*Qs 1: How do I cite or mention the cluster in papers? or what is the preferred method?

...

You could try a trace.
cmake --trace . 2>&1 | tee /tmp/cmakeOut.txt

You may have to explicitly mention the path, For example:
cmake . -DLAPACK_LIBRARIES=/sw/library/lapack/lapack-3.6.0/3.6.0/lib64/liblapack.so -DBLAS_LIBRARIES=/sw/library/blas/CBLAS/lib/cblas_LINUX.so
 
OR:
 cmake . -DLAPACK_LIBRARIES=/sw/library/lapack/lapack-3.6.0/3.6.0/lib64/liblapack.so -DBLAS_LIBRARIES=/sw/library/blas/CBLAS/lib/cblas_LINUX.so -DCMAKE_INSTALL_PREFIX=/sw/simbody/353

Qs28:  How do I check number of CPUs my job is using

You can find out on which compute node your job is running:
qstat -1an|grep snumber
>>>>>>>>>>>>>>>>>>>
e.g:
qstat -1an|grep s2761086
4598354.pbsserv s2761086 workq    DT_k-e_04   21795   1   1   10gb 99999 R 523:2 n010/0
Here you see it is running on n010
Then you can do this:
ssh nodename -t "htop"  or ssh nodename -t "htop -u username" 
e.g.ssh n010 -t "htop -u s2761086"
Press <F2> key, go to "Columns", and add PROCESSOR under "Available Columns".
The currently used CPU ID of each process will appear under "CPU" column.

Qs29:   How to customize an environmental variable using modules

...

Qs 31: Multi Cores are requested and allocated by PBs but job runs only on 1 core. Why is that?

This contribution is from Nicholas Dhal and is acknowledged. Nick is an active Grifith HPC user.

>>>>>>>>>

...

goo.gl/koYII3

>>>>>>>>>>

Qs 32: How to check the remaining licenses on the license server

...

e.g scp -r /export/home/s5284664/folder n061:/lscratch/s5284664/

Qs.56: NCMAS process and application

NCMAS facilities overview and who should apply
https://youtu.be/7ZZVk4HtdDY

NCMAS process and application 2021
https://youtu.be/hmV_j5GFgI0

Qs 57: What kind of storage and compute is available on Griffith HPC

...

Additionally and in parallel, you can also apply directly when the application opens

https://my.nci.org.au/mancini/ncmas/2022/

Please note that projects will be given a fixed allocation which is given per quarter on a use it or loose it basis. Allocations cannot be carried forward or backward into other quarters. Standard disk space per project is 75GB in /scratch and if a project needs more you will need to contact help@nci.org.au.

Students cannot be a lead CI on an NCI project however, for the QCIF share postdocs can be. For NCMAS the lead CI is required to have an ARC or NHMRC grant or equivalent which is why larger groups apply for NCMAS. A grant is not required for a project under QCIF. However, the QCIF allocations are small, around 20-50 thousand per quarter. Larger allocations are only available through NCMAS.

Some applications like Mathematica and Matlab are licensed software. Mathematica is only available to ANU researchers on NCI. For Matlab, Griffith will need to get in contact with NCI to set up their institutional license. At the moment this is not available so one cannot use it. Unless you have your own license. But also in that case you would need to get in touch with NCI first to see if you can use Matlab on Gadi or not.

In general, allocations are given in service units SUs. 1 core hour is charged at 2 SUs. So if you have a calculation running using 4 cores and taking 48 hours then you will be charged 4*48*2=384 SUs for that calculation.

If a larger disk space (e.g 300GB) is needed, you would need to talk to NCI to increase the space in /scratch to accommodate this. If a larger RAM (e.g 400GB ), then you would need to make sure you run in a queue that supports that ram request. They could be charged more than 2 SUs per core hour though, so you would need to factor that in.

But talk to NCI, help@nci.org.au, first to see if you could use the application (e.g Matlab) onNCI before you even consider applying for an allocation on NCI.

Qs69: How to install bioinformatics software in your home directory

...

Reference: https://kb.hlrs.de/platforms/index.php/Batch_System_PBSPro_(vulcan)#DISPLAY:_X11_applications_on_interactive_batch_jobs

The login or head node of each cluster is a resource that is shared by many users. Running a GUI job on the login node is prohibited and may adversely affect other users. X11 Forwarding is only possible for interactive jobs.

Please note that there is a performance penalty when running a GUI job on the compute nodes using the method outlined below. 

Set up X11 forwarding

To use X11 port forwarding, Install Xming X Server on Windows laptop/desktop first. Install the xming fonts package as well.
See instructions here: https://griffith.atlassian.net/wiki/spaces/GHCD/pages/4035477/xming

...

1. http://mobaxterm.mobatek.net/download-home-edition.html
2. putty
3. Filezillia
4. Windows WSL system lets you run the linux versions of ssh under windows.
      wsl --install
   This should get you command line:  ssh,  scp,  and sftp; 

...

To transfer from remote to locally: scp -r remotehostname:/export/home/snumber/FolderName ~/ 

Qs80: Tunnel setup

Tunneling setup:

...

Requests of this type should be directed to IT Service Centre to raise though the Digital Solutions service management system (Cherwell / GSM). 
The easiest way to do this is to email your request to ithelp@griffith.edu.au. The request will then be redirected to the correct team. 
Given the email list is an LML, this will be Identity Services. 
(e.g Reference GSM case Incident#1081850)
The solution provided for this was this:
>>>>>>
Regarding your Service Request 1081850 emails sent to LML email list are not received by me, logged on 7/11/2023 2:49 PM, 
we have the following question or update:

We have noticed a discrepancy in the Group Membership for LML - GHPC and your Staff Azure GroupMembership was missing from this Azure Group used for email.  A re-synchronization of this group has increased the associated Azure Group Membership from 178 to 216 members of which you were one of the people missing. Thank you for notifying us of this anomaly.

You will receive emails for those sent to this group from now on.

None of the other LML - Groups (you have membership for) have Staff Azure/Staff Email as a Target System  and would never generate email.

This Service Request will now be marked resolved on the basis of the action taken and information provided.

>>>>>> 

Qs88: Install perl modules without root access.

Install perl locally

>>>>>>>>installation notes<<<<<<<<<<<<
Download the perl source file and unzip/untar
wget https://www.cpan.org/src/5.0/perl-5.38.2.tar.gz --no-check-certificate  
 ./Configure -des -Dprefix=~/sw/perl/5.38.2 2>&1 | tee configureLogs.txt
   make 2>&1 |tee makeLogs.txt
   make test 2>&1 | tee  maketestLogs.txt
   make install 2>&1 | tee makeInstallLogs.txt
>>>>>>>>End of perl installation<<<<<

echo "check_certificate = off" >> ~/.wgetrc

Edit the .bash_profile file and add the local MODULEPATH
>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
vi ~/.bash_profile
export MODULEPATH=$MODULEPATH:~/sw/Modules
>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
#copy the main perl module file locally
 cp -r /sw/Modules/lang/perl/ ~/sw/Modules
module load perl/5.38.2

You now have a a copy of the perl installation in your ~/sw/perl directory and made a module file from ~/Modules/perl/5.38.2

source /usr/local/bin/s3proxy.sh

I guess you want to install cpan -i File:FindLib
This will install this module now. Simple press return for username and password for proxy.