Misc Updates

docs/source/Access/accessrequest.rst

@@ -3,6 +3,14 @@ Access Requests for DeepThought HPC
 
 Getting access to the HPC is quick and easy process. Follow the steps below to get up and running.
 
+.. attention:: 
+    The HPC now has new URLs for access, specifically to the new web portals. 
+
+    1. deepthought.flinders.edu.au: SSH / Command Line Access
+    2. https://deepweb.flinders.edu.au/:  User Portal
+    3. https://deepweb.flinders.edu.au/jupyter: Jupyter Hub 
+
+
 VPN Requirements
 +++++++++++++++++
 
@@ -12,9 +20,9 @@ When **off campus** you must be connected to the Flinders VPN to access the HPC.
 Flinder Staff / HDR Students 
 -----------------------------
 .. _ServiceOne: https://flindersuni.service-now.com/csp?id=sc_cat_item&sys_id=d95a633cdbf87810062472f5f39619f5 
-.. _(Linux & MacOS/X): access/unix.html 
-.. _Windows Sub-System for Linux: access/unix.html 
-.. _Windows: access/windows.html
+.. _(Linux & MacOS/X): unix.html 
+.. _Windows Sub-System for Linux: unix.html 
+.. _Windows: windows.html
 
 1. Create a `ServiceOne`_ Ticket asking for Access to the HPC
 

docs/source/Access/windows.rst

@@ -1,4 +1,4 @@
-Window Connection Guide 
+Windows Connection Guide 
 ========================
 To connect to Deep Thought a SSH client such as PuTTy is required. 
 Below is a short list of the possible programs you can use as a client to connect to the HPC. 

docs/source/SLURM/SLURMIntro.md

@@ -210,6 +210,8 @@ The DeepThought HPC will set some additional environment variables to manipulate
 This means that if you leave anything in $TMP or $SHM directories it will be *removed when your job finishes*.
 
 To make that abundantly clear. If the Job creates `/local/jobs/$SLURM_USER/$SLURM_JOB_ID/` it will also **delete that entire directory when the job completes**. Ensure that your last step in any job creation is to _move any data you want to keep to /scratch or /home_.
+
+
 |Variable Name                |   Description                                 | Value |
 |-----------------------------|-----------------------------------------------|----------------------------|
 | $TMP                        | The Linux default 'Temp' file path.           | /local/$SLURM_USER/$SLURM_JOB_ID         |
@@ -220,7 +222,7 @@ To make that abundantly clear. If the Job creates `/local/jobs/$SLURM_USER/$SLUR
 | $TEMP_DIR                   | An alias for $TMP| /local/$SLURM_USER/$SLURM_JOB_ID/ |
 | $SCRATCH_DIR                | A Per-Job Folder on the HPC /scratch mount  | /scratch/users/$SLURM_USER/$SLURM_JOB_ID/ |
 | $SHM_DIR                    | A Per-Job Folder on the Compute Node Shared-Memory / Tempfs Mount | /dev/shm/jobs/$USER/ |
-| $OMP_NUM_THREADS            | The OpenMPI CPU Count Environment Variable | $SLURM_CPUS_PER_TASK |
+| $OMP_NUM_THREADS            | The OpenMP CPU Count Environment Variable | $SLURM_CPUS_PER_TASK |
 
 #### $TMPDIR and SLURM Job-Arrays
 
@@ -332,41 +334,50 @@ An excellent guide to [submitting jobs](https://support.ceci-hpc.be/doc/_content
     # job will be scheduled when attempting to backfill jobs. 
     # 
     # The current cluster-wide limit is 14 Days from Start of Execution.
+    # The timer is only active while your job runs, so if you suspend
+    # or pause the job, it will stop the timer.
     #
     # The command format is as follows: #SBATCH --time=DAYS-HOURS
+    # There are many ways to specify time, see the SchedMD Slurm 
+    # manual pages for more. 
     #SBATCH --time=14=0
     #
     ##################################################################
     # How many tasks is your job going to run? 
     # Unless you are running something that is Parallel / Modular or
     # pipelined, leave this as 1. Think of each task as a 'bucket of
-    # resources' that stand alone. Without MPI / IPC you cant talk to 
+    # resources' that stand alone. Without MPI / IPC you can't talk to 
     # another bucket!
     #
     #SBATCH --ntasks=1
+    #
     # If each task will need more that a single CPU, then alter this 
-    # value. Remeber, this is multiplicative, so if you ask for 
+    # value. Remember, this is multiplicative, so if you ask for 
     # 4 Tasks and 4 CPU's per Task, you will be allocated 16 CPU's 
     #SBATCH --cpus-per-task=1
     ##################################################################
     # Set the memory requirements for the job in MB. Your job will be
     # allocated exclusive access to that amount of RAM. In the case it
-    # overuses that amount, Slurm will kill it. The default value is 
+    # overuses that amount, Slurm will kill the job. The default value is 
     # around 2GB per CPU you ask for.
+    #
     # Note that the lower the requested memory, the higher the
     # chances to get scheduled to 'fill in the gaps' between other
     # jobs. Pick ONE of the below options. They are Mutually Exclusive.
-    # You can ask for X Amount of RAM per CPU (MB by default)
+    # You can ask for X Amount of RAM per CPU (MB by default).
+    # Slurm understands K/M/G/T For Kilo/Mega/Giga/Tera Bytes.
+    #
     #SBATCH --mem-per-cpu=4000
     # Or, you can ask for a 'total amount of RAM'. If you have multiple 
     # tasks and ask for a 'total amount' like below, then SLURM will 
     # split the total amount to each task evenly for you.
     ##SBATCH --mem=12G
     ##################################################################
-    # Change the number of GPU's required and the most GPU's that can be 
+    # Change the number of GPU's required for you job. The most GPU's that can be 
     # requested is 2 per node. As there are limited GPU slots, they are heavily 
     # weighted against for Fairshare Score calculations. 
-    # You can request either a 'tesla:X' or a 'gpu:x'
+    # You can request either a 'gpu:telsa_v100:X' or a 'gpu:x'
+    # 
     # You can either request 0, or omit this line entirely if you 
     # a GPU is not needed. 
     #
@@ -376,9 +387,9 @@ An excellent guide to [submitting jobs](https://support.ceci-hpc.be/doc/_content
     # loading them manually, with a space-separated list, or you can 
     # write multiple lines.
     # You will need to uncomment these.
-    #module add miniconda/3.0 cuda10.0/toolkit/10.0.130 
-    #module add miniconda/3.0 
-    #module add cuda10.0/toolkit/10.0.130 
+    #module load miniconda/3.0 cuda10.0/toolkit/10.0.130 
+    #module load miniconda/3.0 
+    #module load cuda10.0/toolkit/10.0.130 
 
     ##################################################################
     # This example script assumes that you have already moved your 
@@ -391,7 +402,8 @@ An excellent guide to [submitting jobs](https://support.ceci-hpc.be/doc/_content
     # directory as a part of your job script. 
 
     # Example using the HPC Set $TMPDIR Variable 
-    cd $TMPDIR
+    cd /local/ 
+    mkdir $SLURM_JOB_ID/ ; cd $SLURM_JOBID
     cp /scratch/user/<FAN>/dataset ./
 
     # A Manual 'Shared' Data-Set Directory
@@ -414,6 +426,6 @@ An excellent guide to [submitting jobs](https://support.ceci-hpc.be/doc/_content
 
     # Using the example above with a shared dataset directory, your final step 
     # in the script should remove the directory folder 
-    # rm -rf $DATADIR
+    # rm -rf /local/$SLURM_JOBID
 
     ##################################################################

docs/source/dataflow/hpcjobdataflow.rst

@@ -5,6 +5,9 @@ HPC Job Data Flow
 To run jobs in an efficient manner on the HPC, there is usually some additional preparation work required. The below diagram will aid you in ascertaining
 what steps to take to ensure that you run your jobs in the quickest manner. 
 
+Depending on your view-screen size 
+you may wish to Right Click -> Open Image in New Tab to view the diagram correctly. 
+
 .. figure:: ../_static/HPC_Job_Data_Flow.svg
     :align: center
     :alt: HPC Job Data Flow Diagram

docs/source/dataflow/hpcresearchdataflow.rst

@@ -2,7 +2,8 @@
 HPC Research Data Flow 
 ************************
 
-The following diagram illustrates the overall location of the HPC in the Research Data Management flow.  
+The following diagram illustrates the overall location of the HPC in the Research Data Management flow. Depending on your view-screen size 
+you may wish to Right Click -> Open Image in New Tab to view the diagram correctly. 
 
 .. figure:: ../_static/HPC_Research_Data_Flow.svg
     :alt: HPC Research Data Flow