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configuration-files.md

@@ -52,38 +52,38 @@ A detailed description of each of the fields can be found below:
 :b: Default set to *redfin.sharcnet.ca*  
 
 **6. Project Root Archive Address**  
-* text   --------------------------------------------    
+* text   ??????????????????????????????????????????  
 :b: :warning: Default of *dtn.sharnet.ca:/work/user_name/project_name* needs to be adjusted for your job.  
 
 **7. Project Root Work Address**  
-* text   ----------------------------------------------------------------  
+* text   ???????????????????????????????????????????????   
 :b: :warning: Default of *dtn.sharnet.ca:/work/user_name/project_name* needs to be adjusted for your job.   
 
 **8. Dependency Address**  
-* text  ----------------------------------------------------------  
+* text  ????????????????????????????????????????????????????   
 :b: :warning: Default of *dtn.sharnet.ca:/work/user_name/project_name/analysis/support/dependencies* needs to be adjusted for your job.
 
  *** 
 
 **9. Archive Mount Directory**  
-* text   -------------------------------------------------------------------    
+* text   ????????????????????????????????????????????????????    
 :b: Default set to *remote_archive*   
 
 **10. Work Mount Directory**  
-* text  ----------------------------------------    
+* text ?????????????????????????????????????????????????????    
 :b: Default set to *remote_work*   
 
  *** 
 
 **11. Miscellaneous Locations**  
-* text  ------------------------------------------  
+* text  ???????????????????????????????????????????????????   
 :b: Default left as    '  '.  
 
  ***  
 
 **12. System Variables**  
 * System variables are custom system commands you can quickly make using the other context configuration variables. 
-* text  ------------------------------------------  
+* text ???????????????????????????????????????????????? 
 For more information visit the [Mounting the Project](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/remote-start-up#mounting-the-project) on the [Managing Remote Projects](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/remote-start-up) page.  
 :b: Default set as:  
         *sshfs [remote_user_name]@[remote_project_archive] [cd]/[mount_archive]  
@@ -117,8 +117,11 @@ This is a drop down menu where you will select one of the following:
 * *Current Base*  
 This designates the job to be completed locally.
 * *Sq_Sub*  
-This designates the job to be completed on the Sharcnet.  
-  * Other schedulers are currently being developed including qSub and Slurm.  
+This designates the job to be completed on the Sharcnet using the sqsub wrapper scheduler.  
+* *q_Sub*  
+This designates the job to be completed on the Sharcnet using the qsub scheduler.  
+  * Other schedulers are currently being developed including Slurm and Torque.    
+
 :b: The default depends on whether you loaded the local or remote file.
 
 **2. Replace String**  
@@ -179,10 +182,11 @@ It also contains a loop which will remove the *Fieldtrip* plugin as it will cras
 
 **8. Scheduler Options**  
 * This section contains a series of characters to communicate the job specifications to the remote server, such as memory and time. Click on the field and look at the information box below to see the specific commands. If you are running a project locally you can leave this field blank.   
-:b: Remote default is *-r 4h --mpp 6G*  for Octave Scripts and *-r 4h -q -mpi 1G* for amica files.
+:b: Remote default is *-r 4h --mpp 6G*  for Octave Scripts and *-r 3h --mpp 1G --ppn 1 -q mpi -n 8* for AMICA files when selecting sqsub. For qsub the defaults would be *-q serial -l nodes=1:ppn=1,pvmem=6gb,walltime=4:00:00* for Octave Files, and *-q mpi -l nodes=1:ppn=8,pvmem=1gb,walltime=3:00:00* for AMICA.
 These should be adjusted based on what server you are running your jobs on as well as the kind of process you are preforming. Some jobs will require more time and some will require more memory. These also effect the que time your jobs will have in the scheduler. Most of the time jobs with shorter time and lower memory will get into que faster, but you also don't want your job to crash as you did not give it enough resources.    
 
-The nature of the string also depends on what scheduler you are using. The current systems use qsub or sqsub, but as of April 2017 the new Sharcnet servers will be using Slurm.  
+The nature of the string also depends on what scheduler you are using.   
+:warning:  The current systems use qsub or sqsub, but as of April 2017 the new Sharcnet servers will be using Slurm.  
 
 **9. Software**  
 This is a drop down menu where you can select one of the following: