You may be able to trace your jobs with this command:

tracejob 

type "man tracejob" for syntax.

e.g: tracejob -n4 213883

where n4 indicates to search logs over the past 4 days 
213883 indicates job number.

There is a script to watch a job live. You can run it on gowonda as follows:
watch_jobs.sh

It will ask for node number on which your job is running. This can be got by typing:
qstat -1an 

The last column of the output from above will have the node number. It also needs the job number.

>>>>>>>
cat watch_jobs.sh
echo "==========================="
echo "Please enter Node Number e.g: n004"
read NODE
echo "Please enter Job number  e.g 9066"
read JOBNO
echo "==========================="

ssh $NODE  "tail -f /var/spool/PBS/spool/*$JOBNO*"
>>>>> 

I have put some documentation here:

http://confluence.rcs.griffith.edu.au:8080/display/GHPC/cuda

A sample PBS script is here:
>>>>>>>>>>>>>>
#!/bin/bash

#PBS -N cuda
#PBS -l ngpus=2
#PBS -l walltime=100:00:00
#PBS -q gpu
module load cuda/4.0
echo "Hello from $HOSTNAME: date = `date`"
nvcc --version
echo "Finished at `date`"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>


Basically a queue named gpu has been created and a pbs resource named ngpus created. 
Both needs to be called in the pbs script to send batch jobs to the gpu nodes.

I suggest you do an interactive batch run first to sort out any issues. To do that:

qsub -I -l ngpus=2 -l walltime=100:00:00  -q gpu

This will log you into one of the gpu nodes (you may have to wait if the nodes are busy).

Type this on the gpu node:

 module load cuda/4.0

The cuda binaries are located here: /usr/local/cuda/bin/

If we run this with binaries on the /scratch filesystem ( /scratch/s2594054/LennardJones dir), I get this:

===========================================
Energy = -1622.25

Number of devices is 2
Passed clCreateProgramWithSource
Compute using the CPU

Energy value is -1622.24
Time taken was : 1450 microseconds    <=========  *Check this

Compute using the GPU

Energy value is -1618.35
Time taken was : 837 microseconds     


If I run this with binaries on the /export/home filesystem, this is the timing we get (this result was expected as /export/home is a busy filesystem):
=================================================
Energy = -1622.25

Number of devices is 2
Passed clCreateProgramWithSource
Compute using the CPU

Energy value is -1622.24
Time taken was : 2005 microseconds    <=========  *Check this

Compute using the GPU

Energy value is -1618.35
Time taken was : 1061 microseconds    
======================================================

#!/bin/bash
#PBS -m abe
#PBS -M YOUREMAIL@griffith.edu.au
#PBS -N openCL_GPU_job
#PBS -l ngpus=1
#PBS -l walltime=00:10:00
module load <WhatEver>
##echo "Hello from $HOSTNAME: date = `date`"
cd /scratch/s123456/<yourBinDir>
./<yourProg>
#You may copy data (if any) back and forth if needed.
##e.g:
##./LennardJones pop256dd.xyz

Finding online help

To find a command or library routine that performs a required function, try a “keyword” search.

You may do a keyword search of the online man pages using “man-k keyword”. The command “apropos keyword” also performs this search.
To find details on a command or library

To find details on using a unix command or library use the command “man command_name”

If no man page is found, it is worth trying the “info” tool.
Controlling your unix environment

Using the modules command.

Listing the files and subdirectories in a directory

basic commands: ls, cd, rm.

Use the "ls" command to list the contents of a directory.
Changing the current working directory

The Unix environment (Shell) records a "current working directory" which is initially set to your home directory.

Many programs, (such as ls above) will look in this directory if no other directory requested.

The "current working directory" may be changed using the "cd" command. See the notes below on directory names.
Deleting (Removing) a file

Use the "rm" command to remove a file.
A few note on Unix directory names.

A Unix file full path name is constructed of the directory and subdirectory names separated by slashes "/".

 ie. /export/home/s123456/work/file1

All Unix full path names start with "/", (There are no Drive/Volume names as in Windows). Hence any filename starting with "/" is a full pathname.

A filename containing one or more slash "/" will refer to subdirectory of the "current working directory".

The current working directory may also be referenced as dot "."

 ie. ./subdirectory/file

The directory containing the "current working directory" may be referenced as dot-dot "..

 ie. ../peer-directory/file

cat -tv  pbs.00

#PBS -m abe^M
#PBS -M Email@griffith.edu.au^M
#PBS -N Pile^M
#PBS -l select=1:ncpus=1:mem=4g^M
#PBS -l walltime=03:00:00^M
source $HOME/.bashrc^M
module load matlab/2008b^M
module load ATLAS/3.9.39^M
echo "Starting job"^M
matlab -nodisplay -nodesktop -nosplash < /export/home/s123456/P1_e5f1k4/SBFEmOnePileVerify_04Aug11.m^M
echo "Done with job"^M


dos2unix   pbs.00
dos2unix: converting file pbs.00 to UNIX format ...

cat -tv  pbs.00
#PBS -m abe
#PBS -M Email@griffith.edu.au
#PBS -N Pile
#PBS -l select=1:ncpus=1:mem=4g
#PBS -l walltime=03:00:00
source $HOME/.bashrc
module load matlab/2008b
module load ATLAS/3.9.39
echo "Starting job"
matlab -nodisplay -nodesktop -nosplash < /export/home/s123456/P1_e5f1k4/SBFEmOnePileVerify_04Aug11.m
echo "Done with job"

AARNet introduced un-metered Off Peak traffic in the middle of 2009. At that time, Off Peak was defined as 8:00pm to 8:00am each day, including weekends and public holidays. This resulted in an additional 10% of total traffic being reclassified as un-metered.
 
At the beginning of this 2011, Off Peak was increased to the period from 5:00pm to 9:00am. The effect was that a further 10% of total traffic was reclassified as un-metered. Year-to-date, some 80% of total traffic is now in this category.
 
The AARNet Board has just approved a further extension of Off Peak to include all of the weekend, so that that the period from 5:00pm Friday to 9:00am Monday will then be un-metered. This change will occur from July 1st, and will result in another 5% of total traffic becoming un-metered. That mean that around 85% of total AARNet traffic will soon be un-metered and subscription based.

Check what your stack size is and try increasing it.

ulimit -a
ulimit -s unlimited

#PBS -l walltime=00:10:00 

I'm running a RAxML analysis now (job id: 371395). It is supposed to be an mpi job, but it doesn't seem to be running much faster than it does on my laptop. Is there a way to check that an mpi job is actually running on multiple cores? I tried 'qstat -f 371395', but I can't tell if it's reporting the used memory or the reserved memory.

If you have time, could you please take a look at my submit script, to make sure it's OK: /scratch/s2831058/120524_NIMR_RAxML/120524_NIMR_RAxML_submit.sh

First checked where it is running:

>>>>>>>>>>>>>>>>>>
qstat -1an|grep s1111111
371395.pbsserve s1111111 mpi      nimr_raxml   6915   1   8    8gb 48:00 R 13:08 n003/0*0
>>>>>>>>>>>>>>>>>>>>

This shows it is running on node n003 and has requested 8 cpus. 
Next check if it is actually using all the cpus. 
To find out, you will need to ssh to the node.

ssh n003

You will need to run a tool like "top" to check if it is utilizing these processors. Running "top" shows it is only using 1 CPU.

>>>>>>>>>
top - 11:29:45 up 81 days,  1:30,  1 user,  load average: 1.00, 1.00, 1.00
Tasks: 608 total,   2 running, 606 sleeping,   0 stopped,   0 zombie
Cpu(s):  3.6%us,  0.1%sy,  0.0%ni, 96.3%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Mem:  12189240k total,  3954752k used,  8234488k free,   187132k buffers
Swap:  8193140k total,    45688k used,  8147452k free,   395396k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
 6959 s2831058  20   0 2573m 2.3g 2976 R 100.1 19.8 791:59.76 raxmlHPC-MPI
11248 root      20   0 17492 1680  956 R  0.7  0.0   0:00.04 top
10972 root      20   0     0    0    0 S  0.3  0.0   0:00.68 flush-0:17
11182 root      20   0     0    0    0 S  0.3  0.0   0:00.06 flush-0:19

>>>>>>>>>>>>>>
See the load average is 1.00 when it should be about 8 if it is using 8 processors . 
To get a detailed CPU use report, type "top" and type 1  or "mpstat -P ALL"
(We have hyperthreading enabled and hence you will see 24 CPUs instead of 12 CPUs). 
There is another program called "htop" tjat gives even better visuals about the running processes.

>>>>>>>>>>>>>>>>>
top - 11:42:33 up 81 days,  1:43,  1 user,  load average: 1.04, 1.03, 1.01
Tasks: 608 total,   2 running, 606 sleeping,   0 stopped,   0 zombie
Cpu0  :100.0%us,  0.0%sy,  0.0%ni,  0.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu1  :  0.3%us,  0.3%sy,  0.0%ni, 99.3%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu2  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu3  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu4  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu5  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu6  :  0.0%us,  0.0%sy,  0.0%ni, 99.3%id,  0.7%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu7  :  0.0%us,  0.7%sy,  0.0%ni, 99.3%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu8  :  0.0%us,  0.3%sy,  0.0%ni, 99.7%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu9  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu10 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu11 :  0.0%us,  0.2%sy,  0.0%ni, 99.8%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu12 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu13 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu14 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu15 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu16 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu17 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu18 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu19 :  0.4%us,  0.0%sy,  0.0%ni, 99.6%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu20 :  0.0%us,  0.4%sy,  0.0%ni, 99.6%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu21 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu22 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu23 :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Mem:  12189240k total,  3955736k used,  8233504k free,   187276k buffers
Swap:  8193140k total,    45688k used,  8147452k free,   396956k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
 6959 s2831058  20   0 2573m 2.3g 2976 R 100.1 19.8 804:44.49 raxmlHPC-MPI
11732 root      20   0     0    0    0 S  0.7  0.0   0:00.32 flush-0:17
11680 root      20   0     0    0    0 S  0.3  0.0   0:00.32 flush-0:19
11846 root      20   0 17492 1684  960 R  0.3  0.0   0:00.04 top
24632 ganglia   20   0  143m 1984 1104 S  0.3  0.0   2:05.04 gmond
    1 root      20   0 21400 1276 1044 S  0.0  0.0   0:01.97 init
    2 root      20   0     0    0    0 S  0.0  0.0   0:03.00 kthreadd
    3 root      RT   0     0    0    0 S  0.0  0.0   0:00.03 migration/0

>>>>>>>>>>>>>>>>>
From the mpstat output (see last column), it is pretty much idle.
>>>>>>>>>
 mpstat -P ALL
Linux 2.6.32-131.0.15.el6.x86_64 (n003)         05/25/2012      _x86_64_        (24 CPU)

11:38:55 AM  CPU    %usr   %nice    %sys %iowait    %irq   %soft  %steal  %guest   %idle
11:38:55 AM  all   10.92    0.00    0.61    0.02    0.00    0.00    0.00    0.00   88.45
11:38:55 AM    0   37.80    0.00    1.05    0.19    0.00    0.00    0.00    0.00   60.96
11:38:55 AM    1   35.52    0.00    2.31    0.00    0.00    0.00    0.00    0.00   62.17
11:38:55 AM    2   35.72    0.00    2.28    0.00    0.00    0.00    0.00    0.00   61.99
11:38:55 AM    3   36.64    0.00    1.34    0.00    0.00    0.00    0.00    0.00   62.02
11:38:55 AM    4   33.67    0.00    2.49    0.00    0.00    0.00    0.00    0.00   63.84
11:38:55 AM    5   33.85    0.00    2.51    0.00    0.00    0.00    0.00    0.00   63.64
11:38:55 AM    6   20.58    0.00    0.60    0.18    0.00    0.02    0.00    0.00   78.63
11:38:55 AM    7   18.85    0.00    0.58    0.00    0.00    0.00    0.00    0.00   80.57
11:38:55 AM    8    2.28    0.00    0.25    0.01    0.00    0.00    0.00    0.00   97.47
11:38:55 AM    9    2.43    0.00    0.30    0.02    0.00    0.00    0.00    0.00   97.25
11:38:55 AM   10    2.94    0.00    0.24    0.02    0.00    0.00    0.00    0.00   96.79
11:38:55 AM   11    1.84    0.00    0.25    0.00    0.00    0.00    0.00    0.00   97.91
11:38:55 AM   12    0.01    0.00    0.02    0.00    0.00    0.00    0.00    0.00   99.97
11:38:55 AM   13    0.02    0.00    0.07    0.00    0.00    0.00    0.00    0.00   99.91
11:38:55 AM   14    0.01    0.00    0.02    0.00    0.00    0.00    0.00    0.00   99.98
11:38:55 AM   15    0.00    0.00    0.01    0.00    0.00    0.00    0.00    0.00   99.99
11:38:55 AM   16    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00   99.99
11:38:55 AM   17    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00   99.99
11:38:55 AM   18    0.01    0.00    0.03    0.01    0.00    0.00    0.00    0.00   99.95
11:38:55 AM   19    0.01    0.00    0.10    0.00    0.00    0.00    0.00    0.00   99.89
11:38:55 AM   20    0.01    0.00    0.03    0.01    0.00    0.00    0.00    0.00   99.95
11:38:55 AM   21    0.01    0.00    0.02    0.01    0.00    0.00    0.00    0.00   99.97
11:38:55 AM   22    0.01    0.00    0.03    0.00    0.00    0.00    0.00    0.00   99.96
11:38:55 AM   23    0.01    0.00    0.02    0.00    0.00    0.00    0.00    0.00   99.97
>>>>>>>>>>>

Log into the node that is running your job.
qstan -1an|grep <jobNumber>

This gives the node (last column). Please log into that node (ssh n???) 
and run "top".

The values under RES show the amount of physical memory (RAM) being used by the process. This should be the amount of pmem 
in your job request. If you are not using pmem but using mem, you will have to add up for all processes (1.3g+1.2g+.....=10.2g).
And that was for that instance when top was run.  You requested memory (mem= ) was not enough. 

Please look at the swap line from the output of "top":
 
Swap:  8193140k total,  5132424k used,  3060716k free

Here you can see that it is using 5132424k of swap mem which ideally should be very low (=~ 0 k). So you are using a lot of swap. 

>>>>>>>>>>>>>>>>>>>>>>>
top - 13:29:10 up 81 days,  3:30,  3 users,  load average: 8.00, 8.00, 7.74
Tasks: 621 total,   9 running, 612 sleeping,   0 stopped,   0 zombie
Cpu(s): 33.8%us,  0.2%sy,  0.0%ni, 66.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Mem:  12189240k total, 11812780k used,   376460k free,    14036k buffers
Swap:  8193140k total,  5132424k used,  3060716k free,    38532k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
15095 s2831058  20   0 2640m 1.3g 3164 R 100.0 11.2  44:15.23 raxmlHPC-MPI
15096 s2831058  20   0 2640m 1.2g 3196 R 100.0 10.6  44:08.10 raxmlHPC-MPI
15097 s2831058  20   0 2640m 1.3g 3240 R 100.0 11.2  44:08.22 raxmlHPC-MPI
15098 s2831058  20   0 2640m 1.4g 3224 R 100.0 12.3  44:13.74 raxmlHPC-MPI
15100 s2831058  20   0 2640m 1.6g 3212 R 100.0 13.9  44:11.65 raxmlHPC-MPI
15101 s2831058  20   0 2640m 1.1g 3080 R 100.0  9.8  44:04.24 raxmlHPC-MPI
15094 s2831058  20   0 2640m 1.0g 3196 R 99.7  8.9  44:11.99 raxmlHPC-MPI
15099 s2831058  20   0 2641m 1.3g 3184 R 99.7 11.2  44:20.96 raxmlHPC-MPI
17329 root      20   0     0    0    0 S  2.7  0.0   0:00.91 flush-0:17
17313 s2831058  20   0 17728 1544 1032 S  2.0  0.0   0:01.21 htop
 3161 root      20   0 2940m  17m 2332 S  0.3  0.1 257:23.80 DNA
17371 root      20   0  103m 3816 2972 S  0.3  0.0   0:00.01 sshd
17405 root      20   0 17492 1672  956 R  0.3  0.0   0:00.05 top
    1 root      20   0 21400 1144  980 S  0.0  0.0   0:01.97 init


>>>>>>>>>>>>>>>>>>>>>>>>>
Another tool you can use is "htop". See attached pictures for the swap row. It should be a very short line or no line 
if it is not swapping. If it is swapping heavily, it will have a long line.
 
I would suggest you request more memory. PBS will then dispatch your jobs to the bigger memory nodes. Your jobs may have to wait
a little longer (it will be queued up) but it will then use the appropriate bigger memory nodes (currently our 4 biggest nodes 
have 96 G RAM).

qalter -l select=1:ncpus=12:mem=5gb <jobID>
qalter -l walltime=<hh:mm:ss> <jobid>

To release a job on status "Hold"
qrls -hs <jobid>

qdel `qselect -u username`

Please put this line in the pbs script:

#PBS -W group_list=nimrodusers

or simply use it in qsub as follows:

qsub -l walltime=800:00:00,select=1:ncpus=2 -W group_list=nimrodusers  -N bm2-12 -q gpu -- /export/home/s123456/blade2.sh

If running the same everytime, it is best to use job arrays (rather than running qsub multiple times).

So you could do:
qsub -N <jobname> -J 1-10 job_submit.pbs

To run it 10 times. 

#!/bin/bash
#PBS -J 1-100
#PBS -m abe
#PBS -M YOUREMAIL@griffithuni.edu.au
#PBS -N MQworker
#PBS -l select=1:ncpus=1:mem=2g,walltime=2:00:00
cd  $PBS_O_WORKDIR
./myBinary ${PBS_ARRAY_INDEX} 3600 >> output_${PBS_ARRAY_INDEX}

#Demonstrate the behaviour of job arrays
#!/bin/bash
#PBS -m abe
#PBS -M EMAILID@griffith.edu.au
#PBS -N TestArray
#PBS -l select=1:ncpus=1:mem=1gb,walltime=00:01:00
#PBS -J 1-10
#PBS -q workq
sleep 60

#Make a new Directory for this job in array inside our current directory
mkdir $PBS_O_WORKDIR/Demo$PBS_ARRAY_INDEX

#Change into it
cd $PBS_O_WORKDIR/Demo$PBS_ARRAY_INDEX

#Send some output to a file
printf " This is a job number $PBS_ARRAY_INDEX in the array\n" >job.PBS_ARRAY_INDEX.log

#!/bin/bash
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -N IndyMarxACT_v3
#PBS -q routeq
#PBS -J 1-20
#PBS -l select=1:ncpus=1:mem=1g,walltime=20:00:00
cd $PBS_O_WORKDIR
module load R/4.0.3
R CMD BATCH /export/home/snumber/pbs/array/scripts/script_$PBS_ARRAY_INDEX.R

For an easy reference, here's a list of the most common screen commands that you'll want to know. This isn't exhaustive, but it should be enough for most users to get started using screen happily for most use cases.

screen -d -m -S shared
screen -ls
screen -x shared



    Start Screen: screen
    Detatch Screen: Ctrl-a d
    Re-attach Screen: screen -x or screen -x PID
    Split Horizontally: Ctrl-a S
    Split Vertically: Ctrl-a |
    Move Between Windows: Ctrl-a Tab
    Name Session: Ctrl-a A
    Log Session: Ctrl-a H
    Note Session: Ctrl-a h

First ask the system admin on gowonda to do this:
>>>>>>>>>
usermod -a -G fuse <username>
>>>>>>>>>

You need the SSH server installed and running on the computer you want to mount (for most unix-like OSes including MacOSX, it is a matter of installing openssh-server package). 
Then check that SSH itself is working with:
>>>>>>>>>>>>>>>>>>>>>>
ssh user@remote!P  
>>>>>>>>>>>>>>>>>>>>>>
This will ask for confirmation the first time, then ask for a password every time you try to connect. Once connected, press Ctrl+d to
disconnect, then run the sshfs command 
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sshfs user@remoteiP:/directory/to/mount /mount/point 

e.g 
On gowonda:
mkdir /tmp/mnt1 
sshfs s12345@132.234.1.1:/opt/import  /tmp/mnt1

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
As sshfs uses Fuse. it will refuse to mount onto a non-empty directory, so make sure there's nothing in the mount point beforehand. Now
the contents of the remote directory should be available to you. When you are finished, you unmount the remote directory with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
fusermount -u /mount/point
e.g:
fusermount -u  /tmp/mnt1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
After doing this a couple of times. you will find it incredibly annoying having to type your password in each time. Fortunately, SSH can use keys for logging in. First generate your keys on the local machine with 
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
ssh-keygen -t rsa
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Don't set a password when asked, just press Enter. otherwise you'll defeat the point of creating the key. This creates a pair of files in ~/.ssh. which are your private and public key. Your private key should never be shared, but you need to copy the public one to the remote
computer. with this command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
$ ssh-copy-id -i -/.ssh/id_rsa.pub user@remoteiP
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

This will ask for the password one more time, but after that you can run the above ssh and sshfs commands without being asked for a password again. All of these commands should be run as your normal user. You can omit the user@ part of the ssh and sshfs commands if you have the same username on both computers. 


Source: Linux Format 5 Apr 2016 p.92

Several environment variables are provided to PBS jobs. Some are taken from the user's environment and carried with a job, and others are created by PBS. There are also some environment variables that you can explicitly create for exclusive use by PBS jobs.

All PBS-provided environment variable names start with the characters "PBS_". Some start with "PBS_O_", which indicates that the variable is taken from the job's originating environment (that is, the user's environment).

A few useful PBS environment variables are described in the following list:

PBS_O_WORKDIR - Contains the name of the directory from which the user submitted the PBS job
PBS_O_PATH - Value of PATH from submission environment
PBS_JOBID - Contains the PBS job identifier
PBS_JOBDIR - Pathname of job-specific staging and execution directory
PBS_NODEFILE - Contains a list of vnodes assigned to the job
TMPDIR - The job-specific temporary directory for this job. Defaults to /tmp/pbs.job_id on the vnodes.    

Wwhen the code was compiled for the new node architecture and the app is run on the old nodes, you may get errors like this

Please verify that both the operating system and the processor support Intel(R) MOVBE, F16C, FMA, BMI, LZCNT, AVX2, AVX512DQ, AVX512F, ADX, AVX512CD, AVX512BW and AVX512VL instructions.

Solution:
========
The new nodes are:
gc-prd-hpcn001
gc-prd-hpcn002
gc-prd-hpcn003
gc-prd-hpcn004
gc-prd-hpcn005
gc-prd-hpcn006

To check if the resource is free, please run this command:
pbsnodes  -aSj|egrep "gc-prd-hpcn002|gc-prd-hpcn001|gc-prd-hpcn003|gc-prd-hpcn004|gc-prd-hpcn005|gc-prd-hpcn006"

Let's say gc-prd-hpcn006 has free memory and free cpus.

>>>>>>>>>Here is a sample pbs script to send a job to gc-prd-hpcn006<<<<<<<<<
#!/bin/bash
#PBS -N SpecificHost
###PBS -m abe
###PBS -M ID@griffithuni.edu.au
#PBS -l select=1:ncpus=1:host=gc-prd-hpcn006:mem=8gb,walltime=24:00:00
echo "Starting job: "
cd $PBS_O_WORKDIR
echo "Hello"
sleep 10
>>>>>>>>>>>>>>>>>>>>>>>

For an interactive run, you can do this:

qsub -I -X -q workq  -l select=1:ncpus=1:host=gc-prd-hpcn006:mem=8gb,walltime=24:00:00

If hosts from a range is acceptable:
qsub -I -X -q workq  -l select=1:ncpus=1:host=gc-prd-hpcn001-006:mem=1gb,walltime=00:01:00

PS: If you need to send the job to a different queue. Please find the queue a node belongs to with this command first:
qhost|egrep "gc-prd-hpcn002|gc-prd-hpcn001|gc-prd-hpcn003|gc-prd-hpcn004|gc-prd-hpcn005|gc-prd-hpcn006"

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

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.

mkdir -p ~/sw/Modules
cd ~/sw/Modules

Create a modules file for the application (here it is named xbeach)
>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
vi xbeach

#%Module######################################################################
##
##      XBeach modulefile
##
proc ModulesHelp { } {
        puts stderr "Sets up shell environment to use XBeach  "
        puts stderr " "
}

module load gnu/4.9.2

set base        /gpfs1/groups/gccmss/project/sw/xbeach
set base_path   $base

##prepend-path    INCLUDE             $base_path/include
prepend-path    LD_LIBRARY_PATH     $base_path/lib
prepend-path    PATH         $base_path/bin
##prepend-path    MANPATH      $base_path/man
##setenv          NCBI         $base_path/local
>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

Edit the .bash_profile file and add the local MODULEPATH
>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
vi ~/.bash_profile
export MODULEPATH=$MODULEPATH:~/sw/Modules
>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

Log out and log back in.
Check if the module is available
module avail xbeach

#! /bin/bash
### Template PBS script to submit Delft3d job to queue gccm
#PBS -m e
#PBS -N brisb0809
#PBS  -l  walltime=200:00:00
#PBS  -l  nodes=1:ppn=4:intel,mem=30gb,vmem=30gb
#PBS  -A qris-gu
source $HOME/.bashrc
module load delft3d-rev5624

cd /gpfs1/groups/gccmss/project/delft3d/brisb_aug0809/
##input data file
export MDWFILE=fm_wave.mdw
export ARGFILE=config_flow2d3d.xml
## RUN ##
# start flow
echo "=== start Delft3D-FLOW in the background ==="
#$MPIRUNEXEC -np $NHOSTS d_hydro.exe $ARGFILE &
#deltares_hydro.exe $ARGFILE -keepXML &
#deltares_hydro.exe $ARGFILE  &
d_hydro.exe $ARGFILE &
# start wave
echo "=== start Delft3D-WAVE in the background ==="
#$MPIRUNEXEC -np $NHOSTS wave.exe $MDWFILE 1
wave.exe $MDWFILE 1
echo "=== calculation finished ==="
echo "Finished job "`date`

/usr/local/bin/lmstat -a -c 27006@gc-prd-erslic.corp.griffith.edu.au
/sw/sysadmin/intelflexlm/lmstat -a -c 27006@gc-prd-erslic.corp.griffith.edu.au
/usr/local/bin/lmstat -a -c 27004@gc-prd-erslic.corp.griffith.edu.au

The queue system uses some algorithm to maximize the use of the resources while prioritizing some jobs over others. Normal users can only make their jobs have lower (eg, use negative arguments to p) priority than normal.  This lets you shuffle around the order of your jobs with respect to each other
qalter -p value job 
qalter -p  -1020  101

 qsub -p priority job-script
priority is a number between -1024 and +1023. A higher number means higher priority. The default priority is 0 

Here are some of the HPC resources available to Griffith researchers:

1. Griffith users can use facilities like NCI, Pawsey. 
For NCI, project allocations are usually done on a quarter basis and are on a "use it or lose it" basis. 

To get access please follow the instructions here:
http://nci.org.au/access/user-registration/new-project-application/

You will need to get a new user account first as specified on the page. When you apply for a project please select to propose a new project and select QCIF as the funding body. You will need to write a project proposal and request computational time per quarter. You may contact QCIF representative, Marlies Hankel (m.hankel@uq.edu.au) if you have any questions related NCI, Pawsey etc.

2. The following resources are available through QCIF/QRISCloud:

a. euramoo cluster
b. flashlite cluster
c. special compute nodes with GPUs, big memory etc
d. virtual machines
e. virtual storage

To request an account, please follow the links here:
https://www.qriscloud.org.au/index.php/services

For example, to request an account on the euramoo cluster, please click the link "Register to use Euramoo". To get further imformation about a particular resource, please click on the "more" link besides the link for a particular resource. For example, click on the "more" link beside the "Request to use Flashlite" to get more information about the flashlite cluster.

#!/bin/bash
#PBS -m abe
#PBS -M YOUREMAIL@griffith.edu.au
#PBS  -A qris-gu
#PBS -l nodes=1:ppn=1,mem=3GB,vmem=3GB,walltime=01:00:00
#PBS -N TestOnly
######################################################################

######################################################################
#### This section is setting up and running your executable or script
######################################################################
module load R/3.2.3
module list
cd  $PBS_O_WORKDIR
#Now do some things
echo -n "What time is it ? "; date
echo -n "Who am I ? " ; whoami
echo -n "Where am I ?"; pwd
echo -n "What's my PBS_O_WORKDIR ?"; echo $PBS_O_WORKDIR
echo -n "What's my TMPDIR ?"; echo $TMPDIR
echo "Sleep for a while"; sleep 1m
echo -n "What time is it now ? "; date

To enable you to download R packages from outside Griffith, you may do this:
source /usr/local/bin/s3proxy.sh


Load the R module 
module load R/4.1.3nopkgs
(Older R modules are also available if needee.g module load R/4.0.3, module load R/3.6.1 or module load anaconda3/2019.07py3; source activate R)
Create file named ~/.Renviron

nano ~/.Renviron
## Linux - check version of R/OS
R_LIBS=~/R/x86_64-pc-linux-gnu-library/3.6
OR R_LIBS=~/R/x86_64-pc-linux-gnu-library/4.0

(Create this directory if it doesn't exist:e.g. mkdir -p ~/R/x86_64-pc-linux-gnu-library/3.6)

The .libPaths() command lists the places where R will 
search for libraries, and use the first item of the list as target for 
new package installs.

Try this: module load R/4.1.3nopkgs
R
 > .libPaths()
  [1] "/usr/lib64/R/library" "/usr/share/R/library"

Let's install the dummy package
  > install.packages('dummy')
R tries to install it in the global library
  Installing package(s) into ‘/usr/lib64/R/library’
  (as ‘lib’ is unspecified)
  Warning in install.packages("dummy") :
    'lib = "/usr/lib64/R/library"' is not writable
but quickly notes that it cannot write in the global place, and asks 
whether it should create a local library. Simply answer 'y'.
  Would you like to create a personal library
  '~/R/x86_64-redhat-linux-gnu-library/2.13'
  to install packages into?  (y/n) y

Another example:
install.packages('raster', type='source') 
install.packages('RCurl', type='source')
install.packages('rgdal', type='source',  configure.args="--with-proj-share=~/opt/sw/library/proj/4.8.0/share/proj")

module load R/3.2.3
cd /tmp
Download the packages you want
>>>>>>>>>>
e.g:
wget https://cran.r-project.org/src/contrib/Archive/rgdal/rgdal_1.2-10.tar.gz
wget https://cran.r-project.org/src/contrib/Archive/rgdal/rgdal_1.2-4.tar.gz
wget https://cran.r-project.org/src/contrib/Archive/sp/sp_1.2-2.tar.gz
>>>>>>>>>>>
R CMD INSTALL /tmp/rgdal_1.2-10.tar.gz 
* installing to library '~/R/x86_64-pc-linux-gnu-library/3.2'
ERROR: this R is version 3.2.3, package 'rgdal' requires R >= 3.3.0

Tried with a lower version of rgdal
>>>>>>>>>
R CMD INSTALL rgdal_1.2-4.tar.gz  
* installing to library '/~/R/x86_64-pc-linux-gnu-library/3.2'
ERROR: dependency 'sp' is not available for package 'rgdal'
* removing '/~/R/x86_64-pc-linux-gnu-library/3.2/rgdal'
So I tried:
>>>>>>>>

It said sp package was needed.

Try a lower version of sp

R CMD INSTALL sp_1.2-2.tar.gz 
That worked.
But another error was received:
>>>>>>>>>>>>>>>>>>
R CMD INSTALL rgdal_1.2-4.tar.gz
checking for gdal-config... no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package 'rgdal'
>>>>>>>>>>>>>>
Tried to load this package using the command "module load gdal/2.0.2"

Got another error:

checking for proj_api.h... no

configure: error: proj_api.h not found in standard or given locations.
Try this: module load proj/4.9.1
Still got the error "configure: error: proj_api.h not found in standard or given locations."
A cursory look at the proj/4.9.1 module file showed that it was not set up correctly (module display proj/4.9.1)

Fix it by creating a custom module file:
mkdir ~/.moduleshome
cd ~/.moduleshome

vi ~/.bash_profile
export MODULEPATH=$MODULEPATH:~/.moduleshome
source ~/.bash_profile
Create the custom module file for proj: 
>>>>
mkdir -p ~/.moduleshome/proj/
vi ~/.moduleshome/proj/mine-4.9.1
>>>>>>>>
setenv         PROJHOME /opt/proj 
prepend-path     PATH /opt/proj/bin 
prepend-path     LD_LIBRARY_PATH /opt/proj/lib 
prepend-path     LDFLAGS -L/opt/proj/lib 
prepend-path     LIBRARY_PATH /opt/proj/lib 
prepend-path     PKG_CONFIG_PATH /opt/proj/lib/pkgconfig 
prepend-path     MANPATH /opt/proj/share/man 
prepend-path     INCLUDE /opt/proj/include 
prepend-path     CPLUS_INCLUDE_PATH /opt/proj/include 
prepend-path     CPATH /opt/proj/include 
prepend-path     C_INCLUDE_PATH /opt/proj/include 
prepend-path     FPATH /opt/proj/include 
prepend-path     CFLAGS -I/opt/proj/include 
prepend-path     CPPFLAGS -I/opt/proj/include 
prepend-path     CXXFLAGS -I/opt/proj/include 
prepend-path     FCFLAGS -I/opt/proj/include 
prepend-path     FFLAGS -I/opt/proj/include 
-------------------------------------------------------------------
>>>>>>>>>
Then:
module unload load proj/4.9.1
module load proj/mine-4.9.1
 R CMD INSTALL rgdal_1.2-4.tar.gz
SUCCESS!

You may request an account on Awoonga by going to this link:
https://www.qriscloud.org.au/services

Please click the link "Register to use Awoonga”

Usage:


Griffith users have access to directories /sw/GU and /sw/Modules/GU.
Griffith Support team has write permissions via the group "suppport4".
All others have read access to these directories.

Griffith support team has created modulefiles, under /sw/Modules/GU, 

All users are asked to add this line into their ~/.bashrc file in their home directory:

module use /sw/Modules/GU

Parallel to the several /sw/{support team) directories

We recommend the compiler versions from the SDSC rolls, so
module load gnu or intel
module load any libraries
Build (configure, make, make install)

module avail will list all the modules.

vi  ~/.bashrc
module use /export/home/YOURSNUMBER/sw/Modules/GU
>>>>>>>
mkdir -p ~/sw/Modules/GU
cd ;HOMEDIR=`pwd`;echo $HOMEDIR
echo "module use $HOMEDIR/sw/Modules/GU" >>~/.bashrc
source ~/.bashrc
>>>>>>>

Create a module file like this
vi ~/sw/Modules/GU/postgress

>>>>>>>>>>>
#%Module######################################################################
##
##      PostGress  modulefile
##
proc ModulesHelp { } {
        puts stderr "Sets up shell environment to use Postgress"
        puts stderr " "
}

set base_path   /export/home/snumber/sw/PostgresSQL



prepend-path    PATH            $base_path/bin
#prepend-path    MANPATH         $base_path/share/man
prepend-path    MANPATH         $base_path/share
##setenv         BLASTDB         $dbbase_path/blastdb

prepend-path    LIBRARY_PATH            $base_path/lib
prepend-path    LD_LIBRARY_PATH $base_path/lib
prepend-path    LDFLAGS                 -L$base_path/lib
prepend-path    PKG_CONFIG_PATH         $base_path/lib/pkgconfig
prepend-path    INCLUDE             $base_path/include
prepend-path    CPLUS_INCLUDE_PATH      $base_path/include
prepend-path    CPATH                   $base_path/include
prepend-path    C_INCLUDE_PATH          $base_path/include
prepend-path    FPATH                   $base_path/include
prepend-path    CFLAGS                  -I$base_path/include
prepend-path    CPPFLAGS                -I$base_path/include
prepend-path    CXXFLAGS                -I$base_path/include
prepend-path    FCFLAGS                 -I$base_path/include
prepend-path    FFLAGS                  -I$base_path/include


>>>>>>>>>>>>

source ~/.bashrc

check if it works:
module display postgress

Here is an example to install a python application named busco locally:

>>>>>>>>>>>>>>>>>>>>>
mkdir ~/sw
cd ~/sw
cd /export/home/s2981868/sw/busco
#You may load any version of python we have on the cluster
module load  python/3.6.1
cd ~/sw/busco
python setup.py install --prefix=/export/home/s123456/sw/busco 2>&1 | tee buscoInstallLog.txt

>>>>>>>>>>>>>>>>>>>>>>
That's all.  Now you need to set the PYTHONPATH variable properly

The easiest would be to setup a module file locally. Or to add this in .bashrc 
PYTHONPATH /export/home/s12345/sw/busco/lib/python3.6/site-packages

The preferred option is to add it as a module:
You can do this one time 
>>>>>>>>>>>>>>>setting up custom/local module env<<<<<<<<<<<<<<<<
mkdir ~/sw/Modules
cd ;HOMEDIR=`pwd`;echo $HOMEDIR
echo "module use $HOMEDIR/sw/Modules/" >>~/.bashrc
source ~/.bashrc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Set up the module file
>>>>>>>>>>>>>>>>>>>>>>
Create a module file in /export/home/s12345/sw/Modules/busco

>>>>>>>>>
#%Module######################################################################
##
##      python modulefile
##
proc ModulesHelp { } {
        puts stderr "Sets up paths for busco with python 3.6.1"
}

module-whatis   "adds custom PYTHONPATH directories to PATH etc. "


set base_path           /export/home/s12345/sw/busco
prepend-path    PATH    $python_base/scripts
prepend-path    PYTHONPATH      $python_base/lib/python3.6/site-packages
prepend-path    LD_LIBRARY_PATH $python_base/lib:$python_base/lib/python3.6


>>>>>>>>>
++++++++++++++++
module display busco/custom-busco
-------------------------------------------------------------------
/export/home/s12345/sw/Modules//busco/custom-busco:


module-whatis	 adds custom PYTHONPATH directories to PATH etc.
prepend-path	 PATH /export/home/s12345/sw/busco/scripts
prepend-path	 PYTHONPATH /export/home/s12345/sw/busco/lib/python3.6/site-packages
prepend-path	 LD_LIBRARY_PATH /export/home/s12345/sw/busco/lib:/export/home/s12345/sw/busco/lib/python3.6
-------------------------------------------------------------------

+++++++++++++++++
Simply do this:
module load busco/custom-busco


To run this program:

Now you can do this:
/export/home/s12345/sw/busco/scripts/run_BUSCO.py -i /export/home/s12345/scratch/SRO_trinity.fasta -o SRO_BUSCO -l ~/scratch/metazoa_odb9 -m tran -c 4

Once satisfied, you can write the pbs script and the config.ini (/export/home/s2981868/sw/busco/config/)


>>>>>>>>>>
#!/bin/bash -l
#PBS -m abe
#PBS -M MYEMAIL@griffith.edu.au
#PBS -N BUSCO_SRO
#PBS -l walltime=250:00:00
#PBS -l select=1:ncpus=4:mpiprocs=4
cd $PBS_O_WORKDIR
source $HOME/.bashrc

module load module load python/3.6.1
module display busco/custom-busco

/export/home/s12345/sw/busco/scripts/run_BUSCO.py -i /export/home/s12345/scratch/SRO_trinity.fasta -o SRO_BUSCO -l ~/scratch/metazoa_odb9 -m tran -c 4

In this example, python 2.7.10 is used but this is applicable to any version of python.

module load python/2.7.10

run the netcheck script to log into the internet
sh /sw/sysadmin/netcheck (old cluster)
OR on the new cluster 
source /usr/local/bin/s3proxy.sh

You may use pip/easy_install/python setup.py to install to a local directory

pip
===
pip install --user package_name
pip install --install-option="--prefix=$HOME/scripts" package_name
e.g pip install --install-option="--prefix=/export/home/s2819099/scripts"  nose


easy_install
==========
easy_install --prefix=$HOME/scripts package_name
which will install into $HOME/scripts/lib/pythonX.Y/site-packages
You will need to manually create $HOME/scripts/lib/pythonX.Y/site-packages

and add it to your PYTHONPATH environment variable (otherwise easy_install will complain -- btw run the command above once 
to find the correct value for X.Y).

e.g: 
export PYTHONPATH=/export/home/s2819099/scripts/lib/python2.7/site-packages
easy_install --prefix=/export/home/s2819099/scripts nose

setup.py
========
Source: http://docs.python.org/install/index.html#alternate-installation
python <lxml_distrib_dir>/setup.py install --home=<dir>
e.g:
python setup.py install --home=/export/home/s2819099/scripts

virtualenv
==========
$ curl -O https://raw.github.com/pypa/virtualenv/master/virtualenv.py
$ python virtualenv.py my_new_env
$ . my_new_env/bin/activate
(my_new_env)$ pip install package_name

Source and more info: https://virtualenv.pypa.io/en/latest/installation/

Finish the installation
========================
export PYTHONPATH=$PYTHONPATH:$HOME/scripts/lib/python2.7/site-packages

Please logout of the internet on gowonda, otherwise all internet charges from all users will be charged to your account.
sh /sw/sysadmin/netcheck -logout

 

To change a dependency after you have submitted a job, use qalter -W depend=type:argument jobid; to remove the dependency completely, use qalter -W depend=type jobid (i.e., omit :argument). For example:
       
    athena% qstat -f 1175 | grep depend
    depend = afterok:1171.hydrogen.mit.edu@hydrogen.mit.edu
  
To make 1175 wait for 1172 instead of 1171: 

·                 athena% qalter -W depend=afterok:1172 1175
·                 athena% qstat -f 1175 | grep depend
·                 depend = afterok:1172.hydrogen.mit.edu@hydrogen.mit.edu
       
To clear the dependency: 

·                 athena% qalter -W depend=afterok 1175
·                 athena% qstat -f 1175 | grep depend
·                 athena%
       
 

How do I get access to QCIF share of NCI @Raijin machine?

https://www.qriscloud.org.au/index.php/services/compute#NCI

How do I get access to QCIF GPU machine Wiener (located @UQ)?
Check under "Use Specialised compute"
https://www.qriscloud.org.au/index.php/services/compute#SpecialCompute

You can go through a proxy to access external collections using wget. You may create a file named .wgetrc (vi ~/.wgetrc) with the following contents

use_proxy = on
http_proxy = http://s3proxy.itc.griffith.edu.au:3128/
HTTP_PROXY = http://s3proxy.itc.griffith.edu.au:3128/
https_proxy = https://s3proxy.itc.griffith.edu.au:3128/
HTTPS_PROXY = https://s3proxy.itc.griffith.edu.au:3128/

You may create a file named s3proxy.sh (vi ~/s3proxy.sh) with the following contents
export http_proxy = http://s3proxy.itc.griffith.edu.au:3128/
export HTTP_PROXY = http://s3proxy.itc.griffith.edu.au:3128/
export https_proxy = https://s3proxy.itc.griffith.edu.au:3128/
export HTTPS_PROXY = https://s3proxy.itc.griffith.edu.au:3128/

Simply source this package (~/s3proxy.sh) to get temporary access to external packages. Please note that all downloads are monitored. Also note that your home directory should not go above 200GB in size.

#Gain access to the outside: source /usr/local/bin/s3proxy.sh
#Load the anaconda module e.g module load anaconda3/2022.10)
#Add the following entry into .condarc (nano ~/.condarc)
channels:
  - defaults

#Create the following folders:

mkdir -p ~/.conda/envs
mkdir -p ~/.conda/pkgs

See if the following commands work!
#conda info
#	conda search flask


conda create --name env1
#e.g conda create --name trinity_env --clone root
#To remove an environment, conda remove -n env --all

source activate env1

#e.g source activate trinity_env

Now you can install your packages:
conda search -c bioconda trinity

For example to install version trinity version 2.9.1:

e.g conda install -n trinity_env -c bioconda trinity=2.9.1
conda create --name rstan --channel conda-forge r-dplyr r-rmapshaper r-sf

To check all versions available of the rstan package:
conda search r-rstan --channel conda-forge

You may wish to transfer the app locally due to write issues on the app folder
This can be easily accomplished. Here is an example to transfer SWAAT-CUT app:

cd ~
mkdir ~/sw
cp -r /sw/misc/swatcup ~/sw
Change permission like this

chown -R yoursnumber:yoursnumber ~/sw/swatcup

Now you would have it locally.

Then setup modules to load 
https://conf-ers.griffith.edu.au/display/GHCD/FAQ+-+Gowonda#FAQ-Gowonda-Qs29:Howtocustomizeanenvironmentalvariableusingmodules 

After following the above link and creating the ~/sw/Modules directory, you can simply copy the parent module file and make changes to it where needed.

cp  /sw/Modules/misc/swatcup/swatcup ~/sw/Modules

vi ~/sw/Modules/swatcup
(make the changes)

This module will be available to you on the login. Or if needed immediately, source ~/.bash_profile  

"qhost" ​will list all the nodes. Please note that not all nodes are available to all users. Only a subset is available.

"pbsnodes -aSj" will give an indication of the currently available resources. Again, not all available resources can be used and pbs will determine where and when a job is run.

For example, there are nodes with 72 cores but if 72 cores is requested, your wait time would be a long time (weeks or months) unless the cluster is not busy at all.

"qstat -q" will give the queue configuration.


To view the current cluster status, you can also use the elinks text browser on the login node to view the status:

elinks http://localhost:3000/nodes

elinks http://localhost:3000/jobs

elinks http://localhost:3000/queues

(You can press "Q" to quit from the below text-based browsers

There are many reasons that your job may have to wait in the queue longer than you would like. Here are some of them.

1.System load is high. It’s frustrating for everyone! There are peaks and lows. Unfortunately it is not possible to predict when we will experience this. We have noted that near the beginning of the semester, midway through the semester and at the end of the semester, the load is high. Load is low during the semester break. However this may not be the case all the time.
2.A system downtime has been scheduled and jobs are being held. Check the message of the day, which is displayed every time you login, or emails to the LML - GHPC list.
3. You or your group have used a lot of resources in the last few days, causing your job priority to be lowered (“fairness policy”). Priority is a complicated function of many factors, including the processor count and walltime requested, the length of time the job has been waiting, and how much other computing has been done by the user and their group over the last several days.
4. You or your group are at the maximum processor count or running job count and your job is being held.
5. Your job is requesting specialised resources, such as large memory, gpus or certain software licences, that are in high demand.
6. Your job is requesting a lot of resources. It takes time for the resources to become available.
7. Your job is requesting incompatible or nonexistent resources and can never run. For example, if you request 200GB memory, it will never run as the maximum capacity of a node is 170GB distributed among many jobs. 
8. Job is unnecessarily stuck in batch hold because of system problems (very rare!).

From the new login node (gc-prd-hpclogin1.rcs.griffith.edu.au), you can see your old home and scratch:

ls /ngumbin/home/s123456
You will see tons of files from old home

ls /ngumbin/scratch/s123456

Again you will see a lot of files and folders from your old scratch.

If you wish to copy a folder named FAS-917 located in the old scratch into the new scratch, you can do this on the new login node.

screen
cp -r /ngumbin/scratch/s123456/FAS-917 ~/scratch &
You will see the copy. Just press ENTER and type
screen -d
After this you can even logout and the copy will continue till it is done.

Please note screen is used to run the command even after you logout. 
The mount point to the new home and scrtach is not available on the old login node gowonda/gowonda2 but instead the old home and scratch are available on the new login node "gc-prd-hpclogin1"

You may follow the instructions on the Griffith vpn site.
https://intranet.secure.griffith.edu.au/computing/remote-access/virtual-private-network

You will need to be part of the gpu queues: gpuq, dljun and dlyao group. 
Interactive pbs run
=================
You log into n060 and run this command:
qsub -I -V -q gpuq -l select=1:ncpus=1:ngpus=1:mem=12gb,walltime=10:00:00
(Depending on your need, you may wish to alter the walltime or other resources like memory etc)
It will start a pbs job in interactive mode with a wall time of 10 hours. If there are resource available currently, it would start the job immediately, else you may have to wait.  
Other examples:
qsub -V -I -q gpuq -l select=1:ncpus=1:ngpus=1 -l walltime=0:30:00
qsub -V -I -q dljun -l select=1:ncpus=1:ngpus=1 -l walltime=0:30:00
qsub -V -I -q dlyao -l select=1:ncpus=1:ngpus=1 -l walltime=0:30:00

We offer 3 research storage services at Griffith University for storage of research data. Check out https://research-storage.griffith.edu.au/  for more details.

You can take a short quiz at https://research-storage.griffith.edu.au/compare to see which service is most appropriate for you depending how you would like to use the data. 
Each service has a separate form to request an account on/Project Space request. 
Please follow the links on the page above to get to them. On the HPC there is a 200GB quota set for your account. 
So you would need to upload segments of the data that you wish to analyse. 
This quota can be temporarily increased but is done on a case by case basis and needs to be requested through the HPC administrator 

To transfer files to the the HPC you can read through the FAQs https://conf-ers.griffith.edu.au/display/GHCD/FAQ+-+Griffith+HPC+Cluster
There is a section on this very question in there.

#!/bin/bash 
#PBS -m abe
#PBS -M YOUREMAIL@griffith.edu.au
#PBS -N Inversion
#PBS -l select=1:ncpus=16:mpiprocs=16:mem=1gb,walltime=300:00:00
##     processor cores
slots=16
cd $PBS_O_WORKDIR
module load mpi/openmpi/4.0.2
module load cmake/3.15.5        
echo "Starting job"
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
make clean
make SolveInversion_NoRot
mpiexec $PBS_O_WORKDIR/SolveInversion_NoRot > $PBS_O_WORKDIR/Inversion_export.dat

#!/bin/bash
#PBS -m abe
#PBS -M YOUREMAIL@griffith.edu.au
#PBS -N Inversion
#PBS -l select=1:ncpus=16:mpiprocs=16:mem=1gb,walltime=300:00:00
## The number of chunks is given by the select =<NUM > above
##$PBS_NODEFILE is a node-list file created with select and ncpus options by PBS
PROCS=16
module load intel/2019up5/mpi
module load cmake/3.15.5        
echo "Starting job"
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
cd $PBS_O_WORKDIR
make clean
make SolveInversion_NoRot
mpiexec -n $PROCS    $PBS_O_WORKDIR/SolveInversion_NoRot > $PBS_O_WORKDIR/Inversion_export.dat

module load mpi/mpich/3.3.2-gnu

#!/bin/bash 
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -N  PepDock
#PBS -q dljun@n060
#PBS -W group_list=deeplearning -A deeplearning
### Number of nodes:Number of CPUs:Number of threads per node.
#PBS -l select=1:ncpus=3:mem=12gb,walltime=100:00:00
cd $PBS_O_WORKDIR
NSLOTS=3
##module load  galaxyPepDock
module load misc/galaxypepdock/galaxyPepDock
GalaxyPepDock.centos7 -t test -p ACE2.pdb -s RBD-mimic1.fasta

#!/bin/bash
#PBS -N jobName
####PBS -m abe
####PBS -M YourEmail@griffith.edu.au
#PBS -q routeq
#PBS -l select=1:ncpus=1:mem=2gb,walltime=5:00:00
#======================================================# 
# USER CONFIG
#======================================================#
INPUT_FILE="hello.py"
OUTPUT_FILE="$PBS_JOBNAME.out"
MODULE_NAME="python/3.7.4"
PROGRAM_NAME="python"
# Set as true if you need those /lscratch files.
COPY_SCRATCH_BACK=true
#======================================================#
# MODULE is loaded 
#======================================================#
NP=‘wc -l < $PBS_NODEFILE‘
source /etc/profile.d/modules.sh
module load $MODULE_NAME
cat $PBS_NODEFILE
#======================================================#
# SCRATCH directory is created at the local disks 
#======================================================#
SCRDIR=/lscratch/$LOGNAME/$PBS_JOBID
if [ ! -d "$SCRDIR" ]; then
mkdir $SCRDIR
fi
#======================================================#
# TRANSFER input files to the scratch directory 
#======================================================#
# just copy input file
cp -r $PBS_O_WORKDIR/$INPUT_FILE $SCRDIR
# copy everything (Option) 
#cp -r $PBS_O_WORKDIR/* $SCRDIR
#======================================================#
# PROGRAM is executed with the output or log file
# direct to the working directory
#======================================================#
echo "START TO RUN WORK"
cd $SCRDIR
# Run a system wide sequential program
##$PROGRAM_NAME < $INPUT_FILE >& $PBS_O_WORKDIR/$OUTPUT_FILE
$PROGRAM_NAME $INPUT_FILE >& $SCRDIR/$OUTPUT_FILE
###$PROGRAM_NAME $INPUT_FILE >& $PBS_O_WORKDIR/$OUTPUT_FILE
# Run a MPI program (Option)
###For openmpi, use the following syntax####
#module load mpi/openmpi/4.0.2
#mpiexec $PROGRAM NAME < $INPUT FILE >& $OUTPUT FILE
####For intel mpi, use the following syntax####
#module load intel/2019up5/mpi
#mpiexec -n $NP  $PROGRAM NAME < $INPUT FILE >& $OUTPUT FILE
# mpirun -np $NP $PROGRAM NAME < $INPUT FILE >& $OUTPUT FILE
# Run a OpenMP program(Option) # export OMP NUM THREADS=$NP
# $PROGRAM NAME < $INPUT FILE >& $OUTPUT FILE
sleep 60
#======================================================# 
# RESULTS are migrated back to the working directory
#======================================================#
if [[ "$COPY_SCRATCH_BACK" == *true* ]]
then
    echo "COPYING SCRACH FILES TO " $PBS_O_WORKDIR/$PBS_JOBID 
    cp -rp $SCRDIR/* $PBS_O_WORKDIR
    if [ $? != 0 ]; then
        {
             echo "Sync ERROR: problem copying files from $tdir to $PBS_O_WORKDIR;" 
                     echo "Contact HPC admin for a solution."
             exit 1
        }
    fi
fi
#======================================================#
# DELETING the local scratch directory 
#======================================================#
cd $PBS_O_WORKDIR
if [[ "$SCRDIR" == *scratch* ]]
then
    echo "DELETING SCRATCH DIRECTORY" $SCRDIR
    rm -rf $SCRDIR
    echo "ALL DONE!"
fi
#======================================================#
# ALL DONE 
#======================================================#
##  End-of-job summary
echo "qstat -H $PBS_JOBID"
echo "qstat -xf $PBS_JOBID"

These commands can help

1.List nodes and usage: pbsnodes -aSj
2. qhost
3. Jobs queued and Running: qstat -1an
4. license info: 
comsol: /usr/local/bin/lmstat -a -c 27006@gc-prd-erslic.corp.griffith.edu.au
abacus: /usr/local/bin/lmstat -a -c 27005@gc-prd-erslic.corp.griffith.edu.au
ArcGis: /usr/local/bin/lmstat -a -c 27004@gc-prd-erslic.corp.griffith.edu.au
Matlab: /usr/local/bin/lmstat -a -c 27001@gc-prd-erslic.corp.griffith.edu.au
Ansys: /sw/ansys/2020R2/shared_files/licensing/linx64/ansysli_util -liusage
Ansys: /sw/ansys/2020R2/shared_files/licensing/linx64/ansysli_util -statli 2325@gc-prd-erslic.corp.griffith.edu.au

5. Different queues: qstat -q
6. Additional Info: pqueues, pjobs and pnodes

License issued:

/usr/local/bin/lmstat -a -c 27005@gc-prd-erslic.corp.griffith.edu.au|grep 'Users of standard'

Users of standard:  (Total of 10 licenses issued;  Total of 10 licenses in use)


Remaining licenses
/usr/local/bin/lmstat -a -c 27005@gc-prd-erslic.corp.griffith.edu.au|grep 'Users of standard' | awk '{ printf("%d\n", $6-$11); }'
0

Example:
module load R/4.0.3

> library(plyr)

> library(doParallel)

Loading required package: foreach

Loading required package: iterators

Loading required package: parallel

> cores <- detectCores()

> cores

[1] 72

> registerDoParallel(cores=12)

> fake_func <- function(x) {

+   Sys.sleep(0.1)

+   return(x)

+ }

> 

> library(microbenchmark)

> microbenchmark(

+   serial = llply(1:24, fake_func),

+   parallel = llply(1:24, fake_func, .parallel = TRUE),

+   times = 1

+ )

Unit: milliseconds

     expr       min        lq      mean    median        uq       max neval

   serial 2424.3580 2424.3580 2424.3580 2424.3580 2424.3580 2424.3580     1

 parallel  226.2199  226.2199  226.2199  226.2199  226.2199  226.2199     1

> 

Use this variable:  export CUDA_CACHE_DISABLE=1
This can be added to your pbs script or from command line (for interactive runs)
make sure you use the /lscratch directory for all runs. 
It looks to me that our /scratch and /export/home are too slow . Here is an explanation from the link above

Cache stored on a Slow Network Share
============================
On Linux, the default location of the CUDA JIT cache is in your home directory. On clusters, it is not uncommon to mount home directories
 with relatively poor performance to the compute nodes (by using the Lustre file system for scratch space, but only NFS for the home directory, 
for example). We have seen cases where this relatively slow connection to the home directory (and thus the JIT cache) resulted in very long 
application start-up times when the application was not built with code for the right SM version. Even more confusing, start-up time can vary 
from node to node due to intricacies of the NFS set up.

In this situation, it is best to build the application to avoid JIT entirely, and alternatively, to set CUDA_CACHE_PATH to point to a 
location on a fast file system.

If errors like "Program received signal SIGSEGV: Segmentation fault - invalid memory reference." are received, you may force a core dump to be generated by simply running the program on the login node outside of pbs
e.g:
module load quantum-espresso/6.7.0
PRE='Fe'
turbo_eels.x < ${PRE}tddft.in > ${PRE}tddft.out
This generated a core dump. To analyse a core dump
gdb program coredump
(gdb) where
(gdb)  bt full
Please google "analysing core dump" for various techniques.

e.g gdb turbo_eels.x core.36881

GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-114.el7
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /sw/quantum-espresso/6.7.0/bin/turbo_eels.x...(no debugging symbols found)...done.
[New LWP 36881]
Core was generated by `turbo_eels.x'.
Program terminated with signal 11, Segmentation fault.
#0  0x000000000040d7d1 in lr_alloc_init_k.3770 ()
Missing separate debuginfos, use: debuginfo-install blas-3.4.2-8.el7.x86_64 fftw-libs-double-3.3.3-8.el7.x86_64 glibc-2.17-260.el7_6.6.x86_64 lapack-3.4.2-8.el7.x86_64 libgfortran-4.8.5-36.el7_6.2.x86_64 zlib-1.2.7-18.el7.x86_64
 (gdb) where
#0  0x000000000040d7d1 in lr_alloc_init_k.3770 ()
#1  0x0000000000413ea0 in lr_alloc_init_ ()
#2  0x0000000000406bde in MAIN__ ()
#3  0x0000000000408fec in main ()

Other stuff:
===========
readelf -Wa core.36881
objdump -s  core.36881

I have submitted two jobs in the n060 node. But one of my job is in the queue. Same case is happened in the gpuq. But I saw that some gpus are available. Now What I need to do?

>>>>>>>
Please run the command qstatt to check what is running on n060:

>>>>>
qstatt

94437.gc-prd-hp s5084400 dljun    KF_RD_F2    37878   1   1  100gb 100:0 R 20:41 n060/1

94493.gc-prd-hp s5084397 dljun    OUR         17110   1   1  100gb 200:0 R 01:41 n060/2

94501.gc-prd-hp s5084400 dljun    KF_PN_F2_3  20741   1   1  100gb 100:0 R 00:18 n060/0

94503.gc-prd-hp s5084397 dljun    OUR_2_32      --    1   1  100gb 200:0 Q   --   -- 

94504.gc-prd-hp s5084397 gpuq     Our_2_32      --    1   1  100gb 200:0 Q   --   -- 

>>>>
The other command to run is:
gpustat

n060  Thu Mar 25 11:09:19 2021

[0] Tesla V100-PCIE-32GB | 54'C,  90 % | 31114 / 32480 MB | s5084400(31103M)

[1] Tesla V100-PCIE-32GB | 51'C,  91 % | 31114 / 32480 MB | s5084397(31103M)

[2] Tesla V100-PCIE-32GB | 33'C,   0 % |     0 / 32480 MB |

[3] Tesla V100-PCIE-32GB | 32'C,   0 % |     0 / 32480 MB |

[4] Tesla V100-PCIE-32GB | 49'C,  92 % | 31114 / 32480 MB | s5084400(31103M)

[5] Tesla V100-PCIE-32GB | 33'C,   0 % |     0 / 32480 MB |

[6] Tesla V100-PCIE-32GB | 31'C,   0 % |     0 / 32480 MB |

[7] Tesla V100-PCIE-32GB | 33'C,   4 % |     0 / 32480 MB |


>>>>>>>>>>>>>>>>
Run the command "free" to find how much total memory is available
free

              total        used        free      shared  buff/cache   available

Mem:      395591556    17993044    40322676      710764   337275836   375287544

Swap:       2097148       17408     2079740



>>>>>>>>>>>>>>>>
gpustat shows free gpus
The command qstatt shows what is running.
If you look at it, there are 3 jobs running each with 100GB memory request. Which means a total of 300GB for these jobs. (Never mind if they are using that memory or not)

The problem is clear. For the queued job, you have requested  100GB. The command "free" tells you the maximum amount of memory on that node which is 375GB (the last column). So already 300GB is being used with the running jobs.
Additional jobs request will have to be below 75GB. The queued jobs requests additional 100GB each. It obviously does not have this as it will put it over the max 375GB. So, you must wait for the other remaining jobs to finish or reduce your memory requirements (e.g to less than 75GB in this case).

The bottleneck could be the CPUs,walltime, GPUs, memory (as in this example), etc.
I hope this explains why the jobs are still queued.


 There are cloud options (eg Microsoft Azure) that are available to all researchers on a paid basis if your research group has the funding for it

#!/bin/bash
#PBS -m abe
#PBS -M i.siva@griffith.edu.au
#PBS -N SimpleTest
#PBS -q workq
#PBS -l select=1:ncpus=8:mem=1g,walltime=01:01:10
module load intel/intelParallelStudio2019
export OMP_NUM_THREADS=$NCPUS
cd $PBS_O_WORKDIR
./hello_world.exe

#define NPROCS 8

int main (int argc, char *argv[]) {

   int nthreads, num_threads=NPROCS, tid;

  /* Set the number of threads */
  omp_set_num_threads(num_threads);

  /* Fork a team of threads giving them their own copies of variables */
#pragma omp parallel private(nthreads, tid)
  {

  /* Each thread obtains its thread number */
  tid = omp_get_thread_num();

  /* Each thread executes this print */
  printf("Hello World from thread = %d\n", tid);

  /* Only the master thread does this */
  if (tid == 0)
     {
      nthreads = omp_get_num_threads();
      printf("Total number of threads = %d\n", nthreads);
     }

   }  /* All threads join master thread and disband */

}

./hello_world.exe
Hello World from thread = 4
Hello World from thread = 0
Total number of threads = 8
Hello World from thread = 2
Hello World from thread = 3
Hello World from thread = 5
Hello World from thread = 6
Hello World from thread = 7
Hello World from thread = 1

Requirement: Install fastqc v0.11.9 ,samtools v1.15.1, bcftools v1.15.1 ,bwa v0.7.17 (r1188), bwa-mem2 v2.2.1, GATK v4.2.6.1  
Please check to make sure if these packages are available through conda.
Once that is confirmed, do this:

To get internet access from the cluster, run this command:
source /usr/local/bin/s3proxy.sh

Load the anaconda module to create virtual environment to install the given software (if available through conda)
module load anaconda3/2022.10 

conda search -c bioconda gatk4
We get the following results. Repeat the same for the other applications if needed.
(fastqc                        0.11.9               0  bioconda )
(samtools                      1.15.1      h1170115_0  bioconda)
(bcftools                      1.15.1      h0ea216a_0  bioconda)
(bwa                           0.7.17      pl5.22.0_2  bioconda )
(bwa-mem2                       2.2.1      he513fc3_0  bioconda)
(gatk                             3.8          py36_4  bioconda)
(gatk4                        4.2.6.1      hdfd78af_0  bioconda  )
As you can see all are available for the version required.

If you do not have a virtual environment already, you may create one like this by specifying the version of python needed if required.

>>>>>>
mkdir -p ~/.conda/envs;mkdir -p ~/.conda/pkgs

Edit the ~/.condarc file (nano ~/.condarc) and place the following content:

channels:
  - defaults


The do the following to create the virtual environment
conda create --name environmentName
e.g 
conda create --name javed

Activate this environment by doing this:

source activate javed

>>>>>>>
Once you are in the virtual environment, you simply use the conda command to install the version of the application you need.
e.g
conda install -c bioconda fastqc=0.11.9
conda install -c bioconda samtools=1.15.1
conda install -c bioconda bcftools=1.15.1
conda install -c bioconda bwa=0.7.17
conda install -c bioconda bwa-mem2=2.2.1
conda install -c bioconda gatk4=4.2.6.1

Once installed, these applications would be available in your pbs script by having these 2 lines in the pbs script

module load anaconda3/2021.11 
source activate javed  (or whatever the name of the virtual env)


Sometimes a particular virtual environment may conflict with the install request due to other applications already installed in that environment conflicting with the the requirement. Simply install a new virtual environment to install the problem application.

source deactivate javed
conda create --name javed2
source activate javed2
You may have to load further modules to enable it to install. (e.g module load library/zlib/1.2.12 ) or install updated versions through conda of dependencies. (e.g:conda install zlib=1.2.12)

Now that you have installed everything, you can now use it in a pbs script (see below for cat ~/pbs/pbs.01). 
To submit the job, you can do this "qsub pbs.01".


#!/bin/bash
#PBS -N MyTest
#PBS -m abe
#PBS -M myEmail@griffithuni.edu.au
#PBS -q workq
#PBS -l select=1:ncpus=1:mem=12gb,walltime=5:00:00
module load anaconda3/2021.11
source activate javed
echo "Starting job: "
cd  $PBS_O_WORKDIR
tensorboard -help

#On the login node which has been sshed into with X11 forwarding, run the following command to submit an interactive pbs job:

qsub -I -X -q workq  -l select=1:ncpus=1:mem=8gb,walltime=24:00:00

If you need a specific node, you can mention the node as follows
qsub -I -X -q workq  -l select=1:ncpus=1:host=gc-prd-hpcn006:mem=8gb,walltime=24:00:00

From your local computer
ssh -Y snumber@10.250.250.3

Once you log in, make sure you are able to open "xclock"

Once you are happy xclock works, 
cd <dataDirectory>
Start pbs with X11 forwarding and in interactive mode (this is only possible in interactive mode)
e.g: 
qsub -X -I -l select=1:ncpus=1:mem=12gb,walltime=5:00:00

Once the job has been placed in a compute node, you wil be taken there.
The prompt will change from snumber@gc-prd-hpclogin1 to one of the compute node snumber@gc-prd-hpcn003

Now, type "xclock" to make sure all is well.

Then do this:
cd $PBS_O_WORKDIR
module load misc/febio/3.6
module load matlab/2021a
module load anaconda3/2021.11
source activate nataliya
cp ~/pathdef.m .
#Run your matlab here
matlab -nodisplay -nosplash -nodesktop -r "run('/export/home/snumber/FEA_scripts/Mat_Visco_PinkySil/C_inverse_FEA_uniaxial_viscoelastic.m');exit;"

mkdir ~/Containers
cp -i /sw/Containers/singularity/images/trinityrnaseq.v2.14.0.simg ~/Containers

mkdir ~/scratch/jobs
create a run file inside this folder (nano ~/scratch/jobs/trinity.sh)
cat trinity.sh

dir=/scratch/jobs/sz_ons_totalRNA
out_dir=/scratch/jobs/trinity_out
Trinity --seqType fq --max_memory 19G --normalize_reads --left $dir/100020001_1P.fastq --right $dir/100020001_2P.fastq --SS_lib_type RF --CPU 15 --output $out_dir/10201_r1r2_trinity_out

Make it an executable:
chmod +x  trinity.sh

Make sure data is available inside: /export/home/s123456/scratch/jobs
(or wherever in scratch)

https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

Exporting the environment.yml file
Note

If you already have an environment.yml file in your current directory, it will be overwritten during this task.

Activate the environment to export: 

Note

Replace myenv with the name of the environment. 

module load anaconda3/2021.11

source activate myenv

Export your active environment to a new file:

conda env export > environment.yml
Note

This file handles both the environment's pip packages and conda packages.

Email or copy the exported environment.yml file to the other person.



To setup this environment:
module load anaconda3/2021.11
source /usr/local/bin/s3proxy.sh
conda env create -n ENVNAME --file ENV.yml
e.g
conda env create -n labmcdougall --file /tmp/environment.yml
conda env create -n labmcdougallRoot --file /tmp/environment.yml
#To remove an environment, conda remove -n env --all

ssh -o ProxyCommand="ssh  -W %h:%p s123456@gc-prd-bastion-1.itc.griffith.edu.au" s123456@10.250.250.3

OR
ssh -l s123456 \
      -o 'ProxyCommand ssh -l s123456 %h nc 10.250.250.3 22' \
      -o 'HostKeyAlias 10.250.250.3' \
      gc-prd-bastion-1.itc.griffith.edu.au

You may update your ~/.ssh/config file and make the command simpler.

Host hpclogin1
        Hostname 10.250.250.3
        ProxyCommand ssh s123456@gc-prd-bastion-1.itc.griffith.edu.au -W %h:%p
 
Now all I have to do is type the following ssh command 
ssh s123456@hpclogin1

Note 1:
=======
OpenSSH version 7.3 or above: If there are multiple jump hosts, you can set multiple jump host using a comma-separated list and the servers will be visited in the order listed:

Host hpclogin1
        Hostname 10.250.250.3
        ProxyCommand ssh gc-prd-bastion-1.itc.griffith.edu.au,na-prd-bastion-1.itc.griffith.edu.au -W %h:%p
        User s123456

Note 2: Multihop transfers
===========================

sftp -o ProxyCommand="ssh  -W %h:%p s123456@gc-prd-bastion-1.itc.griffith.edu.au" s123456@10.250.250.3

scp -o ProxyCommand="ssh -W %h:%p user1@server1" user2@server2:/<remotePath> <localpath>

To copy a file named core.10437 from HPC login node to local machine:
=====================================================================
scp -o ProxyCommand="ssh -W %h:%p s123456@gc-prd-bastion-1.itc.griffith.edu.au" s123456@10.250.250.3:/export/home/s123456/core.10437 . 

To copy a directory named tmp2 from local machine to HPC login node
====================================================================
scp -o ProxyCommand="ssh -W %h:%p s123456@gc-prd-bastion-1.itc.griffith.edu.au" -r tmp2 s123456@10.250.250.3:/export/home/s123456/

n061 nvidia driver is 530.30.02 and cuda toolkit 12.1. As this is the latest (as of March 2023), pytorch was not compatible. The nvidia drivers have been downgraded to 520.61.05 and cuda toolkit 11.8. Even after the downgrade, torch still could not detect a cuda device.The workaround was to manually compile it 

Here is the installation notes:
>>>>>>
Edit ~/.condarc (vi ~/.condarc)
>>>>>>
channels:
  - defaults

envs_dirs:
  - /lscratch/s12345/.conda/envs
  - /export/home/s12345/.conda/envs

>>>>>>>
source /usr/local/bin/s3proxy.sh
module load anaconda3/2022.10
module load gcc/11.2.0
module load cmake/3.26.4
module load cuda/11.4
#If you have an existing environment, you can use it. If not create it with: conda create -n myTorch
source activate modelT5b
conda install astunparse numpy ninja pyyaml mkl mkl-include setuptools  cffi typing_extensions future six requests dataclasses #cmake
conda install -c pytorch magma-cuda118

mkdir  /tmp/bela  #Any name is fine. Here I named it bela. It is temp dir
cd /tmp/bela
git clone --recursive https://github.com/pytorch/pytorch
cd pytorch
git checkout v1.13.1 # Or any version you want
git submodule sync
git submodule update --init --recursive
export CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
python setup.py install 2>&1 | tee pythonSetupLogs.txt
>>>>>>>

Now you can test your installation:
source activate myenv
python
Python 3.10.11 (main, Apr 20 2023, 19:02:41) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
>>> torch.cuda.is_available()
True
>>>

Another test:
python isCuda.py 

CUDA AVILABLE

>>>>cat isCuda.py<<<<<
import torch
if torch.cuda.is_available():
    print('CUDA AVILABLE')
else:
    print('NO CUDA')
>>>>>>>>>>>>>>>>>>
 
To install torchvision from source:
conda install -c conda-forge libjpeg-turbo
git clone https://github.com/uploadcare/pillow-simd
cd pillow-simd
python setup.py install 2>&1 | tee pythonInstallPillowSimd.txt
git clone https://github.com/pytorch/vision.git
cd vision
git checkout v0.14.1
python setup.py install 2>&1  | tee pythonInstalltorchvision.txt
 For tensorflow:
conda install -c conda-forge tensorflow=2.12.0=gpu_py310hfda07e1_0

ssh n061
#Check if they work first
cd /lscratch/sw/Containers
singularity  shell  --nv /lscratch/sw/Containers/tensorflow_23.05-tf2-py3mine.sif
python
import tensorflow as tf
physical_devices = tf.config.list_physical_devices('GPU')
print("Num GPUs:", len(physical_devices))

#use it in a pbs script
Check: https://griffith.atlassian.net/wiki/spaces/GHCD/pages/4030761/Singularity

# You can create your own containers
#https://catalog.ngc.nvidia.com/containers
singularity pull  docker://nvcr.io/nvidia/tensorflow:22.01-tf2-py3  # Get the version you desire
singularity  shell  --nv <container.sif>

You can temporarily use the local scratch to install application and run data out of.
#Please note /lscratch is temporary storage and will disappear next time the server is imaged. So always have a backup.

To install from /lscratch, you can do the following:
mkdir -p /lscratch/s12345/.conda/envs
mkdir -p /lscratch/s12345/.conda/pkgs

Edit ~/.condarc (vi ~/.condarc)
>>>>>>
channels:
  - defaults

envs_dirs:
  - /lscratch/s12345/.conda/envs
  - /export/home/s12345/.conda/envs
>>>>>>

module use /lscratch/sw/Modules  #put it in your ~/.bashrc if you are going to use this often
module load anaconda3/2023.03
source /usr/local/bin/s3proxy.sh
conda create -n A100local   #any name will do
source activate A100local
Now you can install the packages with
conda search -c pytorch pytorch #example of a package 
conda search -c pytorch-nightly  pytorch #example of a package from development site
conda search tensorflow #example of a package 
conda install <package> 
e.g: conda install -c pytorch pytorch=2.0.1=py3.11_cuda11.8_cudnn8.7.0_0
e.g: conda install  -c pytorch-nightly tensorflow=2.12.0=gpu_py310hfda07e1_0

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.

>>>>>>