> scontrol show job #JOBID

 > sprio -j #JOBID

In order to use the available libraries dynamically, you have to add the library directory to the path list of the environment variable $LD_LIBRARY_PATH before the execution of your job starts. To see your library path, please load the library module and then use 

 > module show <libraryname> 

Then export or set the path:

...

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:<path>

set LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:<path>    (csh)

• Error invalid account when submitting a job: Invalid account or account/partition combination specified.

• The error Invalid account might depend on the lack of resources associated to your project or there is an error with the account name in your batch script. Just use the saldo command.  If the account is correct and valid, are you lunching the job on the right partition? To see which partition is right for your case and account, please consult the Summary paragraph inside the System Specific Guide.

• How can I list all my jobs currently in the queue?

 > squeue -u $USER

...

• Can I modify SLURM settings of a waiting job?

Some Slurm settings of a pending job can be modified using the command scontrol update. For example, setting the new job name and time limit of the pending job: 

...

• How can I place and release a job from hold state?

In order to place a job on hold type 

 > scontrol hold JOB_ID. 

To release the job from the hold state, issue 

...

• Jobs in interactive mode: launching the program with srun but it remains stuck

After creating an interactive job with srun command

    srun -N 1 -n X ... --pty /bin/bash

if I launch my job with srun

    srun -n X program

...

salloc -N 1 -n X

...

for KEYAL in ssh-rsa ecdsa-sha2-nistp256; do for n in 1 2 5 7; do ssh-keyscan -t $KEYAL login0${n}-ext.leonardo.cineca.it | sed s"/0${n}-ext/\*/" >> ~/.ssh/known_hosts; done; done

foreach ($key in "ssh-rsa", "ecdsa-sha2-nistp256") {foreach ($node in "1", "2", "5", "7"){ssh-keyscan -t $key "login0$node-ext.leonardo.cineca.it" | foreach {$_ -replace ("0$node-ext", "*")} | Add-Content -Path "$HOME\.ssh\known_hosts"}}

     export LANGUAGE=en_US.UTF-8
     export LANG=en_US.UTF-8
     export LC_ALL=en_US.UTF-8

 > scontrol show job #JOBID

 > sprio -j #JOBID

In order to use the available libraries dynamically, you have to add the library directory to the path list of the environment variable $LD_LIBRARY_PATH before the execution of your job starts. To see your library path, please load the library module and then use 

 > module show <libraryname> 

Then export or set the path:

• export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:<path>

• set LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:<path>    (csh)

  
  

• Error invalid account when submitting a job: Invalid account or account/partition combination specified.

• The error Invalid account might depend on the lack of resources associated to your project or there is an error with the account name in your batch script. Just use the saldo command.  If the account is correct and valid, are you lunching the job on the right partition? To see which partition is right for your case and account, please consult the Summary paragraph inside the System Specific Guide.

• How can I list all my jobs currently in the queue?

 > squeue -u $USER

and you will see the list of your running or pending jobs.

• Can I modify SLURM settings of a waiting job?

Some Slurm settings of a pending job can be modified using the command scontrol update. For example, setting the new job name and time limit of the pending job: 

> scontrol update JobId=2543 Name=newtest TimeLimit=00:10:00

• How can I place and release a job from hold state?

In order to place a job on hold type 

 > scontrol hold JOB_ID. 

To release the job from the hold state, issue 

> scontrol release JOB_ID.

• Jobs in interactive mode: launching the program with srun but it remains stuck

After creating an interactive job with srun command

    srun -N 1 -n X ... --pty /bin/bash

if I launch my job with srun

    srun -n X program

the command remains stuck and nothing happens.

This is because the resources requested with the second srun are already allocated for the first srun and the command remains stuck waiting for the resources to be freed.
There are two possible solutions:

1.  create the interactive job with salloc instead of srun

   salloc -N 1 -n X

   please refer to this page with more details about how to use salloc.
   
   
2. launch the second command with the flag --overlap
   

   srun -n X --overlap program
   
   

Note: if you use mpirun instead of srun to launch your program inside an interactive job allocating more than one node you will encounter the same error. If you would like/need to use mpirun on multiple nodes, you can follow the first solution above (salloc). On a single node, instead, the command will work (because in this last case mpirun does not call srun).

• I get the following message: "srun: Warning: can't honor --ntasks-per-node set to xx which doesn't match the requested tasks yy with the number of requested nodes yy. Ignoring --ntasks-per-node." What does it mean?

  This is a message that can appear when using mpirun and Intelmpi parallel environment. It is a known problem that can be safely ignored,since mpirun does not read the proper Slurm variables and thinks that the environment is not set properly, thus generating the warning: in reality, the instance of srun behind it will respect the setting you requested with your Slurm directives.
  While there are workarounds for this, the best solution (apart from ignoring the message) is to use srun instead of mpirun: with this command, the Slurm environment is read properly and the warning does not appear.

• I'm trying to setup a conda environment but I get connection errors from the package repository. How can I solve this?

  Due to the recent modifications to Anaconda's Terms of Service, the use of the anaconda public package repository on CINECA platforms is no more permitted without the purchase of a license for commercial use. As a consequence, the service was disrupted by Anaconda. Please create your environment using alternative channels, such as conda-forge, adding the --override-channels flag and add the channel to your conda
  environment (.condarc) via:

  $  conda config --add channels conda-forge

  As an alternative you may recur to python virtual environment and pip installations.

Performance:

• I have found performance problems, what should I do?

First, you should find a method to reproduce the problem and confirm after some tests that it is reproducible. After that, you should provide all relevant information to the Support Team by e-mail together with instructions on how to reproduce your tests. Support Team will investigate the issue and contact you as soon as possible.

Note: if you use mpirun instead of srun to launch your program inside an interactive job allocating more than one node you will encounter the same error. If you would like/need to use mpirun on multiple nodes, you can follow the first solution above (salloc). On a single node, instead, the command will work (because in this last case mpirun does not call srun).

• I get the following message: "srun: Warning: can't honor --ntasks-per-node set to xx which doesn't match the requested tasks yy with the number of requested nodes yy. Ignoring --ntasks-per-node." What does it mean?

  This is a message that can appear when using mpirun and Intelmpi parallel environment. It is a known problem that can be safely ignored,since mpirun does not read the proper Slurm variables and thinks that the environment is not set properly, thus generating the warning: in reality, the instance of srun behind it will respect the setting you requested with your Slurm directives.
  While there are workarounds for this, the best solution (apart from ignoring the message) is to use srun instead of mpirun: with this command, the Slurm environment is read properly and the warning does not appear.

Performance:

• I have found performance problems, what should I do?

First, you should find a method to reproduce the problem and confirm after some tests that it is reproducible. After that, you should provide all relevant information to the Support Team by e-mail together with instructions on how to reproduce your tests. Support Team will investigate the issue and contact you as soon as possible.

Cloud

• How to add/delete a user in your virtual linux machine

In order to add the user and set his/her password  use following commands

sudo /usr/sbin/adduser <username> 

sudo chage -d 0 <username>

After you need to modify the file /etc/ssh/sshd_config, enabling the PasswordAuthentication and then restart and check the SSH deamon:

Ubuntu: 

sudo systemctl restart sshd.service

sudo systemctl status sshd.service

CentOS:

sudo systemctl restart sshd.service

sudo systemctl status sshd.service

In order to delete a user and his/her HOME directory just execute the command:

deluser --remove-home <username>

• • How to grant a user root privileges in your virtual machine

  It is possible to grant a user with root privileges using O the command adduser instead of useradd when the new user is created: 

  sudo /urs/sbin/adduser <username> sudo

  Otherwise you can add the following line in the section #User privilege specification of  the file /etc/sudoers:

• <username> ALL=(ALL:ALL) ALL

...

• How to mount remote filesystem with FUSE (Filesystem in USEr space) on CentOS or Ubuntu

On CentOS:  - You will need to install a few packages that are not available in the standard CentOS repository. So, you must enable the EPEL repo:

yum install epel-release -y 

- Install FUSE (Filesystem in USEr space) and SSHFS packages 

yum install fuse sshfs
- Load the FUSE module

modprobe fuse

- Confirm that the FUSE module is loaded 

lsmod | grep fuse
fuse                  84368    2

...

echo "modprobe fuse" >> /etc/rc.local 

- Using SSHFS. Once the FUSE module is loaded, you can mount your remote partition using SSHFS:

sshfs user@remote_host:/remote_directory  /local_mount_partition

If you have configured the login via ssh key authorization, you can use the following command:

sshfs user@remote_host:/remote_directory  /local_mount_partition -o IdentityFile=<absolute-path-with-key>

Note: If appear the following error 

fuse: bad mount point `/local_mount_partition': Transport endpoint is not connected

execute:      sudo fusermount -u /local_mount_partition

On Ubuntu:  - First you have to install FUSE and SSHFS packages with the apt-get comand:

apt-get install fuse 

apt-get install sshfs

Once the FUSE module is loaded, you can mount your remote partition using SSHFS:

sshfs user@remote_host:/remote_directory  /local_mount_partition

If you have configured the login via ssh key authorization, you can use the following command:

sshfs user@remote_host:/remote_directory  /local_mount_partition -o IdentityFile=<absolute-path-with-key>

Note: If appear the following error 

fuse: bad mount point `/local_mount_partition': Transport endpoint is not connected

execute :  sudo fusermount -u /local_mount_partition

How to mount remote filesystem  on Ubuntu 

...

apt-get install fuse 

apt-get install sshfs

Using SSHFS. Once the FUSE module is loaded, you can finally mount your remote partition using SSHFS:

sshfs user@remote_host:/remote_directory  /local_mount_partition

If you have configured the login via ssh key authorization, you can use the following command:

sshfs user@remote_host:/remote_directory  /local_mount_partition -o IdentityFile=<absolute-path-with-key>

Note: If appear the following error 

fuse: bad mount point `/local_mount_partition': Transport endpoint is not connected

execute:       sudo fusermount -u /local_mount_partition

• How to use and configure Docker in your virtual machine

To use Docker in your virtual machine please set the MTU value at 1400 in the file  /etc/docker/daemon.json.  More in particular edit the file /etc/docker/daemon.json and then set

{

"mtu" : 1400

...