- Working on Wynton - Part 2
+ Working on Wynton
+ Part 2
Natalie Elphick
April 16th, 2024
@@ -580,7 +587,7 @@ document.addEventListener('DOMContentLoaded', function(e) {
Introductions
Natalie Elphick
Bioinformatician I
-
Alex Pico
+
Alex Pico (TA)
Bioinformatics Core Director
@@ -607,8 +614,8 @@ Bioinformatics Core Director
Custom Containers
-
-Motivation
+
+Motivation
- Compute heavy jobs (high RAM, multiple cores) should be run on
compute nodes
@@ -620,7 +627,7 @@ Rocky 8 Linux
- Improves reproducibility
-![Compute Jobs]()
+![Compute Jobs]()
Dockerfile Basics
@@ -726,18 +733,20 @@ command, -t, to set the name of the docker image
[alice@dev1 ~]$ apptainer pull docker://docker_hub_user/seurat-harmony:1.0
-
-Notes on Building Custom Images
+
+Notes on Building Custom Images
-- Time consuming process and uses a lot of RAM on your local
+
- Time consuming process and can use a lot of RAM on your local
machine
- A good base image can save you a lot of time
-- You must run
apt-get update and
-apt-get install in the same command
+ - You must run apt-get update and apt-get
+install in the same command
- Otherwise you will encounter caching issues
+- These are only for Ubuntu, for other OS run the equivalent package
+list retrieval and install commands together
-- Remember to use
apt-get install -y
+ - Remember to use apt-get install -y
- You will have no control over the process while it’s building
@@ -949,7 +958,7 @@ development node.
bioinformatics analysis pipelines
- The most commonly used one is the RNA-seq pipeline
-![RNA-seq]()
+![RNA-seq]()
Example - RNA-seq Pipeline
diff --git a/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd b/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd
index 779310b..f20e2ac 100644
--- a/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd
+++ b/working-on-wynton-hpc/Working_on_Wynton_Part_1.Rmd
@@ -1,5 +1,6 @@
---
-title: "Working on Wynton - Part 1"
+title: "Working on Wynton"
+subtitle: "Part 1"
author: "Natalie Elphick"
date: "April 15th, 2024"
knit: (function(input, ...) {
@@ -28,7 +29,7 @@ output:
**Natalie Elphick**
Bioinformatician I
-**Alex Pico**
+**Alex Pico (TA)**
Bioinformatics Core Director
@@ -50,7 +51,7 @@ Bioinformatics Core Director
# What is Wynton HPC?
-## High-performance Computing Cluster
+## High-performance Computing Cluster {.smaller-picture}
- A collection of specialized computers (nodes) connected together on a fast local network
@@ -75,7 +76,7 @@ Bioinformatics Core Director
- **Login:** Submit and query jobs. SSH to development nodes. File management.
- **Development:** Compile and install software. Test job scripts. Submit and query jobs. Version control. File management.
-- **Compute:** Running short and long-running job scripts.
+- **Compute:** Running job scripts.
- **Transfer:** Fast in- & outbound file transfers. File management.
## The Login Nodes {.small-bullets}
@@ -92,8 +93,8 @@ log1, log2 and plog (for PHI users)
## Login {.small-bullets}
-- Make sure you are on the UCSF or Gladstone WiFi networks (or the respective VPN)
-- **ssh [your-username]@[node-name].wynton.ucsf.edu**
+- Connect to the UCSF or Gladstone WiFi networks (or the respective VPN) or using [2FA](https://wynton.ucsf.edu/hpc/get-started/duo-signup.html)
+- **ssh [your-username]@[node].wynton.ucsf.edu**
```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
echo "{local}$ ssh alice@log1.wynton.ucsf.edu
@@ -108,7 +109,7 @@ alice@log1.wynton.ucsf.edu's password:
- Has a set of [core software](https://wynton.ucsf.edu/hpc/software/core-software.html) installed
- e.g. git, vim, nano, make and python
-- Also has access to [software repositories](https://wynton.ucsf.edu/hpc/software/software-repositories.htmll) some which are maintained by other users or research groups
+- Also has access to [software repositories](https://wynton.ucsf.edu/hpc/software/software-repositories.html) some which are maintained by other users or research groups
- e.g. matlab, R and openjdk
- Cannot be logged in to directly, only from a login node
```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
@@ -138,14 +139,15 @@ dt1 and dt2
-## Compute Nodes {.small-bullets .big-picture}
+## Compute Nodes {.small-bullets}
- Can **not** be logged in to directly
+- No internet or UCSF network access
- Used to run non-interactive compute job scripts
- The software to run the job script is provided using a container
-
+
@@ -161,9 +163,6 @@ dt1 and dt2
-
-
-
## BeeGFS {.small-bullets}
- Wynton uses a *parallel* shared file system called BeeGFS
@@ -196,18 +195,18 @@ dt1 and dt2
- Prefer fewer, large files over many small ones
- Distribute reading and writing over several directories
- Including compute job output and error files
-- Use local scratch (/scratch) when possible
+- Use local scratch (**/scratch**) when possible
- Don't include anything in **/wynton** in your default LD_LIBRARY_PATH
-
-
## Storage {.small-bullets}
- **Wynton storage is not backed up**
-- /wynton/**[group_name]**/**[user]**
+- /wynton/home/**[group_name]**/**[user]**
+ - PHI users : /wynton/protected/home/**[group_name]**/**[user]**
- User home directory - limited to 500 GiB
-- /wynton/**[group_name]**
+- /wynton/group/**[group_name]**
+ - PHI users : /wynton/protected/group/**[group_name]**
- User group directory - disk quota varies by group
- Use this directory for any analysis you want to share with your lab
- [More information on disk quotas](https://wynton.ucsf.edu/hpc/howto/storage-size.html#file-sizes-and-disk-quotas)
@@ -220,9 +219,10 @@ echo 'beegfs-ctl --getquota --storagepoolid=12 --gid "$(id --group)"'
-## Scratch - Temporary Storage
+## Scratch - Temporary Storage {.small-bullets}
- Local **/scratch** - 0.1-1.8 TiB/node storage unique to each compute node
- - Can only be accessed from the specific compute node
+ - Can only be accessed from the specific compute node
+ - Use this to store intermediate files only needed for a job
- **/wynton/scratch** and **/wynton/protected/scratch** (for PHI users)
- 703 TiB storage accessible from everywhere
- No quotas
@@ -245,8 +245,10 @@ echo 'beegfs-ctl --getquota --storagepoolid=12 --gid "$(id --group)"'
## Storage Advice
- Always back up anything you store under **/wynton**
-- Use **/gladstone** if you have access to it for all of your work since it is automatically backed up
-- Use the scratch directories to store temporary files so they do not count against your group or user quotas
+- Back up your data on **/gladstone** if you have access to it
+ - A large number of jobs reading and writing to these directories will be slower since it is NFS mounted not BeeGFS
+- Use the scratch directories to store temporary files
+
# Data Transfer
@@ -372,26 +374,23 @@ echo '[alice@dev1 ~]$ nextflow -v'
-
-
# Containers
-## Motivation {.small-bullets}
+## Motivation {.small-bullets .small-picture}
- Compute heavy jobs (high RAM, multiple cores) should be run on compute nodes
- Containers allow us to make additional software available to the compute nodes
- Also allows the use of software that might be hard to install on Rocky 8 Linux
- Improves reproducibility
-
+
## Definitions {.small-bullets}
-- **Virtualization:** When software mimics the functions of physical hardware to run virtual machines
-- **Containers:** Implements virtualization using an *image* as its base
-- **Images:** An ordered collection of root filesystem changes and the corresponding execution parameters for use within a container runtime
+- **Containers:** An isolated environment for running software that is created from an *image* file, preventing conflicts with the host system.
+- **Images:** An ordered collection of root filesystem changes that contain all necessary dependencies, ensuring software run identically across various computing platforms.
## Apptainer {.small-bullets}
diff --git a/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd b/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd
index 341da38..523c03c 100644
--- a/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd
+++ b/working-on-wynton-hpc/Working_on_Wynton_Part_2.Rmd
@@ -1,5 +1,6 @@
---
-title: "Working on Wynton - Part 2"
+title: "Working on Wynton"
+subtitle: "Part 2"
author: "Natalie Elphick"
date: "April 16th, 2024"
knit: (function(input, ...) {
@@ -28,7 +29,7 @@ output:
**Natalie Elphick**
Bioinformatician I
-**Alex Pico**
+**Alex Pico (TA)**
Bioinformatics Core Director
@@ -53,14 +54,14 @@ Bioinformatics Core Director
# Custom Containers
-## Motivation {.small-bullets}
+## Motivation {.small-bullets .small-picture}
- Compute heavy jobs (high RAM, multiple cores) should be run on compute nodes
- Containers allow us to make additional software available to the compute nodes
- Also allows the use of software that might be hard to install on Rocky 8 Linux
- Improves reproducibility
-
+
@@ -125,13 +126,14 @@ echo "docker push docker_hub_user/seurat-harmony:1.0"
echo "[alice@dev1 ~]$ apptainer pull docker://docker_hub_user/seurat-harmony:1.0"
```
-## Notes on Building Custom Images {.code-small}
+## Notes on Building Custom Images {.small-bullets}
-- Time consuming process and uses a lot of RAM on your local machine
+- Time consuming process and can use a lot of RAM on your local machine
- A good base image can save you a lot of time
-- You must run `apt-get update` and `apt-get install` in the same command
+- You must run **apt-get update** and **apt-get install** in the same command
- Otherwise you will encounter caching issues
-- Remember to use `apt-get install -y`
+ - These are only for Ubuntu, for other OS run the equivalent package list retrieval and install commands together
+- Remember to use **apt-get install -y**
- You will have no control over the process while it's building
# Compute Jobs
diff --git a/working-on-wynton-hpc/renv.lock b/working-on-wynton-hpc/renv.lock
index a000798..abbdc26 100644
--- a/working-on-wynton-hpc/renv.lock
+++ b/working-on-wynton-hpc/renv.lock
@@ -9,49 +9,6 @@
]
},
"Packages": {
- "DBI": {
- "Package": "DBI",
- "Version": "1.2.2",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "methods"
- ],
- "Hash": "164809cd72e1d5160b4cb3aa57f510fe"
- },
- "MASS": {
- "Package": "MASS",
- "Version": "7.3-60.0.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "grDevices",
- "graphics",
- "methods",
- "stats",
- "utils"
- ],
- "Hash": "b765b28387acc8ec9e9c1530713cb19c"
- },
- "Matrix": {
- "Package": "Matrix",
- "Version": "1.6-5",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "grDevices",
- "graphics",
- "grid",
- "lattice",
- "methods",
- "stats",
- "utils"
- ],
- "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
- },
"R6": {
"Package": "R6",
"Version": "2.5.1",
@@ -62,36 +19,6 @@
],
"Hash": "470851b6d5d0ac559e9d01bb352b4021"
},
- "RColorBrewer": {
- "Package": "RColorBrewer",
- "Version": "1.1-3",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R"
- ],
- "Hash": "45f0398006e83a5b10b72a90663d8d8c"
- },
- "askpass": {
- "Package": "askpass",
- "Version": "1.2.0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "sys"
- ],
- "Hash": "cad6cf7f1d5f6e906700b9d3e718c796"
- },
- "backports": {
- "Package": "backports",
- "Version": "1.4.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R"
- ],
- "Hash": "c39fbec8a30d23e721980b8afb31984c"
- },
"base64enc": {
"Package": "base64enc",
"Version": "0.1-3",
@@ -102,63 +29,6 @@
],
"Hash": "543776ae6848fde2f48ff3816d0628bc"
},
- "bit": {
- "Package": "bit",
- "Version": "4.0.5",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R"
- ],
- "Hash": "d242abec29412ce988848d0294b208fd"
- },
- "bit64": {
- "Package": "bit64",
- "Version": "4.0.5",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "bit",
- "methods",
- "stats",
- "utils"
- ],
- "Hash": "9fe98599ca456d6552421db0d6772d8f"
- },
- "blob": {
- "Package": "blob",
- "Version": "1.2.4",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "methods",
- "rlang",
- "vctrs"
- ],
- "Hash": "40415719b5a479b87949f3aa0aee737c"
- },
- "broom": {
- "Package": "broom",
- "Version": "1.0.5",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "backports",
- "dplyr",
- "ellipsis",
- "generics",
- "glue",
- "lifecycle",
- "purrr",
- "rlang",
- "stringr",
- "tibble",
- "tidyr"
- ],
- "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c"
- },
"bslib": {
"Package": "bslib",
"Version": "0.6.1",
@@ -191,31 +61,6 @@
],
"Hash": "c35768291560ce302c0a6589f92e837d"
},
- "callr": {
- "Package": "callr",
- "Version": "3.7.5",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "R6",
- "processx",
- "utils"
- ],
- "Hash": "9f0e4fae4963ba775a5e5c520838c87b"
- },
- "cellranger": {
- "Package": "cellranger",
- "Version": "1.1.0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "rematch",
- "tibble"
- ],
- "Hash": "f61dbaec772ccd2e17705c1e872e9e7c"
- },
"cli": {
"Package": "cli",
"Version": "3.6.2",
@@ -227,127 +72,6 @@
],
"Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
},
- "clipr": {
- "Package": "clipr",
- "Version": "0.8.0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "utils"
- ],
- "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
- },
- "colorspace": {
- "Package": "colorspace",
- "Version": "2.1-0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "grDevices",
- "graphics",
- "methods",
- "stats"
- ],
- "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
- },
- "conflicted": {
- "Package": "conflicted",
- "Version": "1.2.0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "cli",
- "memoise",
- "rlang"
- ],
- "Hash": "bb097fccb22d156624fd07cd2894ddb6"
- },
- "countdown": {
- "Package": "countdown",
- "Version": "0.4.0",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "htmltools",
- "prismatic",
- "utils",
- "whisker"
- ],
- "Hash": "b44ad5a5e287637c3b8ca0e9bb64bb18"
- },
- "cpp11": {
- "Package": "cpp11",
- "Version": "0.4.7",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R"
- ],
- "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
- },
- "crayon": {
- "Package": "crayon",
- "Version": "1.5.2",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "grDevices",
- "methods",
- "utils"
- ],
- "Hash": "e8a1e41acf02548751f45c718d55aa6a"
- },
- "curl": {
- "Package": "curl",
- "Version": "5.2.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R"
- ],
- "Hash": "411ca2c03b1ce5f548345d2fc2685f7a"
- },
- "data.table": {
- "Package": "data.table",
- "Version": "1.15.2",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "methods"
- ],
- "Hash": "536dfe4ac4093b5d115caed7a1a7223b"
- },
- "dbplyr": {
- "Package": "dbplyr",
- "Version": "2.5.0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "DBI",
- "R",
- "R6",
- "blob",
- "cli",
- "dplyr",
- "glue",
- "lifecycle",
- "magrittr",
- "methods",
- "pillar",
- "purrr",
- "rlang",
- "tibble",
- "tidyr",
- "tidyselect",
- "utils",
- "vctrs",
- "withr"
- ],
- "Hash": "39b2e002522bfd258039ee4e889e0fd1"
- },
"digest": {
"Package": "digest",
"Version": "0.6.35",
@@ -359,48 +83,6 @@
],
"Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
},
- "dplyr": {
- "Package": "dplyr",
- "Version": "1.1.4",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "R6",
- "cli",
- "generics",
- "glue",
- "lifecycle",
- "magrittr",
- "methods",
- "pillar",
- "rlang",
- "tibble",
- "tidyselect",
- "utils",
- "vctrs"
- ],
- "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
- },
- "dtplyr": {
- "Package": "dtplyr",
- "Version": "1.3.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "cli",
- "data.table",
- "dplyr",
- "glue",
- "lifecycle",
- "rlang",
- "tibble",
- "tidyselect",
- "vctrs"
- ],
- "Hash": "54ed3ea01b11e81a86544faaecfef8e2"
- },
"ellipsis": {
"Package": "ellipsis",
"Version": "0.3.2",
@@ -423,25 +105,6 @@
],
"Hash": "daf4a1246be12c1fa8c7705a0935c1a0"
},
- "fansi": {
- "Package": "fansi",
- "Version": "1.0.6",
- "Source": "Repository",
- "Repository": "RSPM",
- "Requirements": [
- "R",
- "grDevices",
- "utils"
- ],
- "Hash": "962174cf2aeb5b9eea581522286a911f"
- },
- "farver": {
- "Package": "farver",
- "Version": "2.1.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Hash": "8106d78941f34855c440ddb946b8f7a5"
- },
"fastmap": {
"Package": "fastmap",
"Version": "1.1.1",
@@ -461,22 +124,6 @@
],
"Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
},
- "forcats": {
- "Package": "forcats",
- "Version": "1.0.0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "cli",
- "glue",
- "lifecycle",
- "magrittr",
- "rlang",
- "tibble"
- ],
- "Hash": "1a0a9a3d5083d0d573c4214576f1e690"
- },
"fs": {
"Package": "fs",
"Version": "1.6.3",
@@ -488,64 +135,6 @@
],
"Hash": "47b5f30c720c23999b913a1a635cf0bb"
},
- "gargle": {
- "Package": "gargle",
- "Version": "1.5.2",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "cli",
- "fs",
- "glue",
- "httr",
- "jsonlite",
- "lifecycle",
- "openssl",
- "rappdirs",
- "rlang",
- "stats",
- "utils",
- "withr"
- ],
- "Hash": "fc0b272e5847c58cd5da9b20eedbd026"
- },
- "generics": {
- "Package": "generics",
- "Version": "0.1.3",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "methods"
- ],
- "Hash": "15e9634c0fcd294799e9b2e929ed1b86"
- },
- "ggplot2": {
- "Package": "ggplot2",
- "Version": "3.5.0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "MASS",
- "R",
- "cli",
- "glue",
- "grDevices",
- "grid",
- "gtable",
- "isoband",
- "lifecycle",
- "mgcv",
- "rlang",
- "scales",
- "stats",
- "tibble",
- "vctrs",
- "withr"
- ],
- "Hash": "52ef83f93f74833007f193b2d4c159a2"
- },
"glue": {
"Package": "glue",
"Version": "1.7.0",
@@ -557,95 +146,6 @@
],
"Hash": "e0b3a53876554bd45879e596cdb10a52"
},
- "googledrive": {
- "Package": "googledrive",
- "Version": "2.1.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "cli",
- "gargle",
- "glue",
- "httr",
- "jsonlite",
- "lifecycle",
- "magrittr",
- "pillar",
- "purrr",
- "rlang",
- "tibble",
- "utils",
- "uuid",
- "vctrs",
- "withr"
- ],
- "Hash": "e99641edef03e2a5e87f0a0b1fcc97f4"
- },
- "googlesheets4": {
- "Package": "googlesheets4",
- "Version": "1.1.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "cellranger",
- "cli",
- "curl",
- "gargle",
- "glue",
- "googledrive",
- "httr",
- "ids",
- "lifecycle",
- "magrittr",
- "methods",
- "purrr",
- "rematch2",
- "rlang",
- "tibble",
- "utils",
- "vctrs",
- "withr"
- ],
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/* Decrease size of image, remove border, shadow and center align*/
.reveal img {
- max-width: 60%;
+ max-width: 70%;
border: none !important;
box-shadow: none !important;
display: block !important;
@@ -164,6 +164,15 @@ small {
}
+.small-picture img{
+ max-width: 65%;
+
+}
+.smaller-picture img{
+ max-width: 60%;
+
+}
+
/* Chage link color to sky blue */
.reveal a {
color: #0c74dc;
