From 737ac053ad4a9d77fac05195ad6c9d1bfb18dc4c Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 30 Aug 2023 12:51:21 +0200 Subject: [PATCH] FAQ on locale issue with R (#105) Also, update of Python version. --- .github/workflows/mkdocs-deploy.yml | 19 +- .github/workflows/mkdocs-test.yml | 17 +- Pipfile | 2 +- Pipfile.lock | 734 ++++++++++++++++++++++------ bih-cluster/docs/help/faq.md | 99 +++- bih-cluster/mkdocs.yml | 2 +- 6 files changed, 686 insertions(+), 187 deletions(-) diff --git a/.github/workflows/mkdocs-deploy.yml b/.github/workflows/mkdocs-deploy.yml index 32c8eb452..11d5a9e26 100644 --- a/.github/workflows/mkdocs-deploy.yml +++ b/.github/workflows/mkdocs-deploy.yml @@ -3,24 +3,25 @@ name: "mkdocs: deploy to gh-pages" on: push: branches: - - master + - main jobs: deploy: - runs-on: ubuntu-18.04 + runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - name: Setup Python - uses: actions/setup-python@v1 + - name: Setup Python 3.10 + uses: actions/setup-python@v4 with: - python-version: '3.6' - architecture: 'x64' + python-version: '3.10' + cache: "pipenv" + cache-dependency-path: | + Pipfile.lock - name: Install dependencies run: | - python3 -m pip install pipenv - pipenv --python python3.6 + python -m pip install --upgrade pipenv wheel pipenv install - run: cd bih-cluster && pipenv run mkdocs build diff --git a/.github/workflows/mkdocs-test.yml b/.github/workflows/mkdocs-test.yml index 7eaee77cc..99780a3e1 100644 --- a/.github/workflows/mkdocs-test.yml +++ b/.github/workflows/mkdocs-test.yml @@ -6,20 +6,21 @@ on: jobs: check: - runs-on: ubuntu-18.04 + runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - name: Setup Python - uses: actions/setup-python@v1 + - name: Setup Python 3.10 + uses: actions/setup-python@v4 with: - python-version: '3.6' - architecture: 'x64' + python-version: '3.10' + cache: "pipenv" + cache-dependency-path: | + Pipfile.lock - name: Install dependencies run: | - python3 -m pip install pipenv - pipenv --python python3.6 + python -m pip install --upgrade pipenv wheel pipenv install - run: cd bih-cluster && pipenv run mkdocs build diff --git a/Pipfile b/Pipfile index 3d745b8e3..4c7c4f4d9 100644 --- a/Pipfile +++ b/Pipfile @@ -14,4 +14,4 @@ pymdown-extensions = "*" mkdocs-git-revision-date-localized-plugin = "*" [requires] -python_version = "3.6" +python_version = "3.10" diff --git a/Pipfile.lock b/Pipfile.lock index bfb129fb0..739491d85 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "31bbcf3de4700411b2e99481e36449afd08b038c67a53f0c7caf663ef166e4ab" + "sha256": "a3746d5a9041b5f947cddffa8540e203f95c4bacdc4e06ed674c3faf76efc023" }, "pipfile-spec": 6, "requires": { - "python_version": "3.6" + "python_version": "3.10" }, "sources": [ { @@ -18,240 +18,686 @@ "default": { "babel": { "hashes": [ - "sha256:1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38", - 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ExitCode ------------- ---------- ---------- ---------- ---------- ---------- -------- -_JOBID_ snakejob.+ medium hpc-ag-xx+ 4 TIMEOUT 0:0 -_JOBID_.bat+ batch hpc-ag-xx+ 4 CANCELLED 0:15 -_JOBID_.ext+ extern hpc-ag-xx+ 4 COMPLETED 0:0 + JobID JobName Partition Account AllocCPUS State ExitCode +------------ ---------- ---------- ---------- ---------- ---------- -------- +_JOBID_ snakejob.+ medium hpc-ag-xx+ 4 TIMEOUT 0:0 +_JOBID_.bat+ batch hpc-ag-xx+ 4 CANCELLED 0:15 +_JOBID_.ext+ extern hpc-ag-xx+ 4 COMPLETED 0:0 ``` Use the `--long` flag to see all fields (and probably pipe it into `less` as: `sacct -j JOBID --long | less -S`). @@ -105,7 +105,7 @@ For example, the following tells us that the given job was above its elapsed tim ---------- ---------- 01:00:00 01:00:12 01:00:13 - 01:00:12 + 01:00:12 ``` Use `man sacct`, `sacct --helpformat`, or see the [Slurm Documentation](https://slurm.schedmd.com/sacct.html) for options for the `--format` field of `sacct`. @@ -139,7 +139,7 @@ The solution is to use `xvfb-run` (xvfb = X11 virtual frame-buffer). Here is the content of an example script: ```terminal -$ cat img.R +$ cat img.R #!/usr/bin/env Rscript png('cars.png') @@ -151,8 +151,8 @@ dev.off() Here, it fails without X11: ```terminal -$ ./img.R -Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width, : +$ ./img.R +Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width, : unable to start device PNG Calls: png In addition: Warning message: @@ -163,9 +163,9 @@ Execution halted Here, it works with `xvfb-run`: ```terminal -$ xvfb-run ./img.R -null device - 1 +$ xvfb-run ./img.R +null device + 1 $ ls cars.png foo.png img.R Rplots.pdf ``` @@ -232,15 +232,15 @@ Second, inspect the node states: ```bash res-login-1:~$ sinfo -n med030[1-4] -PARTITION AVAIL TIMELIMIT NODES STATE NODELIST -debug* up 8:00:00 0 n/a -medium up 7-00:00:00 0 n/a -long up 28-00:00:0 0 n/a -critical up 7-00:00:00 0 n/a -highmem up 14-00:00:0 0 n/a -gpu up 14-00:00:0 1 drng med0304 -gpu up 14-00:00:0 3 mix med[0301-0303] -mpi up 14-00:00:0 0 n/a +PARTITION AVAIL TIMELIMIT NODES STATE NODELIST +debug* up 8:00:00 0 n/a +medium up 7-00:00:00 0 n/a +long up 28-00:00:0 0 n/a +critical up 7-00:00:00 0 n/a +highmem up 14-00:00:0 0 n/a +gpu up 14-00:00:0 1 drng med0304 +gpu up 14-00:00:0 3 mix med[0301-0303] +mpi up 14-00:00:0 0 n/a ``` This tells you that med0301 to med0303 have jobs running ("mix" indicates that there are free resources, but these are only CPU cores not GPUs). @@ -249,16 +249,16 @@ Let's look what's going on there. ```bash hl_lines="10 18" res-login-1:~$ scontrol show node med0304 -NodeName=med0304 Arch=x86_64 CoresPerSocket=16 +NodeName=med0304 Arch=x86_64 CoresPerSocket=16 CPUAlloc=2 CPUTot=64 CPULoad=1.44 AvailableFeatures=skylake ActiveFeatures=skylake Gres=gpu:tesla:4(S:0-1) NodeAddr=med0304 NodeHostName=med0304 Version=20.02.0 - OS=Linux 3.10.0-1127.13.1.el7.x86_64 #1 SMP Tue Jun 23 15:46:38 UTC 2020 + OS=Linux 3.10.0-1127.13.1.el7.x86_64 #1 SMP Tue Jun 23 15:46:38 UTC 2020 RealMemory=385215 AllocMem=1024 FreeMem=347881 Sockets=2 Boards=1 State=MIXED+DRAIN ThreadsPerCore=2 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A - Partitions=gpu + Partitions=gpu BootTime=2020-06-30T20:33:36 SlurmdStartTime=2020-07-01T09:31:51 CfgTRES=cpu=64,mem=385215M,billing=64 AllocTRES=cpu=2,mem=1G @@ -523,6 +523,57 @@ Have a look at our [How-To: Debug Software](../how-to/misc/debug-software.md) an Yes, please also refer to these guides on possible approaches to find the problem. +## My R sessions is always crashing! + +We are aware of issues for macOS users that are related to locales. +You might see something like the following in your R session or logs. + +Note that this is not macOS specific by itself but by macOS using a locale that R does not understand. + +Try using `export LC_ALL=C` before calling R. +If the problem goes away, you can add the following lines to your `~/.bashrc` file to make this permanent. +Note that this is actually a good idea so your locale settings are fixed. + +```bash +# Fix all locale settings to "C" for robustness. +export LC_ALL=C +``` + +!!! note "ChatGPT on Unix Locales" + + Let's se what ChatGPT 3.5 tells us about Unix locale. + + **Me: Please explain the concept of Unix locales to me.** + + > Certainly! Unix locales are a set of environment variables and settings that define how various aspects of software and user interactions should be handled to accommodate different languages, regions, and cultural conventions. They play a crucial role in enabling software to adapt to local preferences for displaying text, formatting numbers, handling dates, and more. + > + > In a Unix-like operating system (such as Linux or macOS), locales provide a way to customize how programs behave based on the user's language, country, and cultural norms. Here are some of the key components of Unix locales: + > + > 1. **Language:** The primary language used for messages, menus, prompts, and system output. For instance, if you set your locale to "en_US", messages and interfaces will be in English (United States). + > + > 2. **Region:** The country or region that defines conventions for aspects like date and time formatting, number formatting (decimal point or comma, thousands separator, etc.), and currency symbols. For example, "en_GB" represents English (Great Britain). + > + > 3. **Character Encoding:** Specifies how characters are encoded, which is vital for correctly displaying and handling text in various scripts and languages. Common encodings include UTF-8 for Unicode text. + > + > 4. **Collation:** Defines how strings should be sorted. Different languages have different sorting orders for characters, and the locale determines the appropriate collation rules. + > + > 5. **Numeric and Date Formats:** Specifies how numbers, dates, and times should be formatted. Different regions have different conventions for date formats (dd/mm/yyyy vs. mm/dd/yyyy) and numerical representations (commas vs. periods as decimal points). + > + > 6. **Currency Symbols:** Defines the symbol or abbreviation used for representing currency. This is important for currency formatting in software. + > + > Unix locales are typically identified by a combination of language and region codes, like "en_US" for American English or "fr_FR" for French (France). These locales are stored in files on the system, and they contain the necessary rules and data for proper localization. + > + > Users and administrators can set the system's default locale, and individual users can override this setting in their environment. Here are some common commands used to manage locales: + > + > - `locale`: Displays the current locale settings. + > - `locale -a`: Lists all available locales on the system. + > - `export LC_ALL=locale_code`: Temporarily sets the locale for the current session. + > - `update-locale locale_code`: Changes the system-wide default locale. + > + > Programs that are designed to be locale-aware use these settings to display messages, format numbers and dates, and handle other language-dependent features. This allows software to be more user-friendly and relevant to different linguistic and cultural contexts. + > + > In summary, Unix locales provide a framework for adapting software behavior to match the language, region, and cultural preferences of users, ensuring a more inclusive and globally accessible computing experience. + ## Which CUDA version is installed? For this, connect to the node you want to query (via SSH but do not perform any computation via SSH!) diff --git a/bih-cluster/mkdocs.yml b/bih-cluster/mkdocs.yml index 703265092..a7cea208c 100644 --- a/bih-cluster/mkdocs.yml +++ b/bih-cluster/mkdocs.yml @@ -7,7 +7,7 @@ site_url: https://bihealth.github.io/bih-cluster # Repository repo_name: BIH HPC Docs repo_url: https://github.com/bihealth/bih-cluster/ -edit_uri: 'edit/master/bih-cluster/docs/' +edit_uri: 'edit/main/bih-cluster/docs/' # Copyright copyright: 2016-2022, BIH HPC IT