The HLA*IMP software has been amended, in order to accommodate the temp folder that the software likes to use. The previous version required root access to this internal folder, something that is not a good idea on a shared cluster.
The workaround is to create your own temp folder, issued just before you run the software. The precise command is mentioned below.
Unless stated otherwise, this temp folder would be created on your lampredi2 home folder, and should be a one-off process. If you wanted to set a temp folder elsewhere e.g. within the lustre storage then that is possible too.
This temp folder is where the graphs, and other files, are stored during the software run. They don’t appear to be particularly large (your lampredi2 home folder does have a quota level set at 20GB, in order to prevent jobs being run from the login/head node).
https://oxfordhla.well.ox.ac.uk/hla/static/tutorialIMP2.pdf
For our purposes, we are assuming that you will take a copy of the two example data files, mentioned in the tutorial, and will copy them to your lustre area first.
(1)
Log into lampredi2 using Microsoft Remote Desktop Connection (Windows),
CoRD (Mac) or TS Client (Linux – there’s a myriad of names for this
client, depending on the distro you use).
(2)
Click on the Terminal icon and issue the commands:
$ qrsh
$ module load apps/hlaimpbe
$ module load apps/hlaimpfe
Here we issue the new command to create a temp folder that the software can use:
$ mkdir -p $HLAIMPFE_USERTMP
If we are following the tutorial, we can copy the example data we need to our lustre storage. I’m going to use a folder called “hla_test” on my lustre storage area.
$ mkdir -p ~/lustre/hla_test | cp $HLAIMPFEDIR/share/PnP2Pipeline/interface/examples/* ~/lustre/hla_test
(3)
Now we can run the HLA software using:
$ interface.pl
You can follow the tutorial at page 3 on the PDF document. You just need to browse to /users/your_home_folder/lustre/hla_test folder when locating your main data file. Remember that this is also the same as using ~/lustre/hla_test and /mnt/lustre/users/your_home_folder/hla_test
It might seem cumbersome using the example data in this way but it actually avoids us having to “fight” with the GUI, when it comes to declaring where data is to be located.
Lampredi HPC
igm-lampredi-users@ncl.ac.uk
IGM IT
igmithelp@ncl.ac.uk
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