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In general, it costs nothing. Basic access to the Storrs HPC is provided for free to UConn students, staff, and faculty for research purposes. If you would like to have your jobs run more quickly, we offer priority access for a fee. See: How do I get priority access to HPC resources? |
How do I login log in to the Storrs HPC when I am off campus?
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Short answer: First, you need to connect to UConn’s VPN. Then, you should be able to access the HPC. Long Answer: The HPC Cluster only allows the connection of SSH from the campus-wide computers, for example:
In order to connect to the HPC when you are off campus, you will first need to connect to the UConn Virtual Private Network (VPN). After connecting to the VPN, you will be able to login log in to the HPC as you normally do. For instructions on how to install, setupset up, and connect your personal device(s) to UConn’s VPN, please go to this webpage. |
Why am I suddenly getting a “Permission denied” error when I try to ssh
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into the HPC?
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Short answer: One of the login nodes is most likely not working properly. Try to ssh into any of the three login nodes directly. Long Answer: When you ssh into hpc2.storrs.hpc.uconn.edu, you are directed to one of our three login nodes (login4, login5, or login6). Occasionally, one of these three login nodes will be come become faulty. If you ssh into the cluster and your account is directed to the faulty node, then you may be given a “Permission denied” error message. If you experience this problem, we recommend you try to ssh directly into one of the login nodes. Here are the three commands one can use to login into our three login nodes. Please replace netID with your own netID. login4
login5
login6
If one of these allows you to login log in but another gives you a permission denied error, then we can be sure that there is something wrong with one of the login nodes. If you have the time, we’ll ask that you please send us a screenshot of the login node which is giving you a problem so that we can tend to any problems on that faulty node. This will help us ensure that this problem is fixed as soon as possible. If you receive this “Permission denied” error when ssh-ing directly into all three login nodes, then the problem may be with your netID. You may have to reset your netID password which can be done at this link. |
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The node you are on will normally be shown next to your netID when you login log in to the Storrs HPC. For instance, if Jonathan the Husky’s netID was jtk10001, his terminal might look like this.
This would tell us the that Jonathan is on the node called “login6.” Another way to check what node you are on is to use the
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How do I get priority access to HPC resources?
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Short answer: Faculty can purchase priority access for 5 years if they pay the upfront cost for the nodes. Long answer: High-priority access is available under a “condo model,” where faculty are able to purchase semi-dedicated nodes which get made available to all users when there are unused compute cycles. Under the condo model, faculty researchers fund the capital equipment costs of individual compute nodes, while the university funds the operating costs of running these nodes for five years. Faculty who purchase compute nodes receive access to equivalent resources at a higher priority than other researchers. The faculty can designate others to receive access at the same priority level, such as their graduate students, postdoctoral researchers, etc. With priority access, computational jobs are moved higher in the queuing system, and in most cases begin execution within twelve hours, depending upon other FairShare factors. A priority user can utilize their resources indefinitely. All access to resources is managed through the cluster’s job scheduler. When a priority user is not using their assigned resources, the nodes are made available to all UConn researchers for general use. |
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Since installing R packages is important to so many HPC users' research, we have created a brief guide on the installation of R packages which is linked here. |
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We have created a brief guide on the installation of python libraries which can be found here. |
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Long wait times for your jobs? Errors about unavailable resources? We’ve been there and understand how frustrating it can be for jobs to take a long time to run. It’s an unfortunate consequence of having such a strong computational research community at UConn. LOTS of incredible research happens here, but it also means that there are LOTS of people competing for resources. There’s no getting around that problem, but there are a couple of steps we can take to increase the odds that our jobs get on ASAP.
This FAQ will offer guidance on how to do both of those things. Checking for Available Resources The below
The output for that command will look like this, but it will be much longer and provide info on every partition.
The above command gives us an overarching picture of usage on the cluster, and from there, we can use a more targeted command to get more information on individual nodes within a partition, like how many cores or GPUs are in use and how many are available. The base
The column titled “CPUS (A/I/O/T)” tells us how many cores are available. A “A” stands for Allocated, I “I” stands for Idle, and T “T” stands for Total. (O “O” stands for Other but you can ignore that column) Since there are 39 cores in the “Idle” column for GPU21, that means 39 cores are available to use. But all 3 of the GPUs on GPU21 are in use so we can’t use any GPUs on that node. So, that gives us an idea of the resources. If I only needed cores and no GPUs, I could target GPU21. In summary, these two commands can give us a picture of what partitions have resources available, and then what resources are available on individual nodes within that partition. Targeting a specific partition The next step is submitting a job targeting a specific partition. If you’re not sure how to target a specific partition, please visit our SLURM Guide where you will see examples of submission scripts that target different partitions and architectures. Another key part of targeting a specific partition is knowing what partitions you are allowed to use and what “account” and “QOS” you must use to access them. To check what partitions you’re allowed to use and how to access them you can use this command.
This tells me that I have access to 6 partitions. To access the priority-gpu partition, I need to include the below three flags in my the #SBATCH header of my submission script. This will be different for every individual so you will have to modify this with the partitions you have access to and the account and QOS that are associated with your account.
If you have further questions about how to check what resources are available and how to target them, please feel free to contact the Storrs HPC admins by sending an email to hpc@uconn.edu. |
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There are many reasons a job may fail. A good first step is to use the Here’s an example of the output for a job that failed immediately with an
The The next clue to investigate is the
Once you see the job has failed multiple times on the same node, then you can feel confident that a faulty node is likely the cause. Please submit a help request to Storrs HPC including a screenshot from the |
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Short answer: If you received this error, your job most likely failed because the amount of memory (RAM) it needed was larger than the default. We can request more memory for your job using the Long answer: There are several reasons a job may fail due to from insufficient memory. The most likely reason this problem is suddenly affecting you is because that Storrs HPC Admins had to implement a new change to HPC 2.0. We’ll explain why in a moment, but first, let me go over the solution (assuming this is the problem). As of January 2023, the default amount of memory available per CPU is 2 gigabytes. But you can easily override the default using the
Adding this line will tell SLURM to use 3 gigabytes of RAM per CPU you request. That means if we ask for 2 cores (-n 2), then we’ll be allocated 6 gigabytes of RAM total. Please note that the
We encourage users to please adjust the Now, we’ll explain why this problem is suddenly affecting our users. On HPC 1.0, the memory flags didn’t work so there wasn’t a great way to prevent jobs from failing due to insufficient memory. The problem didn’t happen super often though. The memory flags do work on HPC 2.0, and the default settings were a little too strict. SLURM was only letting 1 job run per node because it assumed all jobs needed the entire node’s memory. There were nodes with 128 cores and 500 GB of RAM where only 1 core and 1 gigabyte of RAM being were used. Tons of jobs were piling up in the queue and the job wait times were really long. So, the Storrs HPC Admins reset the default memory available per core to be 2 gigabytes of RAM per core. We had to set it this low because some of the node architectures have much less memory than others. Resetting this variable enabled SLURM to allow more than one job to run on a node and reduced the job wait times, provided there is enough memory on that node. This default mem-per-cpu of 2 GB is okay for many users, but not for all. Some of our users run more RAM-intensive programs, meaning the default is not sufficient. So, now it has to be adjusted manually in the #SBATCH header. For more info on #SBATCH flags, see this link. |
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Short answer: Possibly, it depends on where the files were stored and how long ago they were deleted. Send us an email at hpc@uconn.edu explaining the situation so we can discuss options. Long Answer: Files stored in the /shared/ and /home/ directories are backed up daily at 5:00 am and the data is stored for 30 days. If the accidentally deleted files were stored within either of those directories, and you contact us in under 30 days, then there’s a chance we will be able to help you restore those files. Please contact us at hpc@uconn.edu so we can discuss a way forward. Unfortunately, if the files that were deleted had been stored on /scratch/, we will not be able to restore them. The /scratch/ directory is not backed up ever. If you’re reading this after accidentally deleting files on from scratch, we understand that this news can come as a huge blow. We wish that we could backup back up /scratch/, but we only have enough room to back /shared/ and /home/. We cannot help you fix the current situation, but there are steps we can take to prevent this from happening again. You can follow these links for more info. on HPC data storage, backing up files, or using Globus. |
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Short answer: Some modules can only be run on certain architectures. Try loading that module on a node with the Epyc or Skylake architectures. Long Answer: These GLIBC errors often happen because the software you’re trying to load expects to find a newer GLIBC library than what’s available in your current node’s Red Hat Enterprise Linux (RHEL) version. Older architectures sometimes have older RHEL versions and therefore older GLIBC libraries. Newer architectures typically have newer RHEL versions and GLIBC libraries. Switching to a newer or different architecture may resolve this GLIBC error. See the following guide for instructions on how to target specific architectures. |
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How do I fix an error which says, “Can't open display, Failed initializing GUI, exiting?”
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Short answer: This is an X-forwarding error. The most common fix is to enable X-forwarding when you ssh into the HPC using the
Long Answer: X-forwarding allows programs being run on the HPC to be opened up in a GUI on our local machines. It is convenient and nice to work with but it can take a bit of effort to set up if you are working on a Mac or Windows device. Linux users have it easy because all they normally have to do is use the |
Modules that I installed used to work properly on the original HPC but they are not loading properly on HPC 2.0. How do I resolve this problem?
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There are many reasons this might be occurring, but a common problem with user-installed programs is that the module names and versions have changed slightly between the old HPC and HPC 2.0. It may be that the dependencies your program used to rely on are no longer available on HPC 2.0. For instance, the GCC compilers have been updated and some of the old ones are no longer available. In this case, the ideal situation would be to install your program again using the newer compilers---this is often a good idea anyway because newer compilers sometimes increase the performance and reduce the chance of bugs. If there are extenuating circumstances that prevent you from using a program with new compilers , or are experiencing other module-related problems, we invite you to submit a request for assistance by emailing hpc@uconn.edu. Then we can discuss options of how to set up a module that meets your needs. |
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If the 'module load' command returns the following errors:
This means that the module you want to load conflicts with the currently loaded module, <Module2>. To fix it, please unload <Module2> and then load <Module1> again:
Or
Or, if neither of these workworks, you can purge all the modules with
and start fresh. |
How do I fix an error which says the module I’m trying to load depends on other
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modules?
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If the 'module load' command returns the following errors:
This means that the module you want to load depends on the module <Module2>. To fix it, please load <Module2> prior to <Module1>:
You may encounter the above errors many times. Please load/unload the requested/conflicted modules and try again. |
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If the script could not run via sbatch. The errors usually looks look like this:
It is usually due to the wrong file format. Your file is still in the Windows format but not the Linux format.
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