help > RE: Missing parallelization option?
Jan 10, 2019  12:01 PM | Alfonso Nieto-Castanon - Boston University
RE: Missing parallelization option?
Hi Wilson,

Thanks for the quick reply and additional info. The issue seemed to be that any user-defined HPC configuration settings were only being propagated correctly from one version/release of CONN to the next after an update if either: a) users used the 'check for updates' option in the GUI for the update procedure (but this is currently only available for Matlab releases); or b) if the configuration settings are being saved for individual users instead of for all users (since in the former case those settings are actually stored in each user home directory while in the latter case the settings are saved in the CONN software directory which may easily change from one release to the next). In any way, thanks again, this should help me fix this issue -hopefully for the next release- (and the permissions issue should be fixable either by using chmod to change the CONN installation directory permissions, or, if CONN appears to be trying to save a file into a different directory like a temporary MCR directory, by adding first the directory where run_conn.sh is installed to the system path). 

Best
Alfonso
Originally posted by Wilson Ho:
Hello Alfonso,

Thank you for the quick response. Indeed checking the Default profile has restored the option.
I am using CONN standalone 18b, and I recall the original HPC settings were saved for all users, not only for current. For 18b, I was having permissions issues saving for all users, but this could probably be resolved with sudo. Feel free to let me know if you would like any more info.

Thanks
Wilson


Originally posted by Alfonso Nieto-Castanon:
Hi,

Could you please double-check if the PBS/Torque option is marked as the default parallelization profile (i.e. if the 'Default profile' checkbox is checked for this profile in the HCP configuration menu)? 

also, if this option is not checked and simply checking it solves this issue, could you please still let me know just for debugging purposes if you recall how you originally saved your HCP configuration settings (saved for all users or only current user?, using standalone or Matlab version? that will help me debug this so other users do not run into the same problem)

Best
Alfonso
Originally posted by Wilson Ho:
Hello Alfonso and CONN experts,

I recently switched from the 17.f standalone to the 18.b standalone and I've noticed some great improvements, especially in the interface speed, so thank you for all the work you have put into this!

I have a question with the HPC setup with 18.b. Back in 17.f I had a setup (with PBS/Torque) that worked both in the configuration tests, and for processing steps. In 18.b I noticed that while the PBS/Torque option still shows in the configuration menu (Tools>HPC Options>Configuration) and can be tested successfully, it no longer appears as an option in the dropdown for processing steps (see screenshot). Since no one else has mentioned this I presume it is a glitch with my specific installation. Do you know if there is a way to restore this option? Parallelization has been a life-saver for the dozens of subjects I've had to process, and it would be great to have it back.

Thanks!

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TitleAuthorDate
Wilson Ho Jan 10, 2019
Alfonso Nieto-Castanon Jan 10, 2019
Wilson Ho Jan 10, 2019
RE: Missing parallelization option?
Alfonso Nieto-Castanon Jan 10, 2019