PyRx linux cluster

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PyRx linux cluster

Postby wazeer » Thu Jul 10, 2014 1:07 am

Hi Sargis,

I bought PyRx for x64 linux and I have installed it on the login node of the cluster - the OS is Centos 6.3 with SGE,

I have two concerns,

1- I tried to run a job using the cluster option but it failed with this error message,

ERROR|2014-07-09 17:40:27,489|Error in : <bound method RunVinaPage.TryRun of <PyRx.vinaWizard.RunVinaPage; proxy of <Swig Object of type 'wxPanel *' at 0x65c4de0> >>
Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> noTK
Traceback (most recent call last):
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/wxMainFrame.py", line 338, in TryCommand
retObject = command(*args, **kw)
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/vinaWizard.py", line 416, in TryRun
pbsJob = pbsJobs.startVina(self)
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/pbsJobs.py", line 71, in startVina
parent.TopLevelParent.documentsView.ClosePath(readme)
AttributeError: 'AuiFloatingFrame' object has no attribute 'documentsView'
>>> Traceback (most recent call last):
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/wxMainFrame.py", line 338, in TryCommand
retObject = command(*args, **kw)
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/vinaWizard.py", line 416, in TryRun
pbsJob = pbsJobs.startVina(self)
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/pbsJobs.py", line 71, in startVina
parent.TopLevelParent.documentsView.ClosePath(readme)
AttributeError: 'AuiFloatingFrame' object has no attribute 'documentsView'
>>>
ERROR|2014-07-09 17:35:40,532|Error in : <bound method RunVinaPage.TryRun of <PyRx.vinaWizard.RunVinaPage; proxy of <Swig Object of type 'wxPanel *' at 0x65c4de0> >>
Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> noTK
Traceback (most recent call last):
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/wxMainFrame.py", line 338, in TryCommand
retObject = command(*args, **kw)
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/vinaWizard.py", line 416, in TryRun
pbsJob = pbsJobs.startVina(self)
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/pbsJobs.py", line 71, in startVina
parent.TopLevelParent.documentsView.ClosePath(readme)
AttributeError: 'AuiFloatingFrame' object has no attribute 'documentsView'



2- Then I tried to ssh to one of the nodes and run ./run.sh but nothing happened! Can not I run PyRx on a node and use local option instead ?


Thanks,

Muhammad
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Re: PyRx linux cluster

Postby sargis » Sun Jul 13, 2014 9:54 pm

Hi Muhammad,

Thank you for purchasing PyRx. I've made changes so that PyRx can run with SGE. Please run the following command on the login node of the cluster and (re)start PyRx:
Code: Select all
cd /home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx
svn update


wazeer wrote:2- Then I tried to ssh to one of the nodes and run ./run.sh but nothing happened! Can not I run PyRx on a node and use local option instead ?

Sure, please pass -X option to ssh for X11 forwarding http://itg.chem.indiana.edu/inc/wiki/so ... h/200.html

Thank you for using PyRx!
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Re: PyRx linux cluster

Postby wazeer » Sun Jul 13, 2014 10:49 pm

Thanks Sargis for your help,
I will do that and update you.
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Re: PyRx linux cluster

Postby wazeer » Sun Jul 13, 2014 11:57 pm

For sorry the error still persists, I did svn upgraded the libraries as you said but still I got the below error message,

ERROR|2014-07-13 16:56:41,990|Error in : <bound method RunVinaPage.TryRun of <PyRx.vinaWizard.RunVinaPage; proxy of <Swig Object of type 'wxPanel *' at 0x5fc0be0> >>
Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> noTK
Traceback (most recent call last):
File "/home/muhammad/.PyRx_workspace/update/PyRx/wxMainFrame.py", line 338, in TryCommand
retObject = command(*args, **kw)
File "/home/muhammad/.PyRx_workspace/update/PyRx/vinaWizard.py", line 417, in TryRun
pbsJob = pbsJobs.startVina(self)
File "/home/muhammad/.PyRx_workspace/update/PyRx/pbsJobs.py", line 71, in startVina
parent.TopLevelParent.documentsView.ClosePath(readme)
AttributeError: 'AuiFloatingFrame' object has no attribute 'documentsView'
>>>
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Re: PyRx linux cluster

Postby sargis » Mon Jul 14, 2014 1:49 am

Please remove /home/muhammad/.PyRx_workspace/update folder and try again.
Code: Select all
rm -rf /home/muhammad/.PyRx_workspace/update

It's picking up the code from /home/muhammad/.PyRx_workspace/update instead of /home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx.

Please let me know if the error still persists after you remove /home/muhammad/.PyRx_workspace/update.

Thanks!
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Re: PyRx linux cluster

Postby wazeer » Mon Jul 14, 2014 1:56 am

Hi Sargis,

For sorry the error still persists, here is the new error message,

RROR|2014-07-13 18:55:32,821|Error in : <bound method RunVinaPage.TryRun of <PyRx.vinaWizard.RunVinaPage; proxy of <Swig Object of type 'wxPanel *' at 0x70e35b0> >>
Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> noTK
Traceback (most recent call last):
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/wxMainFrame.py", line 338, in TryCommand
retObject = command(*args, **kw)
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/vinaWizard.py", line 416, in TryRun
pbsJob = pbsJobs.startVina(self)
File "/home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/pbsJobs.py", line 71, in startVina
parent.TopLevelParent.documentsView.ClosePath(readme)
AttributeError: 'AuiFloatingFrame' object has no attribute 'documentsView'

Thanks for your help,

Muhammad
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Re: PyRx linux cluster

Postby sargis » Mon Jul 14, 2014 2:10 am

Hi Muhammad,

Sorry about that. It seems that svn update didn't work. Would you please get http://sourceforge.net/p/pyrx/code/HEAD ... pbsJobs.py and replace /home/muhammad/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/pbsJobs.py with that file.

Thanks!
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Re: PyRx linux cluster

Postby wazeer » Mon Jul 14, 2014 2:33 am

Great, now it works! One last question in this issue, the job is submitted but how to track it and visualized the results ? I submitted the job for one ligand and still I do not see any feedback, also qstat does not give me anything!

Thanks really for your help,

Muhammad
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Re: PyRx linux cluster

Postby sargis » Mon Jul 14, 2014 3:05 am

Good to see it works now. PyRx creates PyRxVinaJob-yourLigandName job file and submits it using qsub command. I've tested this with SGE installed on CentOS6 using instructions from http://wiki.eri.ucsb.edu/sysadm/Sun_Grid_Engine. I don't know how SGE was installed on your cluster. Check your home folder to see if there is any useful log messages there. The PyRxVinaJob file is located in /home/muhammad/.PyRx_workspace/Macromolecules/YourMacromolecule folder, where YourMacromolecule is the name of your macromolecule. Use qsub to run this job file and talk to your sysadmin to debug any possible issues.

PyRx has no options currently to track PBS or SGE jobs. You'll need to use qstat command to track the execution of these jobs. Once these jobs are completed, you can use Forward button to visualized the results.

Hope this helps and thanks for your feedback.
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Re: PyRx linux cluster

Postby wazeer » Mon Jul 14, 2014 4:22 am

Thanks very much for all your help.
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