Difference between revisions of "FAQ"

Latest revision as of 02:11, 17 April 2024

Applications

For questions about specific software such as Python, OpenOnDemand, or Custom Installations, visit Applications FAQ

Accounts and Investment

Q: How do I get a HiPerGator account?

A: HPG accounts must be requested via the account request form and receive a valid sponsor's approval.

Q: How do I purchase HiPerGator resources or reinvest on expired allocations?

A: If you're a sponsor or account manager, please fill out a purchase form at https://www.rc.ufl.edu/get-started/purchase-allocation/

Q: How to add users to a group?

A: All users must submit a ticket via the RC Support Ticketing System with the Subject line in a format similar to "Add (username) to (groupname) group" in order to gain access to a given group.

Q: I can't login to my HPG account.

A: Visit our Blocked Accounts wiki page

Q: How can I find out what allocations have expired or about to expire?

A: Please use the "showAllocation" tool in the 'ufrc' env module. See UFRC_environment_module for reference on all HPG tools.

Q: How many CPUs can I use?

A: Load the module "ufrc" to run the command "slurmInfo", which shows resources for your groups. You can use even more resources by choosing burst qos. Learn more at Account and QOS limits under SLURM. For more information on SLURM, please visit the Scheduler category in our Help Wiki.

Architecture

Nodes

Q: What's the difference between GPU and HWGUI partitions?

A: HWGUI partitions are technically GPU partitions, but HWGUI is more dedicated to interface visualization for software whos GUI requires hardware acceleration, but it's not directed to high performance computing the way GPU partitions are.

Storage

Q: I can't see my (or my group's) /blue or /orange folders!

A: If you are listing /blue or /orange you won't see your group's directory tree. It's automatically connected (mounted) when you try to access it in any way e.g. by using an 'ls' or 'cd' command. E.g. if your group name is 'mygroup' you should list or cd into /blue/mygroup or /orange/mygroup. See also this short video: https://web.microsoftstream.com/video/87698fe6-84df-40dc-9d22-c3a6c63820fa

Q: Why do I see "No Space Left" in job output or application error?

A: If you see a 'No Space Left' or a similar message (no quota remaining, etc) check the path(s) in the error message closely to look for 'home', 'orange', 'blue', or 'red' and check the respective quota for that filesystem. All quota commands are in the 'ufrc' environment module and include 'home_quota', 'blue_quota', 'orange_quota'. See Getting Started and Storage for more help.

A convenient interactive tool to see what's taking up the storage quota is the ncdu command in a bash terminal (also available with the "ufrc" module). You can run that command and delete or move data to a different storage to free up space.

If the data that's taking up most of the space is related to application environments and packages such as conda, pip, or singularity, you can modify your configuration file to update the default directories for custom installs. You can find more information about the .condarc setup here: Conda. You can also select a directory outside your $HOME to store python packages and modules when running "pip install": pip install --install-option="--prefix=/some/path/" package_name. For more info see https://help.rc.ufl.edu/doc/Python

Performance

Q: Why is HiPerGator running so slow?

A: There are many reasons why users may experience unusually low performance while using HPG. First, users should ensure that performance issues are not originated from their Internet service provider, home network, or personal devices.

Once the possible causes above are discarded, users should report the issue as soon as possible via the RC Support Ticketing System. When reporting the issue, please include detailed information such as:

Time when the issue occurred
JobID
Nodes being used, i.e. username@hpg-node$. Note: Login nodes are not considered high performance nodes and intense jobs should not be executed from them.
Paths, file names, etc.
Operating system
Method for accessing HPG: Jupyterhub, Open OnDemand, or Terminal interface used.

Q: How long can I run my job for?

A: There are default time limits set in different partitions. However, users can set their own time limit using the "--time=" flag: #SBATCH --time=4-00:00:00. Note: Walltime in hh:mm:ss or d-hh:mm:ss

For more details visit SLURM Partition Limits

Q: Are there profiling tools installed on HiPerGator that help identify performance bottlenecks?

A: The REMORA is the most generic profiling tool we have on the cluster. More specific tools depend on the application/stack or the language. E.g. cProfile for python code, Nsight Compute for CUDA apps, or VTune for C/C++ + MPI code.

Q: Why is my job still pending?

A: According to SLURM documentation, when a job cannot be started a reason is immediately found and recorded in the job's "reason" field in the squeue output and the scheduler moves on to the next job to consider.

Related article: Account and QOS limits under SLURM

Common reasons why jobs are pending

Priority: Resources being reserved for higher priority job. This is particularly common on Burst QOS jobs.

Refer to the Choosing QOS for a Job page for details.

Resources: Required resources are in use
Dependency: Job dependencies not yet satisfied
Reservation: Waiting for advanced reservation
AssociationJobLimit: User or account job limit reached

AssociationResourceLimit: User or account resource limit reached
AssociationTimeLimit: User or account time limit reached
QOSJobLimit: Quality Of Service (QOS) job limit reached
QOSResourceLimit: Quality Of Service (QOS) resource limit reached
QOSTimeLimit: Quality Of Service (QOS) time limit reached

Scheduler

Q: What does 'OOM', 'oom-kill event(s)', 'out of memory' error(s) in the job log means?

A: Short answer: request more memory when you resubmit the job. Long answer: each HiPerGator job/session is run with CPU core number, memory, and time limits set by the job resource request. Both the memory and time limits are going to result in the termination of the job if exceeded whereas the CPU core number limit can severely affect the performance of the job in some cases, but will not result in job termination. See Account and QOS limits under SLURM for a thorough explanation of resource limits.

@@ Line 1: / Line 1: @@
-=Storage=
+[[Category:Help]][[Category:Essentials]]
-==No Space Left==
+{|align=right
-If you see a 'No Space Left' or a similar message (no quota remaining, etc) check the path(s) in the error message closely to look for 'home', 'orange', 'blue', or 'red' and check the respective quota for that filesystem. All quota commands are in the [[UFRC_environment_module|'ufrc' environment module]] and include 'home_quota', 'blue_quota', 'orange_quota'. See [[Getting Started]] and [[Storage]] for more help.
+  |__TOC__
+  |}
+==Applications==
+For questions about specific software such as Python,  OpenOnDemand, or Custom Installations, visit [[Applications FAQ]]
+==Accounts and Investment==
+'''Q:''' How do I get a HiPerGator account?
-A convenient interactive tool to see what's taking up the storage quota is 'ncdu' in the 'ufrc' env. module.
+:'''A:''' HPG accounts must be requested via the [https://www.rc.ufl.edu/get-started/hipergator/request-hipergator-account/ account request form] and receive a valid sponsor's approval.
-=Applications=
-==Custom Installation==
-Q: I want to have a custom install of an application or python modules.
-A: We recommend creating a [[Conda]] environment and installing needed packages with the 'mamba' tool from the conda environment module. It is possible to mix conda and pip installed packages inside a conda environment as conda/mamba is aware of packages installed via pip, but not vice versa.
+'''Q:''' How do I purchase HiPerGator resources or reinvest on expired allocations?
-==Python==
+:'''A:''' If you're a sponsor or account manager, please fill out a purchase form at https://www.rc.ufl.edu/get-started/purchase-allocation/
-Q: Installed a python package via 'pip install something', but 'import something' results in an error.
-A: A pip install you performed puts the resulting package into your personal directory tree located in the ~/.local/lib/pythonX.Y/site-packages directory tree. A personal pip install can often result in an installation of a python package from a binary archive (wheel) that was built on a system against software libraries that are not compatible with HiPerGator. A typical error message in such case complains about the lack of a particular GLIBC version or some other missing library. Note that the issue can be exacerbated by an incompatible interaction between an environment loaded via an environment module ('module load something') and a personal python package install. To avoid this issue the python package must be installed into an isolated environment. Our approach for creating such environments depends on many factors, but usually results in a Conda or containerized environment.
+'''Q:''' How to add users to a group?
-=Scheduling=
+:'''A:''' All users must submit a ticket via the [https://support.rc.ufl.edu/enter_bug.cgi RC Support Ticketing System] with the Subject line in a format similar to '''"Add (username) to (groupname) group"''' in order to gain access to a given group.
-==Running Jobs==
-Q: Why is my job still pending?
-A: According to SLURM documentation, when a job cannot be started a reason is immediately found and recorded in the job's "reason" field in the squeue output and the scheduler moves on to the next job to consider. Please refer to "[https://help.rc.ufl.edu/doc/Why_is_my_job_not_running Why is my job not running]" for a list of reasons.
+'''Q:''' I can't login to my HPG account.
+:'''A:''' Visit our [https://help.rc.ufl.edu/doc/Blocked_Accounts Blocked Accounts] wiki page
+'''Q:''' How can I find out what allocations have expired or about to expire?
+:'''A:''' Please use the "showAllocation" tool in the 'ufrc' env module. See [[UFRC_environment_module]] for reference on all HPG tools.
+'''Q:''' How many CPUs can I use?
+:'''A:''' Load the module "ufrc" to run the command "slurmInfo", which shows resources for your groups. You can use even more resources by choosing burst qos. Learn more at [https://help.rc.ufl.edu/doc/Account_and_QOS_limits_under_SLURM Account and QOS limits under SLURM]. For more information on SLURM, please visit the [https://help.rc.ufl.edu/doc/Category:Scheduler Scheduler category] in our Help Wiki.
+==Architecture==
+===Nodes===
+'''Q:''' What's the difference between GPU and HWGUI partitions?
+:'''A:''' HWGUI partitions are technically GPU partitions, but HWGUI is more dedicated to interface visualization for software whos GUI requires hardware acceleration, but it's not directed to high performance computing the way GPU partitions are.
+===Storage===
+'''Q:''' I can't see my (or my group's) /blue or /orange folders!
+:'''A:''' If you are listing /blue or /orange you won't see your group's directory tree. It's automatically connected (mounted) when you try to access it in any way e.g. by using an 'ls' or 'cd' command. E.g. if your group name is 'mygroup' you should list or cd into /blue/mygroup or /orange/mygroup. See also this short video: https://web.microsoftstream.com/video/87698fe6-84df-40dc-9d22-c3a6c63820fa
+'''Q:''' Why do I see "No Space Left" in job output or application error?
+:'''A:''' If you see a 'No Space Left' or a similar message (no quota remaining, etc) check the path(s) in the error message closely to look for 'home', 'orange', 'blue', or 'red' and check the respective quota for that filesystem. All quota commands are in the [[UFRC_environment_module|'ufrc' environment module]] and include 'home_quota', 'blue_quota', 'orange_quota'. See [[Getting Started]] and [[Storage]] for more help.
+A convenient interactive tool to see what's taking up the storage quota is the '''ncdu''' command in a bash terminal (also available with the "ufrc" module). You can run that command and delete or move data to a different storage to free up space.
+If the data that's taking up most of the space is related to application environments and packages such as conda, pip, or singularity, you can modify your configuration file to update the default directories for custom installs. You can find more information about the .condarc setup here: [https://help.rc.ufl.edu/doc/Conda Conda]. You can also select a directory outside your $HOME to store python packages and modules when running "pip install": pip install --install-option="--prefix=/some/path/" package_name. For more info see https://help.rc.ufl.edu/doc/Python
+==Performance==
+'''Q:''' Why is HiPerGator running so slow?
+:'''A:''' There are many reasons why users may experience unusually low performance while using HPG. First, users should ensure that performance issues are not originated from their Internet service provider, home network, or personal devices.
+Once the possible causes above are discarded, users should report the issue as soon as possible via the [https://support.rc.ufl.edu/enter_bug.cgi RC Support Ticketing System].
+When reporting the issue, please include detailed information such as:
+* Time when the issue occurred
+* JobID
+* Nodes being used, i.e. username@hpg-node$. '''Note:''' Login nodes are not considered high performance nodes and intense jobs should not be executed from them.
+* Paths, file names, etc.
+* Operating system
+* Method for accessing HPG: Jupyterhub, Open OnDemand, or Terminal interface used.
+'''Q:''' How long can I run my job for?
+:'''A:''' There are default time limits set in different partitions. However, users can set their own time limit using the "--time=" flag: #SBATCH --time=4-00:00:00. '''Note:''' Walltime in hh:mm:ss or d-hh:mm:ss
+:For more details visit [https://help.rc.ufl.edu/doc/SLURM_Partition_Limits SLURM Partition Limits]
+'''Q:''' Are there profiling tools installed on HiPerGator that help identify performance bottlenecks?
+:'''A:''' The [[REMORA]] is the most generic profiling tool we have on the cluster. More specific tools depend on the application/stack or the language. E.g. cProfile for python code, [[Nsight]] Compute for CUDA apps, or VTune for C/C++ + MPI code.
+'''Q:''' Why is my job still pending?
+:'''A:''' According to SLURM documentation, when a job cannot be started a reason is immediately found and recorded in the job's "reason" field in the squeue output and the scheduler moves on to the next job to consider.
+Related article: [https://help.rc.ufl.edu/doc/Account_and_QOS_limits_under_SLURM Account and QOS limits under SLURM]
+* Common reasons why jobs are pending
+{|cellpadding="20"
+|-
+|
+;Priority: Resources being reserved for higher priority job. This is particularly common on Burst QOS jobs.
+* Refer to the [https://help.rc.ufl.edu/doc/Account_and_QOS_limits_under_SLURM#Choosing_QOS_for_a_Job Choosing QOS for a Job] page for details.
+;Resources: Required resources are in use
+;Dependency: Job dependencies not yet satisfied
+;Reservation: Waiting for advanced reservation
+;AssociationJobLimit: User or account job limit reached
+||
+;AssociationResourceLimit: User or account resource limit reached
+;AssociationTimeLimit: User or account time limit reached
+;QOSJobLimit: Quality Of Service (QOS) job limit reached
+;QOSResourceLimit: Quality Of Service (QOS) resource limit reached
+;QOSTimeLimit: Quality Of Service (QOS) time limit reached
+|}
+==Scheduler==
+'''Q:''' What does 'OOM', 'oom-kill event(s)', 'out of memory' error(s) in the job log means?
+:'''A:''' Short answer: request more memory when you resubmit the job. Long answer: each HiPerGator job/session is run with CPU core number, memory, and time limits set by the job resource request. Both the memory and time limits are going to result in the termination of the job if exceeded whereas the CPU core number limit can severely affect the performance of the job in some cases, but will not result in job termination. See [[Account and QOS limits under SLURM]] for a thorough explanation of resource limits.