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wl78
Starting Member
USA
3 Posts |
 Posted - Jul 15 2010 : 09:08:27 AM
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Hello,
I am a beginner and need help.
I can log in one node using qinteract, but I don't know how to mount the experiments using lnexp.
my questions are:
where to put my script and data? in munin or fatt? in my home directory? or any other folder?
I created a folder: //munin/users/wl78/Experiment.01
and I tried "lnexp Experiment.01", but it does not work.
can somebody tell me what i should do?
Another question: I want to use Matlab, will the cluster be much faster than my current desktop, which has 4 cores and 8 G RAM?
thanks in advance!
Wei
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josh.bizzell
BIAC Staff
USA
118 Posts |
Posted - Jul 15 2010 : 09:39:36 AM
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Wei
What is the actual experiment you wish to access? Experiment.01 is just an example; it doesn't actually exist. Put the name of your actual experiment/study instead of "Experiment.01".
lnexp will then create the necessary folders (~/experiments/YourExperiment.01) for you and mount the correct server automatically.
You can also use "mntshare" to mount an entire server, which may be desirable (this is what I do - see this forum post: http://www.biac.duke.edu/forums/topic.asp?TOPIC_ID=1429 ).
It sounds like you have a pretty fast machine, so the cluster may not run Matlab faster, especially if you'll be doing any sort of visualization via Matlab.
-Josh |
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petty
BIAC Staff
USA
453 Posts |
Posted - Jul 15 2010 : 09:43:36 AM
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regarding matlab, your machine will be faster than the interactive nodes. if you wanted to run things non-interactively, and only through submission scripts, then thats a different story. the compute nodes have more processors/ram (8,32GB) than the interact nodes (4,8gb).
the one major difference will be the memory limits. if you have large data sets and are constantly getting "out of memory" errors in windows, then the cluster would be better for you, as matlab's available ram isn't as limited in linux than windows. |
Edited by - petty on Jul 15 2010 09:48:17 AM |
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wl78
Starting Member
USA
3 Posts |
Posted - Jul 15 2010 : 11:25:57 AM
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quote:
Originally posted by josh.bizzell
Wei
What is the actual experiment you wish to access? Experiment.01 is just an example; it doesn't actually exist. Put the name of your actual experiment/study instead of "Experiment.01".
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Yes, this is my question! I don't know how to setup an actual experiment/study :(
BTW, the mntshare works for me. But I just want to use matlab non-interactively, so that I can access more precessors/ram. I want to use qsub rather than qinteract. I use qinteract primarily for debugging purpose. So How I create such an experiment and make it visible for the cluster?
I have access to SysDevelop.16. But I tried to use
qsub -v EXPERIMENT=SysDevelop.16 myShellScript.sh
but it never works for me...
Thanks,
Wei
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
lnexp will then create the necessary folders (~/experiments/YourExperiment.01) for you and mount the correct server automatically.
You can also use "mntshare" to mount an entire server, which may be desirable (this is what I do - see this forum post: http://www.biac.duke.edu/forums/topic.asp?TOPIC_ID=1429 ).
It sounds like you have a pretty fast machine, so the cluster may not run Matlab faster, especially if you'll be doing any sort of visualization via Matlab.
-Josh
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petty
BIAC Staff
USA
453 Posts |
Posted - Jul 15 2010 : 2:10:49 PM
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It looks like your script just worked on node13
everything was mounted correctly and your log shows that your matlab script ran
The only way you can get your own actual experiment is going through the research application process.
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wl78
Starting Member
USA
3 Posts |
Posted - Jul 15 2010 : 2:28:47 PM
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Thanks a lot for your help! I finally solved all the problems.
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dvsmith
Advanced Member
USA
218 Posts |
Posted - Oct 14 2015 : 4:03:26 PM
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Hi -- has lnexp been replaced by a new command?
[dvs3@hugin ~]$ lnexp Imagene.02
-bash: lnexp: command not found
Thanks,
David
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Oct 14 2015 : 4:05:51 PM
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| It's there, you just can't do it on hugin, you need to be on one of the compute nodes. |
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petty
BIAC Staff
USA
453 Posts |
Posted - Oct 14 2015 : 4:06:26 PM
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you can't mount your experiments on the head node ...
however, having said that ... the only thing lnexp actually does is run "findexp" and create a symbolic link for you to that path |
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dvsmith
Advanced Member
USA
218 Posts |
Posted - Oct 14 2015 : 4:08:53 PM
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Ah, woops.... Sorry I forgot the whole "qinteract" thing. I am a little rusty. :-)
Thanks!
David
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rl100
Starting Member
6 Posts |
Posted - Apr 13 2018 : 1:41:57 PM
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| did y'all change lnexp to something else? findexp works but lnexp does not (from an interactive node) |
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petty
BIAC Staff
USA
453 Posts |
Posted - Apr 13 2018 : 1:46:15 PM
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| Don’t use lnexp anymore, that’s just leftover from the days when each individual mount had a unique path ... now the paths are always the same, which is what findexp would return |
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rl100
Starting Member
6 Posts |
Posted - Apr 13 2018 : 2:43:00 PM
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| is it still possible to "mount" an experiment to our experiments folder on the cluster for navigation ease? |
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petty
BIAC Staff
USA
453 Posts |
Posted - Apr 13 2018 : 2:51:12 PM
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lnexp just stands for link experiment .. it was just a symbolic link to your experiment path
You could make that same link if you wanted .. “ln -s” whatever findexp returns
We did away with the links to the home directory because i think it caused issues deleting old account folders if there was a symlink |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Apr 13 2018 : 2:54:58 PM
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quote:
Originally posted by rl100
is it still possible to "mount" an experiment to our experiments folder on the cluster for navigation ease?
If you want to navigate easily to an experiment directory, add this:
chexp() { cd $( findexp $1 ); };
to the end of your ~/.bash_profile file (using nedit or some other cluster-based editor). Then, next time you log in:
chexp Experiment.01
will be the same thing as:
cd /mnt/BIAC/.../Experiment.01
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rl100
Starting Member
6 Posts |
Posted - Apr 13 2018 : 2:57:30 PM
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Great; thanks!
For posterity for folks who aren't the most computer savvy (such as myself), here's what I did:
expath=`findexp MYEXPERIMENTNAME.01`
ln -s $expath
note that it's not single quotes for expath; it's the down tickmark thingie that shares a key with the ~ |
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Topic |
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how to use lnexp?
