| T O P I C R E V I E W |
| djt11 |
Posted - Feb 24 2011 : 1:45:51 PM
Hi,
I am new to working on the BIAC cluster. I was wondering how can I access FSL commands using the cluster.
Thanks
Dipti |
| 15 L A T E S T R E P L I E S (Newest First) |
| petty |
Posted - Mar 11 2011 : 2:25:40 PM
nope .. those will be two seperate mounts, on different nodes, writting to different resulting directories. |
| djt11 |
Posted - Mar 11 2011 : 2:20:19 PM
So if i Submit this first
qsub -v EXPERIMENT=FSE.01 fslvbm.sh here rawdir is FSL03082011
and then I submit this
qsub -v EXPERIMENT=FSE.01 fslvbm.sh here rawdir is FSL03112011
Will this create an issue?
|
| petty |
Posted - Mar 11 2011 : 2:16:19 PM
if you mean in two seperate submissions, which each mount their own experiment, then yes.
But if you mean within the same script in one submission, then no. |
| djt11 |
Posted - Mar 11 2011 : 2:13:19 PM
Chris ,
One quick question, Can i run to experiments simultaneously using the fslvbm.sh script using the qsub command or will they interfere with each other.? |
| petty |
Posted - Mar 08 2011 : 09:55:52 AM
glad it worked ... now i will just have to remember to make this change with every release of FSL ! |
| djt11 |
Posted - Mar 07 2011 : 11:02:29 AM
Hey Chris,
Thanks for all the help on running FSLVBM, I managed to get the results successfully this time with the appropriate design files
Thanks Really Appreciate it |
| djt11 |
Posted - Mar 04 2011 : 1:54:20 PM
Hey thanks for the heads up.
I realized that sometime back though, I have changed the data to match the model and have started processing it again. Hopefully it should work appropriately this time. Thanks Again for all the inputs and help. Really appreciate it |
| petty |
Posted - Mar 04 2011 : 1:13:43 PM
dipti, your vbm from this morning failed at the randomise step, but its because the model had more points than the data.
if you created the correct model, you could actually just run the randomise step |
| djt11 |
Posted - Mar 04 2011 : 11:28:20 AM
Thanks a lot
I guess I confused with the error files it produced yesterday. Sorry about that |
| petty |
Posted - Mar 04 2011 : 11:20:35 AM
dipti .. the corrected version i created this morning is actually still running ( under your name ), so this is a very good sign for you.
time should have no relevance here because the time ( $HOWLONG ) they are referencing corresponds to which cluster queue they are submitting jobs to with fsl_sub. We aren't using fsl_sub at biac at this point due to other constraints. Their fsl_sub command assumes we have our sge grid set-up exactly like theirs, which we don't (yet) |
| djt11 |
Posted - Mar 04 2011 : 10:36:50 AM
Hey Chris,
Thanks a lot for the help.
Though it did go a little further than what I was getting till yesterday, It yet crashed, at fslvbm2c and this time it gave permission denied and command not found.
Also I have been researching, that this could be due to the time it is suppose to remain on each command is only for 15 to 30.I wanted to change that and see to say around 1000 to see if that makes a difference.
So do i need to create completely different scripts for my fslvbm to run on the cluster ?
Thanks
Dipti |
| petty |
Posted - Mar 04 2011 : 07:54:58 AM
i peaked in your results directory to see that it failed in the same place.
however, i was able to see the outputs in the struct directory before they were deleted and i tried a couple things.
i figured out why they were crashing ( hopefully ). It was the way they were trying to run the scripts ... you can't run them that way on a cifs mounted file system. I changed the lines in the source code to a way that would let a script be executed on a cifs system and tested it on the command line.
After that, i resubmitted step 2 and 3 for you ... let me know if it finishes. |
| petty |
Posted - Mar 03 2011 : 4:19:20 PM
you can't edit them directly ... i did however have a thought about your "permission denied" error.
there's 2 parts of fslvbm that write scripts, so i looked into their code and they seem to try and "chmod" a script which they've produced. A normal user wouldn't have permission to do this, hence "permission denied"
I edited the chmod lines in the fslvbm_2_template and fslvbm_3_proc steps ( only in 4.1.5 currently ) ... Give this a shot again and see if you get the same error |
| djt11 |
Posted - Mar 03 2011 : 4:00:02 PM
Hey
Can someone please tell me,if i Need to edit, an fslvbm script, How do i do it? |
| petty |
Posted - Mar 02 2011 : 3:37:26 PM
i would suggest running the fslvbm2c from the command line on the interact node to see what happens |
