Frequently asked questions
Passwords
I forgot my password - what now?
Please contact the support team.
How do I change my password on Star?
You can run the passwd command on the login node to change your password. Please note passwd will have no affect from the compute nodes.
What is the ssh key fingerprint for star.hofstra.edu?
The SHA256 key fingerprint is: SHA256:W0NKVfQBl5FeOlOkoEIKIVsp1+47yIvzJAYMx6ECpwM
If you are more of a visual person, run ssh -p 5010 -o VisualHostKey=yes binary.star.hofstra.edu and compare it to this visual key:
+--[ED25519 256]--+
|E + ++ . .o=.+=.|
|o=.=o..o . . +ooo|
|* +o .. o o .o+ |
|+o .. + = |
|.. . S o o |
| . . o . |
| o... .. |
| ..+o o |
| .oo. . |
+----[SHA256]-----+
Installing software
I need Python package X but the one on Star is too old or I cannot find it
You can choose different Python versions with either the module system or using Anaconda/Miniconda. See here: /software/modules and /software/python_r_perl.
In cases where this still doesn't solve your problem or you would like to install a package yourself, please read the next section below about installing without sudo rights.
If we don't have it installed, and installing it yourself is not a good solution for you, please contact us and we will do our best to help you.
Can I install Python software as a normal user without sudo rights?
Yes. Please see /software/python_r_perl.
Compute and storage quota
How can I check my disk quota and disk usage?
To check the disk quota of your home directory ( /home/username ), you can use the repquota command which prints a summary of the disc usage and quotas for the specified file systems.
$ /usr/sbin/repquota -a -s
$ Block limits File limits
$ User used soft hard grace used soft hard grace
$ cchave6 -- 116M 1024M 1280M 1922 0 0
Here,
Soft Limit -> This is a warning threshold. A user can exceed this limit temporarily, but they must reduce usage back under this limit within a "grace period."
Hard Limit -> This is the absolute maximum disk space or number of files a user can use. The user cannot exceed this limit at all.
Grace Period -> The amount of time a user is allowed to exceed the soft limit before they are required to get back under it. If this period expires, the soft limit becomes enforced like a hard limit.
File limits (inodes) -> These limit the number of files a user can create, regardless of their size.
To check the quota of the main project storage (parallel file system - /fs1/proj/
$ mmlsquota -j <fileset_name> <filesystem_name>
The -j option specifies that you are querying a fileset. Filesets in GPFS are similar to directories that can have independent quota limits.
fileset_name -> This is the name of the fileset whose quota you want to check.
filesystem_name -> The name of the GPFS filesystem in which the fileset resides.
example: mmlsquota -j project_fileset gpfs1
How many CPU hours have I spent?
This command gives you a report of account utilization, including CPU hours, for the specified period.
$ sreport cluster AccountUtilizationByUser start=YYYY-MM-DD end=YYYY-MM-DD
Connecting via ssh
How can I export the display from a compute node to my desktop?
If you need to export the display from a compute node to your desktop you should
- First login to Star with display forwarding.
- Then you should reserve a node, with display forwarding, trough the queuing system.
Here is an example:
$ ssh -Y binary.star.hofstra.edu # log in with port forwarding
$ srun -N 1 -t 1:0:0 --pty bash -I # reserve and log in on a compute node
This example assumes that you are running an X-server on your local desktop, which should be available for most users running Linux, Unix and Mac Os X. If you are using Windows you must install some X-server on your local PC.
How can I access a compute node from the login node?
Please read about Interactive jobs at /jobs/creating-jobs.md/.
My ssh connections are dying / freezing
How to prevent your ssh connections from dying / freezing.
If your ssh connections more or less randomly are dying / freezing, try to add the following to your local ~/.ssh/config file:
ServerAliveCountMax 3
ServerAliveInterval 10
(local means that you need to make these changes to your computer, not on star)
The above config is for OpenSSH, if you're using PUTTY you can take a look at this page explaining keepalives for a similar solution.
Jobs and queue system
I am not able to submit jobs longer than two days
Please read about label_partitions.
Where can I find an example of job script?
You can find job script examples at /jobs/creating-jobs.md/.
Relevant application specific examples (also for beginning users) for a few applications can be found in sw_guides.
When will my job start?
How can I find out when my job will start?
To find out approximately when the job scheduler thinks your job will start, use the command:
squeue --start -j <job_id>
This command will give you information about how many CPUs your job requires, for how long, as well as when approximately it will start and complete. It must be emphasized that this is just a best guess, queued jobs may start earlier because of running jobs that finishes before they hit the walltime limit and jobs may start later than projected because new jobs are submitted that get higher priority.
How can I see the queing situation?
In the command line, see the job queue by using squeue.
Why does my job not start or give me error feedback when submitting?
Most often the reason a job is not starting is that Star is full at the moment and there are many jobs waiting in the queue. But sometimes there is an error in the job script and you are asking for a configuration that is not possible on Star. In such a case the job will not start.
To find out how to monitor your jobs and check their status see monitoring_jobs.
Below are a few cases of why jobs don't start or error messages you might get:
Memory per core
"When I try to start a job with 2GB of memory pr. core, I get the following error:
sbatch: error: Batch job submission failed: Requested node configuration is not availableWith 1GB/core it works fine. What might be the cause to this?"
On Star we have two different configurations available; 16 core and 20 core nodes - with both a total of 32 GB of memory/node. If you ask for full nodes by specifying both number of nodes and cores/node together with 2 GB of memory/core, you will ask for 20 cores/node and 40 GB of memory. This configuration does not exist on Star. If you ask for 16 cores, still with 2GB/core, there is a sort of buffer within SLURM no allowing you to consume absolutely all memory available (system needs some to work). 2000MB/core works fine, but not 2 GB for 16 cores/node.
The solution we want to push in general is this:
#SBATCH -ntasks=80 # (number of nodes * number of cores, i.e. 5*16 or 4*20 = 80)
If you then ask for 2000MB of memory/core, you will be given 16 cores/node and a total of 16 nodes. 4000MB will give you 8 cores/node - everyone being happy. Just note the info about PE accounting; mem-per-cpu 4000MB will cost you twice as much as mem-per-cpu 2000MB.
Please also note that if you want to use the whole memory on a node, do not ask for 32GB, but for 31GB or 31000MB as the node needs some memory for the system itself. For an example, see here: allocated_entire_memory
Step memory limit
"Why do I get
slurmstepd: Exceeded step memory limitin my log/output?"
For slurm, the memory flag is a hard limit, meaning that when each core tries to utilize more than the given amount of memory, it is killed by the slurm-deamon. For example $SBATCH --mem-per-cpu=2GB means that you maximum can use 2 GB of memory per core. With memory intensive applications like Comsol or VASP, your job will likely be terminated. The solution to this problem is to specify the number of tasks irrespectively of cores/node and ask for as much memory you will need.
For instance:
#SBATCH --ntasks=20
#SBATCH --time=0-24:05:00
#SBATCH --mem-per-cpu=6000MB
QOSMaxWallDurationPerJobLimit
QOSMaxWallDurationPerJobLimit means that MaxWallDurationPerJobLimit has been exceeded. Basically, you have asked for more time than allowed for the given QOS/Partition. Please have a look at label_partitions
Priority vs. Resources
Priority means that resources are in principle available, but someone else has higher priority in the queue. Resources means the at the moment the requested resources are not available.
Why is my job not starting on highmem nodes although the highmem queue is empty?
To prevent the highmem nodes from standing around idle, normal jobs may use them as well, using only 32 GB of the available memory. Hence, it is possible that the highmem nodes are busy, although you do not see any jobs queuing or running on squeue -p highmem.
How can I customize emails that I get after a job has completed?
Use the mail command and you can customize it to your liking but make sure that you send the email via the login node.
As an example, add and adapt the following line at the end of your script:
echo "email content" | ssh star-1.local 'mail -s "Job finished: ${SLURM_JOBID}" firstname.lastname@hofstra.edu'
How can I run many short tasks?
The overhead in the job start and cleanup makes it unpractical to run thousands of short tasks as individual jobs on Star.
The queueing setup on star, or rather, the accounting system generates overhead in the start and finish of a job of about 1 second at each end of the job. This overhead is insignificant when running large parallel jobs, but creates scaling issues when running a massive amount of shorter jobs. One can consider a collection of independent tasks as one large parallel job and the aforementioned overhead becomes the serial or unparallelizable part of the job. This is because the queuing system can only start and account one job at a time. This scaling problem is described by Amdahls Law.
If the tasks are extremly short, you can use the example below. If you want to spawn many jobs without polluting the queueing system, please have a look at job_arrays.
By using some shell trickery one can spawn and load-balance multiple independent task running in parallel within one node, just background the tasks and poll to see when some task is finished until you spawn the next:
And here is the dowork.sh script: