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Niagara Quickstart: Difference between revisions
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Access to Niagara is via | Access to Niagara is via SSH (secure shell) only. | ||
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To access Niagara, first open a terminal window (e.g. [[Connecting with | To access Niagara, first open a terminal window (e.g. [[Connecting with PuTTY|PuTTY]] on Windows or [[Connecting with MobaXTerm|MobaXTerm]]), then SSH into the Niagara login nodes with your CC credentials: | ||
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Niagara | Niagara replaces SciNet clusters | ||
*TCS (Tightly Coupled Cluster) decommissioned last fall and | |||
*GPC (General Purpose Cluster) whose compute nodes will be decommissioned on April 21, 2018 and storage space on May 9, 2018. | |||
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Active GPC Users | Active GPC Users have access to Niagara since April 9, 2018. | ||
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It is the user's responsibility to copy | It is the user's responsibility to copy to Niagara any data generated on the GPC after April 5th, 2018. | ||
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$ scp -r SCINETUSERNAME@gpc-logindm01:\$SCRATCH/abc $SCRATCH/abc | $ scp -r SCINETUSERNAME@gpc-logindm01:\$SCRATCH/abc $SCRATCH/abc | ||
</source> | </source> | ||
For many of you, CCUSERNAME and SCINETUSERNAME will be the same. Make sure you use the | For many of you, CCUSERNAME and SCINETUSERNAME will be the same. Make sure you use the backslash (\) before the first <tt>$SCRATCH</tt>; it causes the value of scratch on the remote node (i.e., here, gpc-logindm01) to be used. Note that the gpc-logindm01 will ask for your SciNet password. | ||
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$ scp -r $SCRATCH/abc CCUSERNAME@nia-dm1:\$SCRATCH/abc | $ scp -r $SCRATCH/abc CCUSERNAME@nia-dm1:\$SCRATCH/abc | ||
</source> | </source> | ||
Again, pay attention to the | Again, pay attention to the backslash in front of the last occurrence of <tt>$SCRATCH</tt>. | ||
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Those | Those who are new to SciNet, but have 2018 RAC allocations on Niagara, will have their accounts created and ready for them to login. | ||
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Use the environment variables (HOME, SCRATCH, PROJECT) instead of the actual paths | Use the environment variables (HOME, SCRATCH, PROJECT) instead of the actual paths since these may change in the future. | ||
= Storage= <!--T:39--> | = Storage= <!--T:39--> | ||
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! expiration time | ! expiration time | ||
! backed up | ! backed up | ||
! on login | ! on login nodes | ||
! on compute | ! on compute nodes | ||
|- | |- | ||
| $HOME | | $HOME | ||
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<li>Archive space is on [https://wiki.scinet.utoronto.ca/wiki/index.php/HPSS HPSS], which will be, but is not yet, attached to Niagara.</li> | <li>Archive space is on [https://wiki.scinet.utoronto.ca/wiki/index.php/HPSS HPSS], which will be, but is not yet, attached to Niagara.</li> | ||
<li>Backup means a recent snapshot, not an achive of all data that ever was.</li> | <li>Backup means a recent snapshot, not an achive of all data that ever was.</li> | ||
<li><p><code>$BBUFFER</code> stands for the Burst Buffer, a functionality that is still being set up. This | <li><p><code>$BBUFFER</code> stands for the Burst Buffer, a functionality that is still being set up. This parallel storage tier for temporary data will be the fastest</p></li></ul> | ||
= Moving data = <!--T:42--> | = Moving data = <!--T:42--> | ||
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Use the scp or rsync commands to move data to either niagara.scinet.utoronto.ca or niagara.computecanada.ca. The transfer method depends on the size of the data you need to move. | |||
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*To move | *To move less than 10GB, use login nodes, which are the only ones visible from outside Niagara. Transfers done in this way will time out if data is larger than about 10GB. | ||
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*To move | *To move more than 10GB, use datamover nodes, which are not reachable from the outside. To do so, from a Niagara login node, first ssh into <code>nia-dm1</code> or <code>nia-dm2</code> and initiate transfer from the datamovers. The other side of the transfer (e.g. your machine) must be reachable from the outside. | ||
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If you | If you often move data, consider using [[Globus]], a web-based tool for data transfer. | ||
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You may also want to move data to [https://wiki.scinet.utoronto.ca/wiki/index.php/HPSS HPSS/Archive/Nearline], but this functionality will be implemented later. Storage space on HPSS is allocated through the annual [https://www.computecanada.ca/research-portal/accessing-resources/resource-allocation-competitions Compute Canada RAC allocation]. | You may also want to move data to [https://wiki.scinet.utoronto.ca/wiki/index.php/HPSS HPSS/Archive/Nearline], but this functionality will be implemented at a later date. Storage space on HPSS is allocated through the annual [https://www.computecanada.ca/research-portal/accessing-resources/resource-allocation-competitions Compute Canada RAC allocation]. | ||
= Loading software modules = <!--T:48--> | = Loading software modules = <!--T:48--> | ||
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<li><p>The same [[Modules|software stack available on Compute Canada's General Purpose clusters]] [https://docs.computecanada.ca/wiki/Graham Graham] and [https://docs.computecanada.ca/wiki/Cedar Cedar], compiled (for now) for a previous generation of CPUs:</p> | <li><p>The same [[Modules|software stack available on Compute Canada's General Purpose clusters]] [https://docs.computecanada.ca/wiki/Graham Graham] and [https://docs.computecanada.ca/wiki/Cedar Cedar], compiled (for now) for a previous generation of CPUs:</p> | ||
<source lang="bash">module load CCEnv</source> | <source lang="bash">module load CCEnv</source> | ||
<p>If you want the same default modules loaded | <p>If you want the same default modules as those loaded on Cedar and Graham, also run <code>module load StdEnv</code>.</p></li></ol> | ||
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Oddly named, the module subcommand spider is the search-and- | Oddly named, the module subcommand spider is the search-and-advise facility for modules. | ||
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* | * You may have to provide your own license. | ||
* SciNet and Compute Canada have an extremely large and broad user base of thousands of users, so we cannot provide licenses for everyone's favorite software. | * SciNet and Compute Canada have an extremely large and broad user base of thousands of users, so we cannot provide licenses for everyone's favorite software. | ||
* Thus, the only commercial software installed on Niagara is software that can benefit everyone: | * Thus, the only commercial software installed on Niagara is software that can benefit everyone: compilers, math libraries and debuggers. | ||
* That means no Matlab, Gaussian, IDL, | * That means no Matlab, Gaussian, IDL, | ||
* Open source alternatives like Octave, Python, R are available. | * Open source alternatives like Octave, Python, R are available. | ||