RCSWiki - User contributions [en]

How to get a MARC account

2020-04-09T19:46:37Z

Admin: Created page with "This page describes the process of obtaining an account and how to login to the Marc Cluster. If you are looking for information about the MARC cluster hardware, please see t..."

This page describes the process of obtaining an account and how to login to the Marc Cluster. If you are looking for information about the MARC cluster hardware, please see the [[Marc_Cluster_Guide]].

= Obtaining an Account =
== Prerequisites ==
* Access will only be granted to MARC for those with project shares on SCDS as this is the only to get data into MARC.

== Procedure ==
1. Navigate to the IT Homepage: www.ucalgary.ca/it
2. Click Login in the upper right corner
3. Click "Order Something"
4. Click "Research Computing"
5. Click "Medical Advanced Research Computing (MARC)"
6. Select "Add Access" from the "What would you like to do?" box
7. Choose your SCDS share from the next box
8. Type a synopsis of the work you plan to do into the "Business Reason" box.
9. You may leave the Additional Information box empty
10. Someone should reply to you when your account is ready.

= Logging in to MARC =
== Prerequisites ==
1. An account will be created on the Citrix system for you. This is where you will run the SSH client Putty from. You

MARC Cluster Guide

2020-04-09T19:29:57Z

Admin:

This guide gives an overview of the MARC (Medical Advanced Research Computing) cluster at the University of Calgary.

It is intended to be read by new account holders getting started on MARC, covering such topics as the hardware and performance characteristics, available software, usage policies and how to log in.

If you are looking for how to login to MARC or how to get an account, please see [[MARC_accounts]]

For MARC-related questions not answered here, please write to support@hpc.ucalgary.ca .

'''Cybersecurity awareness at the U of C'''

Please note that there are typically about 950 phishing attempts targeting University of Calgary accounts each month. This is just a reminder to be careful about computer security issues, both at home and at the University. See [https://it.ucalgary.ca/it-security] for more information, such as tips for secure computing and how to report suspected security problems.

== Introduction ==
MARC is a cluster comprised of Linux-based computers purchased in 2019

The MARC cluster has been designed to enable analyses and computations on data requiring Level 3 and Level 4 safeguards as described in the University of Calgary Information Security Classification Standard here: https://www.ucalgary.ca/policies/files/policies/im010-03-security-standard_0.pdf

Due to security requirements for Level 3/4 data, some necessary restrictions have been placed on MARC to prevent accidental (or otherwise) data exfiltration.
* Compute nodes and login nodes have no access to the internet
* All data must be ingested to MARC by first copying it to SCDS (Secure Compute Data Store) and then fetching it from SCDS to MARC.
* Resulting data (outputs of analyses) must be copyied to SCDS and then fetching it from SCDS to wherever it needs to go using established means.
* All file accesses are recorded for auditing purposes.
* ssh connections to MARC must be through the IT Citrix system (Admin VPN is not sufficient nor necessary)
* All accounts must be IT accounts
* A project ID is required to use MARC. This project ID is the same number that is used on SCDS

== Accounts ==
If you have a project you think would be appropriate for MARC, please make a request in the IT Service Catalogue '''TODO: LINK REQUIRED''' To assist you getting started, it would be helpful if you mention what software you plan to use.

== Hardware ==
MARC has compute nodes of two different varieties:
* 8 GPU (Graphics Processing Unit)-enabled nodes containing:
** 40-cores: each node having 2 sockets. Each socket has an Intel Xeon Gold 6148 20-core processor, running at 2.4 GHz.
** The 40 cores on the individual compute nodes share about 750 GB of RAM (memory) but, jobs should request no more than 753000 MB.
** Two Tesla V100-PCIE-16GB GPUs.
* 1 Bigmem Node
** 80-cores: node with 4 sockets. Each socket has an Intel Xeon Gold 6148 20-core processor, running at 2.4 GHz.
** The 80 cores on the node share about 3 TB of RAM (memory), but, jobs should request no more than 3000000 MB.

=== cpu2019 ===
Allows non-GPU jobs to use:
* Up to 38 cpus per node
* No gpus.
* Up to 500GB memory
* Are the same
=== gpu2019 ===
Allows jobs requiring nVidia v100 gpu jobs to use:
* 1 or 2 gpus per node
* Up to 40 cpus per node.
* Up to 750GB memory
=== bigmem ===
For very large memory jobs:
* Up to 80 cpus
* Up to 3TB memory
* No gpus

== Storage ==
About a petabyte of raw disk storage is available to the MARC cluster, but for error checking and performance reasons, the amount of usable storage for researchers' projects is considerably less than that. From a user's perspective, the total amount of storage is less important than the individual storage limits. As described below, there are two storage areas: home and project.

=== Home file system: /home ===
There is a per-user quota of 50 GB under /home. This limit is fixed and cannot be increased. Each user has a directory under /home, which is the default working directory when logging in to MARC. It is expected that most researchers will work from /project and only use home for software and such things. /home is expected to be used only for L1/L2 data and not for your patient identifiable files. The identifiable files go in the appropriate directory under /project.

=== Project file system for larger projects: /project ===
Directories will be created in /project named after your project ID. This name will be the same as your SCDS share name. The expectation is that all files to do with that project will be stored in /rpoject/projectid. Quotas in /project are somewhat flexible. Please write to support@hpc.ucalgary.ca with an estimate of how much space you will require.

== Further Reading ==
See [Running_jobs] for information on starting a job

MARC Cluster Guide

2020-04-09T19:29:14Z

Admin:

This guide gives an overview of the MARC (Medical Advanced Research Computing) cluster at the University of Calgary.

It is intended to be read by new account holders getting started on MARC, covering such topics as the hardware and performance characteristics, available software, usage policies and how to log in.

If you are looking for how to login to MARC or how to get an account, please see [MARC_accounts]

For MARC-related questions not answered here, please write to support@hpc.ucalgary.ca .

'''Cybersecurity awareness at the U of C'''

Please note that there are typically about 950 phishing attempts targeting University of Calgary accounts each month. This is just a reminder to be careful about computer security issues, both at home and at the University. See [https://it.ucalgary.ca/it-security] for more information, such as tips for secure computing and how to report suspected security problems.

== Introduction ==
MARC is a cluster comprised of Linux-based computers purchased in 2019

The MARC cluster has been designed to enable analyses and computations on data requiring Level 3 and Level 4 safeguards as described in the University of Calgary Information Security Classification Standard here: https://www.ucalgary.ca/policies/files/policies/im010-03-security-standard_0.pdf

Due to security requirements for Level 3/4 data, some necessary restrictions have been placed on MARC to prevent accidental (or otherwise) data exfiltration.
* Compute nodes and login nodes have no access to the internet
* All data must be ingested to MARC by first copying it to SCDS (Secure Compute Data Store) and then fetching it from SCDS to MARC.
* Resulting data (outputs of analyses) must be copyied to SCDS and then fetching it from SCDS to wherever it needs to go using established means.
* All file accesses are recorded for auditing purposes.
* ssh connections to MARC must be through the IT Citrix system (Admin VPN is not sufficient nor necessary)
* All accounts must be IT accounts
* A project ID is required to use MARC. This project ID is the same number that is used on SCDS

== Accounts ==
If you have a project you think would be appropriate for MARC, please make a request in the IT Service Catalogue '''TODO: LINK REQUIRED''' To assist you getting started, it would be helpful if you mention what software you plan to use.

== Hardware ==
MARC has compute nodes of two different varieties:
* 8 GPU (Graphics Processing Unit)-enabled nodes containing:
** 40-cores: each node having 2 sockets. Each socket has an Intel Xeon Gold 6148 20-core processor, running at 2.4 GHz.
** The 40 cores on the individual compute nodes share about 750 GB of RAM (memory) but, jobs should request no more than 753000 MB.
** Two Tesla V100-PCIE-16GB GPUs.
* 1 Bigmem Node
** 80-cores: node with 4 sockets. Each socket has an Intel Xeon Gold 6148 20-core processor, running at 2.4 GHz.
** The 80 cores on the node share about 3 TB of RAM (memory), but, jobs should request no more than 3000000 MB.

=== cpu2019 ===
Allows non-GPU jobs to use:
* Up to 38 cpus per node
* No gpus.
* Up to 500GB memory
* Are the same
=== gpu2019 ===
Allows jobs requiring nVidia v100 gpu jobs to use:
* 1 or 2 gpus per node
* Up to 40 cpus per node.
* Up to 750GB memory
=== bigmem ===
For very large memory jobs:
* Up to 80 cpus
* Up to 3TB memory
* No gpus

== Storage ==
About a petabyte of raw disk storage is available to the MARC cluster, but for error checking and performance reasons, the amount of usable storage for researchers' projects is considerably less than that. From a user's perspective, the total amount of storage is less important than the individual storage limits. As described below, there are two storage areas: home and project.

=== Home file system: /home ===
There is a per-user quota of 50 GB under /home. This limit is fixed and cannot be increased. Each user has a directory under /home, which is the default working directory when logging in to MARC. It is expected that most researchers will work from /project and only use home for software and such things. /home is expected to be used only for L1/L2 data and not for your patient identifiable files. The identifiable files go in the appropriate directory under /project.

=== Project file system for larger projects: /project ===
Directories will be created in /project named after your project ID. This name will be the same as your SCDS share name. The expectation is that all files to do with that project will be stored in /rpoject/projectid. Quotas in /project are somewhat flexible. Please write to support@hpc.ucalgary.ca with an estimate of how much space you will require.

== Further Reading ==
See [Running_jobs] for information on starting a job

MediaWiki:Sidebar

2020-04-09T19:27:01Z

Admin:

** RCS_Home_Page|RCS Home Page
* Guides
** ARC_Cluster_Guide|ARC Cluster Guide
** https://hpc.ucalgary.ca/talc|TALC Guide (external link)
** Running_jobs|Running Jobs

MARC Cluster Guide

2020-04-09T19:25:54Z

Admin:

This guide gives an overview of the MARC (Medical Advanced Research Computing) cluster at the University of Calgary.

It is intended to be read by new account holders getting started on MARC, covering such topics as the hardware and performance characteristics, available software, usage policies and how to log in.

For MARC-related questions not answered here, please write to support@hpc.ucalgary.ca .

'''Cybersecurity awareness at the U of C'''

Please note that there are typically about 950 phishing attempts targeting University of Calgary accounts each month. This is just a reminder to be careful about computer security issues, both at home and at the University. See [https://it.ucalgary.ca/it-security] for more information, such as tips for secure computing and how to report suspected security problems.

== Introduction ==
MARC is a cluster comprised of Linux-based computers purchased in 2019

The MARC cluster has been designed to enable analyses and computations on data requiring Level 3 and Level 4 safeguards as described in the University of Calgary Information Security Classification Standard here: https://www.ucalgary.ca/policies/files/policies/im010-03-security-standard_0.pdf

Due to security requirements for Level 3/4 data, some necessary restrictions have been placed on MARC to prevent accidental (or otherwise) data exfiltration.
* Compute nodes and login nodes have no access to the internet
* All data must be ingested to MARC by first copying it to SCDS (Secure Compute Data Store) and then fetching it from SCDS to MARC.
* Resulting data (outputs of analyses) must be copyied to SCDS and then fetching it from SCDS to wherever it needs to go using established means.
* All file accesses are recorded for auditing purposes.
* ssh connections to MARC must be through the IT Citrix system (Admin VPN is not sufficient nor necessary)
* All accounts must be IT accounts
* A project ID is required to use MARC. This project ID is the same number that is used on SCDS

== Accounts ==
If you have a project you think would be appropriate for MARC, please make a request in the IT Service Catalogue '''TODO: LINK REQUIRED''' To assist you getting started, it would be helpful if you mention what software you plan to use.

== Hardware ==
MARC has compute nodes of two different varieties:
* 8 GPU (Graphics Processing Unit)-enabled nodes containing:
** 40-cores: each node having 2 sockets. Each socket has an Intel Xeon Gold 6148 20-core processor, running at 2.4 GHz.
** The 40 cores on the individual compute nodes share about 750 GB of RAM (memory) but, jobs should request no more than 753000 MB.
** Two Tesla V100-PCIE-16GB GPUs.
* 1 Bigmem Node
** 80-cores: node with 4 sockets. Each socket has an Intel Xeon Gold 6148 20-core processor, running at 2.4 GHz.
** The 80 cores on the node share about 3 TB of RAM (memory), but, jobs should request no more than 3000000 MB.

=== cpu2019 ===
Allows non-GPU jobs to use:
* Up to 38 cpus per node
* No gpus.
* Up to 500GB memory
* Are the same
=== gpu2019 ===
Allows jobs requiring nVidia v100 gpu jobs to use:
* 1 or 2 gpus per node
* Up to 40 cpus per node.
* Up to 750GB memory
=== bigmem ===
For very large memory jobs:
* Up to 80 cpus
* Up to 3TB memory
* No gpus

== Storage ==
About a petabyte of raw disk storage is available to the MARC cluster, but for error checking and performance reasons, the amount of usable storage for researchers' projects is considerably less than that. From a user's perspective, the total amount of storage is less important than the individual storage limits. As described below, there are two storage areas: home and project.

=== Home file system: /home ===
There is a per-user quota of 50 GB under /home. This limit is fixed and cannot be increased. Each user has a directory under /home, which is the default working directory when logging in to MARC. It is expected that most researchers will work from /project and only use home for software and such things. /home is expected to be used only for L1/L2 data and not for your patient identifiable files. The identifiable files go in the appropriate directory under /project.

=== Project file system for larger projects: /project ===
Directories will be created in /project named after your project ID. This name will be the same as your SCDS share name. The expectation is that all files to do with that project will be stored in /rpoject/projectid. Quotas in /project are somewhat flexible. Please write to support@hpc.ucalgary.ca with an estimate of how much space you will require.

MARC Cluster Guide

2020-04-08T22:15:10Z

Admin: Created page with "This guide gives an overview of the MARC (Medical Advanced Research Computing) cluster at the University of Calgary. It is intended to be read by new account holders getting..."

This guide gives an overview of the MARC (Medical Advanced Research Computing) cluster at the University of Calgary.

It is intended to be read by new account holders getting started on MARC, covering such topics as the hardware and performance characteristics, available software, usage policies and how to log in.

For MARC-related questions not answered here, please write to support@hpc.ucalgary.ca .

'''Cybersecurity awareness at the U of C'''

Please note that there are typically about 950 phishing attempts targeting University of Calgary accounts each month. This is just a reminder to be careful about computer security issues, both at home and at the University. See [https://it.ucalgary.ca/it-security] for more information, such as tips for secure computing and how to report suspected security problems.

== Introduction ==
MARC is a cluster comprised of Linux-based computers purchased in 2019

The MARC cluster has been designed to enable analyses and computations on data requiring Level 3 and Level 4 safeguards as described in the University of Calgary Information Security Classification Standard here: https://www.ucalgary.ca/policies/files/policies/im010-03-security-standard_0.pdf

Due to security requirements for Level 3/4 data, some necessary restrictions have been placed on MARC to prevent accidental (or otherwise) data exfiltration.
* Compute nodes and login nodes have no access to the internet
* All data must be ingested to MARC by first copying it to SCDS (Secure Compute Data Store) and then fetching it from SCDS to MARC.
* Resulting data (outputs of analyses) must be copyied to SCDS and then fetching it from SCDS to wherever it needs to go using established means.
* All file accesses are recorded for auditing purposes.
* ssh connections to MARC must be through the IT Citrix system (Admin VPN is not sufficient nor necessary)
* All accounts must be IT accounts
* A project ID is required to use MARC. This project ID is the same number that is used on SCDS

== Accounts ==
If you have a project you think would be appropriate for MARC, please make a request in the IT Service Catalogue '''TODO: LINK REQUIRED''' To assist you getting started, it would be helpful if you mention what software you plan to use.

== Hardware ==
MARC has compute nodes of two different varieties:
* 8 GPU (Graphics Processing Unit)-enabled nodes containing:
** 40-cores: each node having 2 sockets. Each socket has an Intel Xeon Gold 6148 20-core processor, running at 2.4 GHz.
** The 40 cores on the individual compute nodes share about 750 GB of RAM (memory) but, jobs should request no more than 753000 MB.
** Two Tesla V100-PCIE-16GB GPUs.
* 1 Bigmem Node
** 80-cores: node with 4 sockets. Each socket has an Intel Xeon Gold 6148 20-core processor, running at 2.4 GHz.
** The 80 cores on the node share about 3 TB of RAM (memory), but, jobs should request no more than 3000000 MB.

=== cpu2019 ===
Allows non-GPU jobs to use:
* Up to 38 cpus per node
* No gpus.
* Up to 500GB memory
* Are the same
=== gpu2019 ===
Allows jobs requiring nVidia v100 gpu jobs to use:
* 1 or 2 gpus per node
* Up to 40 cpus per node.
* Up to 750GB memory
=== bigmem ===
For very large memory jobs:
* Up to 80 cpus
* Up to 3TB memory
* No gpus

== Storage ==
About a petabyte of raw disk storage is available to the MARC cluster, but for error checking and performance reasons, the amount of usable storage for researchers' projects is considerably le\
ss than that. From a user's perspective, the total amount of storage is less important than the individual storage limits. As described below, there are three storage areas: home, scratch an\
d work, with different limits and usage policies.

=== Home file system: /home ===
There is a per-user quota of 50 GB under /home. This limit is fixed and cannot be increased. Each user has a directory under /home, which is the default working directory when logging in to MARC. It is expected that most researchers will work from /project and only use home for software and such things.

=== Scratch file system for large job-oriented storage: /scratch ===
Associated with each job, under the /scratch directory, a subdirectory is created that can be referenced in job scripts as /scratch/${SLURM_JOB_ID}. You can use that directory for temporary fi\
les needed during the course of a job. Up to 30 TB of storage may be used, per user (total for all your jobs) in the /scratch file system. Deletion policy: data in /scratch associated with a \
given job will be deleted automatically, without exception, five days after the job finishes.

=== Work file system for larger projects: /work ===
If you need more space than provided in /home and the /scratch job-oriented space is not appropriate for you case, please write to support@hpc.ucalgary.ca with an explanation, including an ind\
ication of how much storage you expect to need and for how long. If approved, you will then be assigned a directory under /work with an appropriately large quota.

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/* CSS placed here will affect users of the Vector skin */
/* Disables the Discussion (Talk) tab /*
#ca-talk { display:none!important; }
#footer-icons.noprint { display:none!important; }

MediaWiki:Common.css

2020-01-07T05:59:06Z

Admin:

/* CSS placed here will be applied to all skins */
/* Disables the Discussion (Talk) tab /*
#ca-talk { display:none!important; }
#footer-icons.noprint { display:none!important; }

MediaWiki:Common.css

2020-01-07T05:54:58Z

Admin:

/* CSS placed here will be applied to all skins */
/* Disables the Discussion (Talk) tab /*
#ca-talk { display:none!important; }
#footer-icons { display:none!important; }

MediaWiki:Common.css

2020-01-06T22:25:19Z

Admin:

/* CSS placed here will be applied to all skins */
/* Disables the Discussion (Talk) tab /*
#ca-talk { display:none!important; }

MediaWiki:Common.css

2020-01-06T22:24:17Z

Admin: Created page with "/* CSS placed here will be applied to all skins */ #ca-talk { display:none!important; }"

/* CSS placed here will be applied to all skins */
#ca-talk { display:none!important; }

TALC Terms of Use

2019-12-20T21:31:55Z

Admin:

The Teaching and Learning Cluster (TALC) is a computing resource
provided by Information Technologies Research Computing Services (RCS)
in support of approved courses and workshops. Usage of the cluster is
subject to certain conditions as outlined below and detailed on this page.

=Guidelines and Regulations=

Municipal, Provincial and Federal laws and University Policies and
Procedures must not be violated using RCS resources.

If you have not done so, please read the University's policy on
"Acceptable Use of Electronic Resources and Information" found here:
https://www.ucalgary.ca/policies/files/policies/acceptable-use-of-electronic-resources-and-information-policy.pdf

This account is for your use only. It is made available to you
specifically for the course that requires the use of TALC. You must
not share your password or let anyone use your account.

Commercial use of TALC, including digital currency mining, is strictly
prohibited.

TALC is configured for Level 1 and Level 2 data as set forth in the
University of Calgary Information Security Classification
Standard. Information on the University of Calgary Information
Security Classification Standards can be found here:
https://www.ucalgary.ca/policies/files/policies/im010-03-security-standard_0.pdf

TALC is not suitable for Level 3 and Level 4 data (such as personally
identifiable medical information).

RCS reserves the right to examine files, programs and any other
material used on RCS systems at any time without warning.

Evidence of inappropriate use of TALC may result in immediate loss of
access to your TALC account. Pending further investigation, some
offenses may result in further actions taken.

Please note that no backups are performed for data stored on TALC. It
is your responsibility to copy data you need to save elsewhere. By
default, your account and data will be deleted one week after the last
course associated with the account has finished.

Please write to [mailto://support@hpc.ucalgary.ca support@hpc.ucalgary.ca] with your questions and concerns.

TALC Terms of Use

2019-12-20T21:30:18Z

Admin:

The Teaching and Learning Cluster (TALC) is a computing resource
provided by Information Technologies Research Computing Services (RCS)
in support of approved courses and workshops. Usage of the cluster is
subject to certain conditions as outlined below and detailed on this page.

=Guidelines and Regulations=

Municipal, Provincial and Federal laws and University Policies and
Procedures must not be violated using RCS resources.

If you have not done so, please read the University's policy on
"Acceptable Use of Electronic Resources and Information" found here:
https://www.ucalgary.ca/policies/files/policies/acceptable-use-of-electronic-resources-and-information-policy.pdf

This account is for your use only. It is made available to you
specifically for the course that requires the use of TALC. You must
not share your password or let anyone use your account.

Commercial use of TALC, including digital currency mining, is strictly
prohibited.

TALC is configured for Level 1 and Level 2 data as set forth in the
University of Calgary Information Security Classification
Standard. Information on the University of Calgary Information
Security Classification Standards can be found here:
https://www.ucalgary.ca/policies/files/policies/im010-03-security-standard_0.pdf

TALC is not suitable for Level 3 and Level 4 data (such as personally
identifiable medical information).

RCS reserves the right to examine files, programs and any other
material used on RCS systems at any time without warning.

Evidence of inappropriate use of TALC may result in immediate loss of
access to your TALC account. Pending further investigation, some
offenses may result in further actions taken.

Please note that no backups are performed for data stored on TALC. It
is your responsibility to copy data you need to save elsewhere. By
default, your account and data will be deleted one week after the last
course associated with the account has finished.

Please write to mailto://support@hpc.ucalgary.ca with your questions and concerns.

Talctou

2019-12-20T21:29:06Z

Admin: Admin moved page Talctou to TALC Terms of Use

#REDIRECT [[TALC Terms of Use]]

TALC Terms of Use

2019-12-20T21:29:06Z

Admin: Admin moved page Talctou to TALC Terms of Use

=TALC Terms of Use=

The Teaching and Learning Cluster (TALC) is a computing resource
provided by Information Technologies Research Computing Services (RCS)
in support of approved courses and workshops. Usage of the cluster is
subject to certain conditions as outlined below and detailed on this page.

=Guidelines and Regulations=

Municipal, Provincial and Federal laws and University Policies and
Procedures must not be violated using RCS resources.

If you have not done so, please read the University's policy on
"Acceptable Use of Electronic Resources and Information" found here:
https://www.ucalgary.ca/policies/files/policies/acceptable-use-of-electronic-resources-and-information-policy.pdf

This account is for your use only. It is made available to you
specifically for the course that requires the use of TALC. You must
not share your password or let anyone use your account.

Commercial use of TALC, including digital currency mining, is strictly
prohibited.

TALC is configured for Level 1 and Level 2 data as set forth in the
University of Calgary Information Security Classification
Standard. Information on the University of Calgary Information
Security Classification Standards can be found here:
https://www.ucalgary.ca/policies/files/policies/im010-03-security-standard_0.pdf

TALC is not suitable for Level 3 and Level 4 data (such as personally
identifiable medical information).

RCS reserves the right to examine files, programs and any other
material used on RCS systems at any time without warning.

Evidence of inappropriate use of TALC may result in immediate loss of
access to your TALC account. Pending further investigation, some
offenses may result in further actions taken.

Please note that no backups are performed for data stored on TALC. It
is your responsibility to copy data you need to save elsewhere. By
default, your account and data will be deleted one week after the last
course associated with the account has finished.

Please write to mailto://support@hpc.ucalgary.ca with your questions and concerns.

TALC Terms of Use

2019-12-18T18:25:45Z

Admin: Created page with "=TALC Terms of Use= The Teaching and Learning Cluster (TALC) is a computing resource provided by Information Technologies Research Computing Services (RCS) in support of appr..."