For example problems

How do I log on to machines on Linux?

Systems from the UNIX/Linux family usually have programs that allow SSH connections. To log in you need to execute a command:

ssh <login>@<company_machine_name>

where <login> is the name of the user account on the machine and <access_machine name> is the name of the access machine or its IP number.
For example, a user with a novak account on a eagle.man.poznan.pl machine will log in using a command:

 ssh nowak@eagle.man.poznan.pl

How do I log on to machines in Windows?

Windows systems do not have a built-in SSH protocol client. Therefore their users must install additional software.
Recommended programs:
Putty as a client of SSH
WinSCP for file transfer
After logging in to the machine, the user uses the text console, just like when logging in from Unix/Linux machines.

Sample script

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem=4gb
#SBATCH --time=01:00:00

# We set up paths or load appropriate modules
module load plink/1.90

# Set the $TMPDIR variable
export TMPDIR=$HOME/grant_$SLURM_JOB_ACCOUNT/scratch/$USER/$SLURM_JOB_ID

# We set application variables
export SCR=${TMPDIR}

# We set the auxiliary variables
INPUT_DIR="input"
OUTPUT_DIR="output"
OUTPUT_FILE="OUTPUT"

# We create a temporary directory
mkdir -p ${TMPDIR}

# Copy the input data to the directory indicated for the variable $TMPDIR
cp ${SLURM_SUBMIT_DIR}/${INPUT_DIR}/* ${TMPDIR}

# We go to the $TMPDIR directory
cd $TMPDIR

# We make calculations
plink --noweb --file hapmap1

# We finish calculations, copy the contents of the $TMPDIR/output directory 
# to the directory from which the task was sealed.
mkdir $SLURM_SUBMIT_DIR/${OUTPUT_DIR}
cp -r $TMPDIR/* $SLURM_SUBMIT_DIR/${OUTPUT_DIR}/

# We're cleaning the working directory
rm -rf $TMPDIR

Example input:
Below are the files that should be in the input directory.
File:Plink input.zip

How to access PSNC resources

To gain access to the remaining resources of the PSNC, it is necessary to apply from the access to a specific machine (e.g. Eagle) in the portal
To do this, go to https://hpc.man.poznan.pl and log in. to your user account
Then choose:
Calculation grants -> Machines -> Configure passwords on machines -> Configure accounts for of this user
There, we select the machine to which we want to access and send a request for access. Then we wait for the request to be approved by the machine administrator

How to become a user

For details, see How to become a user.

Can I start calculation tasks on the access machine?

It is not permitted to start computation tasks on an access node. Any such task will be interrupted without warning. Tasks can only be started with a queuing system.

How to run a job on more than one processor?

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4

How do you know how many cores a cluster node has?

The scontrol show node command displays detailed information about all nodes.

How do I request XXXX megabytes of memory for my task?

In the queuing system script, you should put a line that specifies the memory size. For 2GB it has a form:

#SBATCH --mem=2gb

How do you specify the exact time that the task will count?

The time parameter is used to specify the exact time needed for the task. The time is given in the format HH:MM:SS. Use in a queueing script (a task that will last 12 hours and 30 minutes):

#SBATCH --time=12:30:00

Why doesn't my job start right away despite my R status in the queue system

The behaviour of the queuing system is correct and results from the fact that the queuing system has been configured in such a way as to minimize the energy consumption of the cluster. This mechanism causes nodes that are not used by the queuing system to be disabled. When the system accepts the task, the nodes are restarted. Switching on a calculation node takes a maximum of 5 minutes and during this time the queuing system shows that the task is running (R) and has the nodes assigned, that are just starting up (not yet available through ssh). In such a situation the calculations should start after maximum 5 minutes. In case one of the nodes is not started correctly, the queuing system should redirect the task eliminating the malfunctioning nodes.

I've lost the ability to make calculations?

When you lose the possibility to perform calculations and the following message appears:

WinSCP: this is end-of-file:0

In this case, you should check at https://hpc.man.poznan.pl/ in the tab 'Calculation grants' then 'Grant list' by selecting the current grant, whether the declared resources on the machine are not exceeded.
When the resources are exceeded, a request to increase the resources (modification of the grant)
should be submitted. Here are the application instructions:
Składnie wniosku o modyfikacje grantu

FAQ

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