Change staging examples to new directory structure

Author: xamberl

_uw-research-computing/apptainer-htc.md

@@ -138,7 +138,7 @@ exit
 Once you are satisfied that your container is built correctly, copy your `.sif` file to your staging directory.
 
 ```
-mv my-container.sif /staging/$USER
+mv my-container.sif /staging/u/username
 ```
 {:.term}
 
@@ -314,7 +314,7 @@ Since Apptainer `.sif` files are routinely more than 1GB in size, we recommend t
 It is usually easiest to move the container file directly to staging while still in the interactive build job:
 
 ```
-mv my-container.sif /staging/$USER
+mv my-container.sif /staging/u/username
 ```
 {:.term}
 

_uw-research-computing/check-quota.md

@@ -53,9 +53,9 @@ This will print a table with your `/home` and `/staging` quotas. An example outp
 
 ```
 [user@ap2002 ~]$ get_quotas
-Path            Disk_Used(GB)  Disk_Limit(GB)  Files_Used  File_Limit
-/home/user      16.0711        40              8039        N/A
-/staging/user   13.4731        100             12          1000
+Path              Disk_Used(GB)  Disk_Limit(GB)  Files_Used  File_Limit
+/home/username        16.0711        40              8039        N/A
+/staging/u/username   13.4731        100             12          1000
 ```
 {:.term}
 
@@ -119,10 +119,10 @@ _____________________________________________________________________
  == NOTICE: THIS NODE IS ON PUPPET ENVIRONMENT "puppet8" ==
 
 Filesystem quota report (last updated 10:33 AM)
-Storage               Used (GB)    Limit (GB)    Files (#)    File Cap (#)    Quota (%)
-------------------  -----------  ------------  -----------  --------------  -----------
-/home/user                29.38            40           94               0        73.46
-/staging/user             50.23          1000          110           10000         5.02
+Storage                     Used (GB)    Limit (GB)    Files (#)    File Cap (#)    Quota (%)
+------------------        -----------  ------------  -----------  --------------  -----------
+/home/username                  29.38            40           94               0        73.46
+/staging/u/username             50.23          1000          110           10000         5.02
 ```
 {:.term}
 

_uw-research-computing/file-avail-largedata.md

@@ -26,7 +26,7 @@ When submitting jobs to the HTC system, large data needs to be stored and handle
    * [Intended use](#intended-use)
    * [User responsibilities](#user-responsibilities)
 - [Stage large data](#stage-large-data)
-   * [Request a `/staging` directory](#request-a-staging-directory)
+   * [Your personal `/staging` directory](#your-personal-staging-directory)
    * [Reduce file counts](#reduce-file-counts)
    * [Use the transfer server](#use-the-transfer-server)
    * [Remove files after jobs complete](#remove-files-after-jobs-complete)
@@ -67,18 +67,24 @@ CHTC staff reserve the right to remove data from our large data staging location
 
 In order to stage large data for use on CHTC's HTC system, users must: 
 
-1. **Request a `/staging` directory**: Use our quota request form.
 1. **Reduce file counts**: Combine and compress files that are used together.
 1. **Transfer files to the HTC system via the transfer server**: Upload your data via our dedicated file transfer server.
 1. **Remove files after jobs complete**: Our data staging space is quota-controlled and not backed up. 
 
-### Request a `/staging` directory
+### Your personal `/staging` directory
 
-Any one with a CHTC account whose data meets the intended use above can request space in our large data staging area by filling out a quota request form. The default quota is 100 GB / 1000 items; if a larger quota is needed, request a higher quota. The created directory will exist at this path: `/staging/username`
+Each user should have a personal `/staging` directory. The created directory will exist in an alphabetized subdirectory based on the **first letter** of your NetID. For example:
+
+| NetID | Path to your personal `/staging` directory |
+| --- | --- |
+| `alice` | `/staging/a/alice` |
+| `bucky` | `/staging/b/bucky` |
 
 We can also create group or shared spaces by request. 
 
-<p style="text-align: center; margin-bottom: 0; font-weight: bold;">Need a <code>/staging</code> directory or higher quota?</p>
+The default quota is 100 GB / 1000 items; if a larger quota is needed, request a higher quota.
+
+<p style="text-align: center; margin-bottom: 0; font-weight: bold;">Need a group <code>/staging</code> directory or higher quota?</p>
 <div class="d-flex mb-3">
 	<div class="p-3 m-auto">
 		<a class="btn btn-primary" style="text-align: center" href="quota-request">Quota request form</a>
@@ -88,7 +94,7 @@ We can also create group or shared spaces by request.
 
 ### Reduce file counts
 
-The file system backing our `/staging`space is optimized to handle small numbers of large files. If your job requires many small files, we recommend placing these files in the `/home` directory or compressing multiple files into a single zip file or tarball. See [this table](htc-job-file-transfer#data-storage-locations) for more information on the differences between `/staging` and `/home`. 
+The file system backing our `/staging` space is optimized to handle small numbers of large files. If your job requires many small files, we recommend placing these files in the `/home` directory or compressing multiple files into a single zip file or tarball. See [this table](htc-job-file-transfer#data-storage-locations) for more information on the differences between `/staging` and `/home`. 
 
 Data placed in our large data `/staging` location should be stored in as few files as possible (ideally, one file per job), and will be used by a job only after being copied from `/staging` into the job working directory. Similarly, large output should first be written to the job's working directory then compressed in to a single file before being copied to `/staging` at the end of the job. 
 
@@ -105,7 +111,7 @@ Uploading or downloading data to `/staging` should only be performed via CHTC's
 
 For example, you can use `scp` to transfer files into your `/staging` directory:
 ```
-$ scp large.file netid@transfer.chtc.wisc.edu:/staging/netid/ 
+$ scp large.file username@transfer.chtc.wisc.edu:/staging/u/username/ 
 ```
 {:.term}
 
@@ -123,7 +129,7 @@ Staged files should be specified in the job submit file using the `osdf:///` or
 depending on the size of the files to be transferred. [See this table for more information](htc-job-file-transfer#transfer-input-data-to-jobs-with-transfer_input_files).
 
 ```
-transfer_input_files = osdf:///chtc/staging/username/file1, file:///staging/username/file2, file3 
+transfer_input_files = osdf:///chtc/staging/u/username/file1, file:///staging/u/username/file2, file3 
 ```
 {:.sub}
 
@@ -136,7 +142,7 @@ Large outputs should be transferred to staging using the same file transfer prot
 
 ```
 transfer_output_files = file1, file2, file3
-transfer_output_remaps = "file1 = osdf:///chtc/staging/username/file1; file2 = file:///staging/username/file2"
+transfer_output_remaps = "file1 = osdf:///chtc/staging/u/username/file1; file2 = file:///staging/u/username/file2"
 ```
 {:.sub}
 
@@ -166,14 +172,14 @@ within the user's `/home` directory:
 ``` {.sub}
 ### Example submit file for a single job that stages large data
 # Files for the below lines MUST all be somewhere within /home/username,
-# and not within /staging/username
+# and not within /staging/u/username
 
 executable = run_myprogram.sh
 log = myprogram.log
 output = $(Cluster).out
 error = $(Cluster).err
 
-transfer_input_files = osdf:///chtc/staging/username/myprogram, file:///staging/username/largedata.tar.gz
+transfer_input_files = osdf:///chtc/staging/u/username/myprogram, file:///staging/u/username/largedata.tar.gz
 
 # IMPORTANT! Require execute servers that can access /staging
 Requirements = (Target.HasCHTCStaging == true)

_uw-research-computing/high-memory-jobs.md

@@ -174,16 +174,13 @@ Altogether, a sample submit file may look something like this:
 ``` {.sub}
 ### Example submit file for a single staging-dependent job
 
-universe = vanilla
-
 # Files for the below lines will all be somewhere within /home/username,
-# and not within /staging/username
+# and not within /staging/u/username
 log = run_myprogram.log
 executable = run_Trinity.sh
 output = $(Cluster).out
 error = $(Cluster).err
 transfer_input_files = trinityrnaseq-2.0.1.tar.gz
-should_transfer_files = YES
 
 # Require execute servers that have large data staging
 Requirements = (Target.HasCHTCStaging == true)
@@ -236,7 +233,7 @@ Altogether, a sample script may look something like this (perhaps called
 #!/bin/bash
 # Copy input data from /staging to the present directory of the job
 # and un-tar/un-zip them.  
-cp /staging/username/reads.tar.gz ./
+cp /staging/u/username/reads.tar.gz ./
 tar -xzvf reads.tar.gz
 rm reads.tar.gz
 
@@ -255,7 +252,7 @@ Trinity --seqType fq --left reads_1.fq \
 # Trinity will write output to the working directory by default, 
 # so when the job finishes, it needs to be moved back to /staging
 tar -czvf trinity_out_dir.tar.gz trinity_out_dir
-cp trinity_out_dir.tar.gz trinity_stdout.txt /staging/username/
+cp trinity_out_dir.tar.gz trinity_stdout.txt /staging/u/username/
 rm reads_*.fq trinity_out_dir.tar.gz trinity_stdout.txt
 
 ### END

_uw-research-computing/htc-docker-to-apptainer.md

@@ -78,7 +78,7 @@ INFO:    Build complete: container.sif
 Because container images are generally large, we require users to move these images into their staging directories. While you are still in your interactive job, move the image to your staging directory.
 
 ```
-mv container.sif /staging/username/
+mv container.sif /staging/u/username/
 ```
 {:.term}
 

_uw-research-computing/htc-job-file-transfer.md

@@ -42,13 +42,6 @@ The HTC system has two primary locations where users can place their files:
 
 The data management mechanisms behind `/home` and `/staging` are different and are optimized to handle different file sizes and numbers of files. It's important to place your files in the correct location to improve the efficiency at which your data is handled and maintain the stability of the HTC file systems.
 
-<p style="text-align: center; margin-bottom: 0; font-weight: bold;">Need a <code>/staging</code> directory?</p>
-<div class="d-flex mb-3">
-	<div class="p-3 m-auto">
-		<a class="btn btn-primary" style="text-align: center" href="quota-request">Request one here</a>
-	</div>
-</div>
-
 
 ## Transfer input data to jobs with `transfer_input_files`
 
@@ -57,8 +50,8 @@ To transfer files to jobs, we must specify these files with `transfer_input_file
 | Input File Size (Per File)* | File Location |  Submit File Syntax to Transfer to Jobs |
 | ----------- | ----------- | ----------- | ----------- |
 | 0 - 1 GB | `/home`       | `transfer_input_files = input.txt`       |
-| 1 - 30 GB  | `/staging`        | `transfer_input_files = osdf:///chtc/staging/NetID/input.txt`        | 
-| 30 - 100 GB     | `/staging`        | `transfer_input_files = file:///staging/NetID/input.txt`        | 
+| 1 - 30 GB  | `/staging`        | `transfer_input_files = osdf:///chtc/staging/u/username/input.txt`        | 
+| 30 - 100 GB     | `/staging`        | `transfer_input_files = file:///staging/u/username/input.txt`        | 
 | 1 - 100 GB | `/staging/groups`<sup>†</sup>        | `transfer_input_files = file:///staging/groups/group_dir/input.txt`        | 
 | 100 GB+ | | Contact the facilitation team about the best strategy to stage your data |
 
@@ -73,7 +66,7 @@ Multiple input files and file transfer protocols can be specified and delimited
 ```
 # My job submit file
 
-transfer_input_files = file1, osdf:///chtc/staging/username/file2, file:///staging/username/file3, dir1, dir2/
+transfer_input_files = file1, osdf:///chtc/staging/u/username/file2, file:///staging/u/username/file3, dir1, dir2/
 
 requirements = (HasCHTCStaging == true)
 
@@ -120,7 +113,7 @@ transfer_output_files = output_file, output/output_file2, output/output_file3
 
 To transfer files back to `/staging` or a specific directory in `/home`, you will need an additional line in your HTCondor submit file, with each item separated by a semicolon (;):
 ```
-transfer_output_remaps = "output_file = osdf:///chtc/staging/NetID/output1.txt; output_file2 = /home/netid/outputs/output_file2"
+transfer_output_remaps = "output_file = osdf:///chtc/staging/u/username/output1.txt; output_file2 = /home/u/username/outputs/output_file2"
 ```
 {:.sub}
 
@@ -133,7 +126,7 @@ Make sure to only include one set of quotation marks that wraps around the infor
 If you want to transfer *all* files to a specific destination, use `output_destination`:
 
 ```
-output_destination = osdf:///chtc/staging/netid/
+output_destination = osdf:///chtc/staging/u/username/
 ```
 {:.sub}
 
@@ -146,7 +139,7 @@ The `osdf:///` file transfer plugin is powered by the [Pelican Platform](https:/
 To transfer and unpack files, append a `?pack=auto` at the end of the plugin path of the compressed object to be transferred.
 
 ```
-transfer_input_files = osdf:///chtc/staging/netid/filename.tar.gz?pack=auto, input1.txt, input2.txt
+transfer_input_files = osdf:///chtc/staging/u/username/filename.tar.gz?pack=auto, input1.txt, input2.txt
 ```
 
 This feature is only availble for Pelican-based plugins (`osdf://`, `pelican://`) and is not available for `file://` or normal file transfers. This feature is also not recommended for compressed files larger than 30 GB.

_uw-research-computing/htc-overview.md

@@ -163,9 +163,9 @@ Each of the disk space values are given in megabytes (MB), which can be converte
 
 ### Check `/staging` Quota and Usage
 
-To see your `/staging` quota and usage, use the `get_quotas <NetID>` command. For example, 
+To see your `/staging` quota and usage, use the `get_quotas` command. For example, 
 ```
-[NetID@ap2001 ~]$ get_quotas /staging/NetID
+[NetID@ap2001 ~]$ get_quotas
 ```
 {:.term}
 
@@ -178,8 +178,8 @@ Alternatively, the `ncdu` command can also be used to see how many
 files and directories are contained in a given path:
 
 ``` 
-[NetID@ap2001 ~]$ ncdu /home/NetID
-[NetID@ap2001 ~]$ ncdu /staging/NetID
+[NetID@ap2001 ~]$ ncdu /home/username
+[NetID@ap2001 ~]$ ncdu /staging/u/username
 ```
 {:.term}
 

_uw-research-computing/htc-uwdf-researchdrive.md

@@ -84,7 +84,7 @@ transfer_output_files = outputfile1.txt, outputfile2.txt, outputfile3.txt
 You can use `transfer_output_remaps` to place files in different locations:
 
 ```
-transfer_output_remaps = "outputfile1.txt = pelican://chtc.wisc.edu/researchdrive/<PI NetID>/CHTC/outputfile1.txt; outputfile2.txt = osdf:///chtc/staging/<NetID>/outputfile2.txt"
+transfer_output_remaps = "outputfile1.txt = pelican://chtc.wisc.edu/researchdrive/<PI NetID>/CHTC/outputfile1.txt; outputfile2.txt = osdf:///chtc/staging/u/username/outputfile2.txt"
 ```
 
 The example above remaps the output files such that only `outputfile1.txt` is placed in ResearchDrive, `outputfile2.txt` is placed in `/staging`, and `outputfile3.txt` is placed in the submit directory on `/home`.