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FNNDSC / projectman

FNNDSC project manager
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setup brain chris instance #44

Closed NicolasRannou closed 9 years ago

NicolasRannou commented 9 years ago

'brain.chpc.ac.za', user: rpienaar.

A good exercise to make sure the wiki is up to date.

NicolasRannou commented 9 years ago

We need to contact the help desk, might be a firewall issue: port 443 is blocked.

In the meanwhile, using regular http connection.

nico@vpn-17218216-151:~$ telnet brain.chpc.ac.za 80
Trying 196.24.44.34...
Connected to brain.chpc.ac.za.
Escape character is '^]'.
^C
Connection closed by foreign host.
nico@vpn-17218216-151:~$ telnet brain.chpc.ac.za 443
Trying 196.24.44.34...
telnet: connect to address 196.24.44.34: Operation timed out
telnet: Unable to connect to remote host
NicolasRannou commented 9 years ago

sudo su was not passwordless for chris user

updated the wiki: http://durban/wiki/index.php/ChRISMEGABUNDLE#If_a_VM_is_given_with_Ubuntu_already_installed

NicolasRannou commented 9 years ago

findsession plugin was there, which makes everything crash because can not generate XML output.

$> tail -f /var/log/apache2/error.log
[Fri Mar 06 10:17:45.850659 2015] [:error] [pid 30294] [client 134.174.21.27:4879] PHP Warning:  SimpleXMLElement::__construct(): Entity: line 1: parser error : Start tag expected, '<' not found in /home/chris/src/chrisreloaded/controller/plugin.controller.php on line 164, referer: http://brain.chpc.ac.za/
[Fri Mar 06 10:17:45.850995 2015] [:error] [pid 30294] [client 134.174.21.27:4879] PHP Warning:  SimpleXMLElement::__construct(): Traceback (most recent call last):  File "/home/chris/src/chrisreloaded/plugins/ in /home/chris/src/chrisreloaded/controller/plugin.controller.php on line 164, referer: http://brain.chpc.ac.za/
[Fri Mar 06 10:17:45.851155 2015] [:error] [pid 30294] [client 134.174.21.27:4879] PHP Warning:  SimpleXMLElement::__construct(): ^ in /home/chris/src/chrisreloaded/controller/plugin.controller.php on line 164, referer: http://brain.chpc.ac.za/
[Fri Mar 06 10:17:45.851819 2015] [:error] [pid 30294] [client 134.174.21.27:4879] PHP Fatal error:  Uncaught exception 'Exception' with message 'String could not be parsed as XML' in /home/chris/src/chrisreloaded/controller/plugin.controller.php:164\nStack trace:\n#0 /home/chris/src/chrisreloaded/controller/plugin.controller.php(164): SimpleXMLElement->__construct('Traceback (most...')\n#1 /home/chris/src/chrisreloaded/view/plugin.view.php(82): PluginC::getUI('findsession')\n#2 /home/chris/src/chrisreloaded/controller/plugin.controller.php(72): PluginV::getHTML(Array)\n#3 /home/chris/src/chrisreloaded/index.php(73): PluginC::getHTML()\n#4 /home/chris/src/chrisreloaded/index.php(195): homePage()\n#5 {main}\n  thrown in /home/chris/src/chrisreloaded/controller/plugin.controller.php on line 164, referer: http://brain.chpc.ac.za/

Deeper investigation:

chris@brain:~/src/chrisreloaded/plugins/findsession$ ./findsession --xml
Traceback (most recent call last):
  File "./findsession", line 110, in <module>
    plugin.add_parameter('Advanced', Plugin.STRING, '--findsessionscript', action='store', dest='FindSessionScript', default=plugin.envVars['ENV_FINDSESSION_SCRIPT'], help='The find session script')
KeyError: 'ENV_FINDSESSION_SCRIPT'
``
NicolasRannou commented 9 years ago

need to hook up a chris_push between BCH and Brain: 1- passwordless shh 2- email service 3- add targets in both configurations

rudolphpienaar commented 9 years ago

Good work, Nico...

I'll look into the passwordless ssh and email right now...

NicolasRannou commented 9 years ago

ZIP package on brain VM was missing...

NicolasRannou commented 9 years ago

freesurfer was missing

NicolasRannou commented 9 years ago

neuro-fs script must be modified:

-export PACKAGEDIR=/neuro/arch/${HOSTTYPE}-${OS}/packages
+export PACKAGEDIR=/lustre/SCRATCH5/cubic/chris/packages
NicolasRannou commented 9 years ago

libxmu not available anymore on ubuntu, use: sudo apt-get install libxmu6

NicolasRannou commented 9 years ago

fsl was missing

NicolasRannou commented 9 years ago

packages/scripts/dcmanon_meta.bash and dicom_dirSend.bash must be modified to point to right certificate for anonymization

NicolasRannou commented 9 years ago

keys in anonymize_keys were not correct, error updated in wiki CA_cert.pem instead of CA_cert.cer

NicolasRannou commented 9 years ago

in wiki error: CA_cert.pem instead of CA_cert.cer

rudolphpienaar commented 9 years ago

Ugh... there are so many little niggling things!!

NicolasRannou commented 9 years ago

missing files for the mri_deface in freesurfer directory on sun...:

GCAread(/lustre/SCRATCH5/cubic/chris/packages/freesurfer/stable/average/talairach_mixed_with_skull.gca): could not open file