127.0.0.1       master  master

127.0.0.1 localhost

::1 ip6-localhost ip6-loopback

fe00::0 ip6-localnet

ff00::0 ip6-mcastprefix

ff02::1 ip6-allnodes

ff02::2 ip6-allrouters

ff02::3 ip6-allhosts

192.168.30.228 master

192.168.0.71 master

192.168.0.72 worker1

192.168.0.73 worker2

192.168.0.74 worker3

192.168.0.75 worker4

192.168.0.76 worker5

192.168.0.77 worker6

192.168.0.78 worker7



thanks 


Il giorno lunedì 13 febbraio 2017 15:32:36 UTC+1, John Flavin ha scritto:
How did you set up your pipeline engine? Did you run the pipeline setup script? The reason I ask is that the server http://localhost:8080/ is a default value that the pipeline engine uses if you have not told it a different address for your server.

Flavin

On Feb 11, 2017, at 10:14 AM, piero.chia...@gmail.com wrote:

Hi xnat experts,
I try to lunch a pipeline but 've this message:

/media/NAS/qNATitab/data/qnat/pipeline/bin/schedule /media/NAS/qNATitab/data/qnat/pipeline/bin/XnatPipelineLauncher -pipeline /media/NAS/qNATitab/data/qnat/pipeline/catalog/xnat-pipelines/QAP/qap_anat_processing.xml -id qNAT_E00001 -host http://192.168.30.228:8080 -u 9356b705-aa6a-4aba-a3d8-8dfe2854aa34 -pwd ******** -dataType xnat:mrSessionData -recordWorkflow false -label sub01_MR1 -supressNotification -project "test01" -parameterFile /media/NAS/qNATitab/data/qnat/build/test01/20170211_150430/sub01_MR1/sub01_MR1_params_20170211.xml -notify p.chiacc...@unich.it -notify in...@ser-ve.it -parameter mailhost='xxxxxxx' -parameter userfullname='xxxxxxxxx' -parameter builddir='/media/NAS/qNATitab/data/qnat/build/test01/20170211_150430' -parameter xnatserver='qNAT' -parameter adminema...@ser-ve.it' -parameter useremail='p....@unich.it'
Scheduling Command: /media/NAS/qNATitab/data/qnat/pipeline/bin/XnatPipelineLauncher -pipeline  /media/NAS/qNATitab/data/qnat/pipeline/catalog/xnat-pipelines/QAP/qap_anat_processing.xml  -id  qNAT_E00001  -host  http://192.168.30.228:8080  -u  9356b705-aa6a-4aba-a3d8-8dfe2854aa34  -pwd  '20170211_150430'  qNAT_E00001_wrk.xml  -dataType  xnat:mrSessionData  -recordWorkflow  false  -label  sub01_MR1  -supressNotification  -project  test01  -parameterFile  /media/NAS/qNATitab/data/qnat/build/test01/20170211_150430/sub01_MR1/sub01_MR1_params_20170211.xml  -notify  p.chiacc...@unich.it  -notify  xxxxxxxxt  -parameter  mailhost=xxxxxxx  -parameter  userfullname=xxxxxxx  -parameter  builddir=/media/NAS/qNATitab/data/qnat/build/test01/20170211_150430  -parameter  xnatserver=xNAT  -parameter  adminem...@ser-ve.it  -parameter  useremail=p.c...@unich.it  -config  /media/NAS/qNATitab/data/qnat/pipeline/pipeline.config  -catalogPath  /media/NAS/qNATitab/data/qnat/pipeline/catalog




thanks

John Flavin

chưa đọc,
10:59:41 13 thg 2, 201713/2/17
đến xnat_discussion
The errors you are seeing in that log indicate to me that the pipeline engine can't connect to your XNAT. It appears that it first tries to connect at http://localhost:8080/, and then at http://192.168.30.228:8080/ (which was specified as the "-host" argument when the pipeline was launched), and fails to connect to either address.

It also appears that you are using a custom schedule script to submit your pipeline jobs to a grid engine. Is that grid engine running on a different machine than your XNAT server? If it is outside your local network, than local addresses (like the two noted above) will not work. Can you log in to that machine and verify that you can connect to XNAT at the addresses noted above?

Flavin

piero.chia...@gmail.com

chưa đọc,
11:15:45 13 thg 2, 201713/2/17
đến xnat_discussion
The XNAT server and Pipeline engine are on the same machine also the Grid Engine runs on the same machine

thanks

Il giorno lunedì 13 febbraio 2017 16:59:41 UTC+1, John Flavin ha scritto:
The errors you are seeing in that log indicate to me that the pipeline engine can't connect to your XNAT. It appears that it first tries to connect at http://localhost:8080/, and then at http://192.168.30.228:8080/ (which was specified as the "-host" argument when the pipeline was launched), and fails to connect to either address.

It also appears that you are using a custom schedule script to submit your pipeline jobs to a grid engine. Is that grid engine running on a different machine than your XNAT server? If it is outside your local network, than local addresses (like the two noted above) will not work. Can you log in to that machine and verify that you can connect to XNAT at the addresses noted above?

Flavin

On Feb 13, 2017, at 9:34 AM, piero.chia...@gmail.com wrote:

So i download the xnat-pipeline-1.7.2.zip 

then i modified the gradle.properties:

piero.chia...@gmail.com

chưa đọc,
11:44:47 13 thg 2, 201713/2/17
đến xnat_discussion


schedule file :

-----------------------------------------------------------------

#!/bin/bash


log_file=/media/NAS/qNATitab/data/qnat/home/logs/grid-queue.log


logstart () {

 echo `date` >> $1

 echo -------------------------------------------------- >> $1

}



logend () {

 echo -------------------------------------------------- >> $1

}



logstart $logfile

      echo /media/NAS/qNATitab/data/qnat/pipeline/bin/PipelineJobSubmitter $*  $

      /media/NAS/qNATitab/data/qnat/pipeline/bin/PipelineJobSubmitter $*

logend $logfile

 



exit 0;

----------------------------------------------------------------------------------------------------------------



PipelineJobSubmitter.config   file: 
--------------------------------------------------------------------------------------------
################################################################
#Uncomment the following and customize for your project
#
PIPELINE_JOB_SUBMITTER_OPTS="-Dpipeline.tmp=/media/NAS/qNATitab/data/qnat/pipeline/tmp -DuserShell=sh -DaliasHost=http://localhost:8080 -Dout.location=:/media/NAS/qNATitab/data/qnat/home/logs/SGE -Dcwd.location=/media/NAS/qNATitab/data/qnat/build "
################################################################

--------------------------------------------------------------------------------------------

PipelineJobSubmitter file:


--------------------------------------------------------------------------------------------
#!/bin/bash

source "/media/NAS/qNATitab/data/qnat/pipeline"/config/PipelineJobSubmitter.config

java $PIPELINE_JOB_SUBMITTER_OPTS -classpath "/media/NAS/qNATitab/data/qnat/pipeline"/lib/com.noelios.restlet-1.1rc1.jar:"/media/NAS/qNATitab/data/qnat/pipeline"/lib/org.restlet-1.1rc1.jar:"/media/NAS/qNATitab/data/qnat/pipeline"/lib/saaj-1.jar:"/media/NAS/qNATitab/data/qnat/pipeline"/lib/commons-discovery-0.5.jar:"/media/NAS/qNATitab/data/q$

--------------------------------------------------------------------------------------------



Il giorno lunedì 13 febbraio 2017 16:59:41 UTC+1, John Flavin ha scritto:
The errors you are seeing in that log indicate to me that the pipeline engine can't connect to your XNAT. It appears that it first tries to connect at http://localhost:8080/, and then at http://192.168.30.228:8080/ (which was specified as the "-host" argument when the pipeline was launched), and fails to connect to either address.

It also appears that you are using a custom schedule script to submit your pipeline jobs to a grid engine. Is that grid engine running on a different machine than your XNAT server? If it is outside your local network, than local addresses (like the two noted above) will not work. Can you log in to that machine and verify that you can connect to XNAT at the addresses noted above?

Flavin

On Feb 13, 2017, at 9:34 AM, piero.chia...@gmail.com wrote:

So i download the xnat-pipeline-1.7.2.zip 

then i modified the gradle.properties:
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