diff --git a/doc.zih.tu-dresden.de/docs/archive/beegfs_on_demand.md b/doc.zih.tu-dresden.de/docs/archive/beegfs_on_demand.md index 9ccbb99dd41d26e69845455e88f527640d1560b8..f7804c5fc7e5792b9dab3ef722e6a6e8bf83a754 100644 --- a/doc.zih.tu-dresden.de/docs/archive/beegfs_on_demand.md +++ b/doc.zih.tu-dresden.de/docs/archive/beegfs_on_demand.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # BeeGFS Filesystem on Demand (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md b/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md index f023572624c9af646ca5b332272990720dd4a5c9..3bd425ac022341fa0845dd3daded70e16bb51b7a 100644 --- a/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md +++ b/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Bioinformatics (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/cxfs_end_of_support.md b/doc.zih.tu-dresden.de/docs/archive/cxfs_end_of_support.md index 10be6b2c8744c958ea714781f028a991ddb2c91d..9fceac76f460a348fd1bd1895d19479627c07749 100644 --- a/doc.zih.tu-dresden.de/docs/archive/cxfs_end_of_support.md +++ b/doc.zih.tu-dresden.de/docs/archive/cxfs_end_of_support.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Changes in the CXFS Filesystem (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/install_jupyter.md b/doc.zih.tu-dresden.de/docs/archive/install_jupyter.md index 89783636d7ba76dfd0825906eb26cc7e6582f906..b5687bc08b658648a1e3d9896843ad30e15e87ec 100644 --- a/doc.zih.tu-dresden.de/docs/archive/install_jupyter.md +++ b/doc.zih.tu-dresden.de/docs/archive/install_jupyter.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Jupyter Installation (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/knl_nodes.md b/doc.zih.tu-dresden.de/docs/archive/knl_nodes.md index c374e20d26ac15c5c9b7c2cbcdf0b96d690cfcd7..48a91a44145efd2724e15f1a450301a0ee79f5d3 100644 --- a/doc.zih.tu-dresden.de/docs/archive/knl_nodes.md +++ b/doc.zih.tu-dresden.de/docs/archive/knl_nodes.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Intel Xeon Phi (Knights Landing) (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/load_leveler.md b/doc.zih.tu-dresden.de/docs/archive/load_leveler.md index 7723f6baa455fc13ea114cdbf71c9e18ea69be87..797e9d0a2f1af93e9130c9c746dd90e5e46d8262 100644 --- a/doc.zih.tu-dresden.de/docs/archive/load_leveler.md +++ b/doc.zih.tu-dresden.de/docs/archive/load_leveler.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # LoadLeveler - IBM Tivoli Workload Scheduler (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/migrate_to_atlas.md b/doc.zih.tu-dresden.de/docs/archive/migrate_to_atlas.md index c3c37852a10563d6a49f853af8a0b9b5767ac555..ab44cf9bcba0898c0461be3b0d3774d61cd8d6a4 100644 --- a/doc.zih.tu-dresden.de/docs/archive/migrate_to_atlas.md +++ b/doc.zih.tu-dresden.de/docs/archive/migrate_to_atlas.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Migration from Deimos to Atlas (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/no_ib_jobs.md b/doc.zih.tu-dresden.de/docs/archive/no_ib_jobs.md index 8bf78779bdedf8b68d7efd60999878373da3edea..93394d5b8f14c12d8acfda5604066d14e39790ad 100644 --- a/doc.zih.tu-dresden.de/docs/archive/no_ib_jobs.md +++ b/doc.zih.tu-dresden.de/docs/archive/no_ib_jobs.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Jobs without InfiniBand (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/overview.md b/doc.zih.tu-dresden.de/docs/archive/overview.md index 7cd1e76cb566ecf7821464f4cf7e2b9ef72dbc0a..5da5b965a4ebc6751c5bd8f8f496a502a7ba6748 100644 --- a/doc.zih.tu-dresden.de/docs/archive/overview.md +++ b/doc.zih.tu-dresden.de/docs/archive/overview.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Archive (Outdated) A warm welcome to the **archive**. You probably got here by following a link from within the compendium diff --git a/doc.zih.tu-dresden.de/docs/archive/phase2_migration.md b/doc.zih.tu-dresden.de/docs/archive/phase2_migration.md index 55e6c007dde110f38f5a3bb56d5bc2ab992e09fc..4144b652a3181e7fd2acd9c484208d22a3e52777 100644 --- a/doc.zih.tu-dresden.de/docs/archive/phase2_migration.md +++ b/doc.zih.tu-dresden.de/docs/archive/phase2_migration.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Migration towards Phase 2 (Outdated) ## How to copy your data from an old scratch (Atlas, Venus, Taurus I) to our new scratch (Taurus II) diff --git a/doc.zih.tu-dresden.de/docs/archive/platform_lsf.md b/doc.zih.tu-dresden.de/docs/archive/platform_lsf.md index 3e3bdbe9d1ca130f50804ad3275ebe055f4971f7..c0894e2654974fe1d1d3775b0d043ca7e6c98398 100644 --- a/doc.zih.tu-dresden.de/docs/archive/platform_lsf.md +++ b/doc.zih.tu-dresden.de/docs/archive/platform_lsf.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Platform LSF (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/scs5_software.md b/doc.zih.tu-dresden.de/docs/archive/scs5_software.md index 5fc53caf9c7682fb3588283a4fdabceec5026974..5aadc995ef4c07d5009cc959388e61889edd3a86 100644 --- a/doc.zih.tu-dresden.de/docs/archive/scs5_software.md +++ b/doc.zih.tu-dresden.de/docs/archive/scs5_software.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # SCS5 Migration Hints (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/system_altix.md b/doc.zih.tu-dresden.de/docs/archive/system_altix.md index 0ba3c245aea097c8bdf7681ad59d87040c3dfe26..0c7b8a9cecbe079e032b24a926556e17bbf97a4e 100644 --- a/doc.zih.tu-dresden.de/docs/archive/system_altix.md +++ b/doc.zih.tu-dresden.de/docs/archive/system_altix.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # SGI Altix (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/system_atlas.md b/doc.zih.tu-dresden.de/docs/archive/system_atlas.md index f57024308f2a6f54d9f0e19d34b9a38937d8b6a9..e8a63ab236196b0853b9a1e6f90c809cfc567be5 100644 --- a/doc.zih.tu-dresden.de/docs/archive/system_atlas.md +++ b/doc.zih.tu-dresden.de/docs/archive/system_atlas.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # MEGWARE PC-Farm Atlas (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/system_deimos.md b/doc.zih.tu-dresden.de/docs/archive/system_deimos.md index 66da7a2cc4e138780e6d7dfb850467343e9d84bc..b36a9348138dc808273c83501afe92c99872a155 100644 --- a/doc.zih.tu-dresden.de/docs/archive/system_deimos.md +++ b/doc.zih.tu-dresden.de/docs/archive/system_deimos.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Linux Networx PC-Farm Deimos (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/system_phobos.md b/doc.zih.tu-dresden.de/docs/archive/system_phobos.md index 008cf4f7c4c5e9ea5362edd5849437d011051d4c..3519c36b876b15ea8b57146f112207ad0b5dd9f7 100644 --- a/doc.zih.tu-dresden.de/docs/archive/system_phobos.md +++ b/doc.zih.tu-dresden.de/docs/archive/system_phobos.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Linux Networx PC-Cluster Phobos (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/system_titan.md b/doc.zih.tu-dresden.de/docs/archive/system_titan.md index 2424f1a41ff653dbfb571bda719e57f4d10a6f45..d08dcd41de987cc11dd2fec0063b7bfd72a75a6e 100644 --- a/doc.zih.tu-dresden.de/docs/archive/system_titan.md +++ b/doc.zih.tu-dresden.de/docs/archive/system_titan.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Windows HPC Server 2008 Cluster Titan (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/system_triton.md b/doc.zih.tu-dresden.de/docs/archive/system_triton.md index bd5aa7bfea573013e60054f6d3ec8d8654f18339..147d99cd1c0571edb1ecd0f52dd863c0135b8290 100644 --- a/doc.zih.tu-dresden.de/docs/archive/system_triton.md +++ b/doc.zih.tu-dresden.de/docs/archive/system_triton.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # IBM-iDataPlex Cluster Trition (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/system_venus.md b/doc.zih.tu-dresden.de/docs/archive/system_venus.md index a3fa33107b7508589f12842b9183f8819a655de7..72882bb7d827eaba2a68fb84c9932efdfc5dca66 100644 --- a/doc.zih.tu-dresden.de/docs/archive/system_venus.md +++ b/doc.zih.tu-dresden.de/docs/archive/system_venus.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # SGI UV2000 / Venus (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/systems_switched_off.md b/doc.zih.tu-dresden.de/docs/archive/systems_switched_off.md index 929bcd44de2e225a4cd8c9b030c5fa90d89f7174..34880dfe3da0a57c6729ae813ac14142d96f460a 100644 --- a/doc.zih.tu-dresden.de/docs/archive/systems_switched_off.md +++ b/doc.zih.tu-dresden.de/docs/archive/systems_switched_off.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Switched-Off Systems (Outdated) HPC at ZIH has a quite long history and several systems have been installed and operated. diff --git a/doc.zih.tu-dresden.de/docs/archive/unicore_rest_api.md b/doc.zih.tu-dresden.de/docs/archive/unicore_rest_api.md index 2d0ae507fb1fa838f03265c7fd8cfd64c0326864..da9e42c45fe4b56b3b9994a7b130e8b451cd7c7c 100644 --- a/doc.zih.tu-dresden.de/docs/archive/unicore_rest_api.md +++ b/doc.zih.tu-dresden.de/docs/archive/unicore_rest_api.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # UNICORE access via REST API (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/vampirtrace.md b/doc.zih.tu-dresden.de/docs/archive/vampirtrace.md index e2b8030e0f47bc88378c29e80f8b27f13b4eada0..bd6be6ad9c5bbdd59b98041ce651f82f1baec338 100644 --- a/doc.zih.tu-dresden.de/docs/archive/vampirtrace.md +++ b/doc.zih.tu-dresden.de/docs/archive/vampirtrace.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # VampirTrace (Outdated) !!! warning diff --git a/doc.zih.tu-dresden.de/docs/archive/windows_batch.md b/doc.zih.tu-dresden.de/docs/archive/windows_batch.md index df4e0b259cd1345ea2ae3c34496e5878e73e6c88..7cb0a1753611fb68c56b44612f57dde46b876104 100644 --- a/doc.zih.tu-dresden.de/docs/archive/windows_batch.md +++ b/doc.zih.tu-dresden.de/docs/archive/windows_batch.md @@ -1,3 +1,8 @@ +--- +search: + boost: 0.00001 +--- + # Batch System on the Windows HPC Server (Outdated) !!! warning @@ -38,8 +43,8 @@ reasons during the job monitoring phase. - `C:\htitan\<LoginName>` - `C:\titan\HOME_(TITAN)\<LoginName>` -- `\\titan\hpcms-files\HOME_(TITAN)\<LoginName>` -- `\\hpcms\hpcms-files\HOME_(TITAN)\<LoginName>` +- `\titan\hpcms-files\HOME_(TITAN)\<LoginName>` +- `\hpcms\hpcms-files\HOME_(TITAN)\<LoginName>` - `Z:\HOME_(TITAN)\<LoginName>` (only available at login node) ### Job Queues diff --git a/doc.zih.tu-dresden.de/docs/contrib/content_rules.md b/doc.zih.tu-dresden.de/docs/contrib/content_rules.md index eb8beb7b97cd3b10d24c2df10f77b6e38096691c..1f54cd072b71e92e975864be51f2e7701a0bcd1c 100644 --- a/doc.zih.tu-dresden.de/docs/contrib/content_rules.md +++ b/doc.zih.tu-dresden.de/docs/contrib/content_rules.md @@ -424,3 +424,31 @@ understanding. This holds especially for Slurm options, but also other commands. |----|-------| | `srun --nodes=2 --ntasks-per-node=4 [...]`| `srun -N 2 -n 4 [...]` | | `module load [...]` | `ml [...]` | + +### Customize Search + +The +[documentation for the search plugin](https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/) +of the material theme is quite comprehensive. The search is realized as client-side search using the +open-source tool on [lunr](https://lunrjs.com/). The ranking of pages in search results bases on +so-called scoring. Please refer to +[lunrjs documentation](https://lunrjs.com/guides/searching.html#scoring) for details. + +From time to time it might be necessary to **tweak the search priority of certain pages**. +For example, pages from the archive section should be ranked very low in search results. This can be +achieved by adding the front matter `search.boost` property added to the top of the Markdown file of +interest: + +```Markdown +--- +search: + boost: 2 +--- + +# Document Title + +[...] +``` + +The documentation of this plugin gives no range for the boost values. We recommend to use this +feature carefully starting with low values. diff --git a/doc.zih.tu-dresden.de/docs/index.md b/doc.zih.tu-dresden.de/docs/index.md index 6c0f7fb7fc104f60629293c870009759dff01a5a..c22ef202a4408ab09d938219fa9be8b896cd7ae1 100644 --- a/doc.zih.tu-dresden.de/docs/index.md +++ b/doc.zih.tu-dresden.de/docs/index.md @@ -1,20 +1,28 @@ # ZIH HPC Documentation This is the documentation of the HPC systems and services provided at -[TU Dresden/ZIH](https://tu-dresden.de/zih/). This documentation is work in progress, since we try -to incorporate more information with increasing experience and with every question you ask us. The -HPC team invites you to take part in the improvement of these pages by correcting or adding useful -information. +[TU Dresden/ZIH](https://tu-dresden.de/zih/). + +This documentation will be continuously updated, since we try +to incorporate more information with increasing experience and with every question you ask us. + +If the provided HPC systems and services helped to advance your research, please cite us. Why this +is important and acknowledgment examples can be found in the section +[Acknowledgement](https://doc.zih.tu-dresden.de/application/acknowledgement/). ## Contribution -Your contributions are highly welcome. The easiest way for you to contribute is to report issues via +The HPC team invites you to take part in the improvement of these pages by correcting or adding +useful information. Your contributions are highly welcome! + +The easiest way for you to contribute is to report issues via the GitLab [issue tracking system](https://gitlab.hrz.tu-chemnitz.de/zih/hpcsupport/hpc-compendium/-/issues). Please check for any already existing issue before submitting your issue in order to avoid duplicate issues. -Please also find out the other ways you could contribute in our [guidelines how to contribute](contrib/howto_contribute.md). +Please also find out the other ways you could contribute in our +[guidelines how to contribute](contrib/howto_contribute.md). !!! tip "Reminder" diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/alpha_centauri.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/alpha_centauri.md index 5a0e15613665ececfaa2d0915fd7022c742a9288..b5b09281dd9ab9fdde89c7ae4ffe9ad4ec48c089 100644 --- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/alpha_centauri.md +++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/alpha_centauri.md @@ -12,6 +12,14 @@ The hardware specification is documented on the page The NVIDIA A100 GPUs may only be used with **CUDA 11** or later. Earlier versions do not recognize the new hardware properly. Make sure the software you are using is built with CUDA11. +There is a total of 48 physical cores in each node. SMT is also active, so in total, 96 logical +cores are available per node. + +!!! note + + Multithreading is disabled per default in a job. + See the [Slurm page](slurm.md) on how to enable it. + ### Modules The easiest way is using the [module system](../software/modules.md). diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/hardware_overview.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/hardware_overview.md index c4bd1c7909fda4fa27703c00c68e284be07a4cb0..538296b4ea52aee6c99f132811af8112803adcf9 100644 --- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/hardware_overview.md +++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/hardware_overview.md @@ -26,7 +26,7 @@ users and the ZIH. - 34 nodes, each with - 8 x NVIDIA A100-SXM4 Tensor Core-GPUs - - 2 x AMD EPYC CPU 7352 (24 cores) @ 2.3 GHz, Multithreading disabled + - 2 x AMD EPYC CPU 7352 (24 cores) @ 2.3 GHz, Multithreading available - 1 TB RAM - 3.5 TB local memory on NVMe device at `/tmp` - Hostnames: `taurusi[8001-8034]` @@ -36,7 +36,7 @@ users and the ZIH. ## Island 7 - AMD Rome CPUs - 192 nodes, each with - - 2 x AMD EPYC CPU 7702 (64 cores) @ 2.0 GHz, Multithreading enabled, + - 2 x AMD EPYC CPU 7702 (64 cores) @ 2.0 GHz, Multithreading available - 512 GB RAM - 200 GB local memory on SSD at `/tmp` - Hostnames: `taurusi[7001-7192]` diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md index adaf75cdf9a356307f023a85620fbc9f482dc019..98063cb50337c5396ee3125e245d9d929abe0679 100644 --- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md +++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md @@ -1,3 +1,8 @@ +--- +search: + boost: 2.0 +--- + # Batch System Slurm ZIH uses the batch system Slurm for resource management and job scheduling. Compute nodes are not @@ -316,6 +321,32 @@ provide a comprehensive collection of job examples. * Submisson: `marie@login$ sbatch batch_script.sh` * Run with fewer MPI tasks: `marie@login$ sbatch --ntasks=14 batch_script.sh` +## Using Simultaneous Multithreading (SMT) + +Most modern architectures offer simultaneous multithreading (SMT), where physical cores of a CPU are +split into virtual cores (aka. threads). This technique allows to run two instruction streams per +physical core in parallel. + +At ZIH systems, SMT is available at the partitions `rome` and `alpha`. It is deactivated by +default, because the environment variable `SLURM_HINT` is set to `nomultithread`. +If you wish to make use of the SMT cores, you need to explicitly activate it. +In principle, there are two different ways: + +1. Change the value of the environment variable via `export SLURM_HINT=multithread` in your current + shell and submit your job file, or invoke your `srun` or `salloc` command line. + +1. Clear the environment variable via `unset SLURM_HINT` and provide the option `--hint=multithread` + to `sbatch`, `srun` or `salloc` command line. + +??? warning + + If you like to activate SMT via the directive + ``` + #SBATCH --hint=multithread + ``` + within your job file, you also have to clear the environment variable `SLURM_HINT` before + submitting the job file. Otherwise, the environment varibale `SLURM_HINT` takes precedence. + ## Heterogeneous Jobs A heterogeneous job consists of several job components, all of which can have individual job diff --git a/doc.zih.tu-dresden.de/docs/software/performance_engineering_overview.md b/doc.zih.tu-dresden.de/docs/software/performance_engineering_overview.md index 564db230ca699fbc309a1e50b1ffb6d361e28828..0807db9ac0b6474b9a8051639fbad6466a03df09 100644 --- a/doc.zih.tu-dresden.de/docs/software/performance_engineering_overview.md +++ b/doc.zih.tu-dresden.de/docs/software/performance_engineering_overview.md @@ -1,3 +1,8 @@ +--- +search: + boost: 450.0 +--- + # Performance Engineering Overview !!! cite "Walter J. Doherty, 1970 [^1]" diff --git a/doc.zih.tu-dresden.de/mkdocs.yml b/doc.zih.tu-dresden.de/mkdocs.yml index 098c08b74461bd678d2745b9013e95513591c8bf..d05959ffab8c63bfcdbf9718e04a4a602b52d002 100644 --- a/doc.zih.tu-dresden.de/mkdocs.yml +++ b/doc.zih.tu-dresden.de/mkdocs.yml @@ -185,6 +185,7 @@ theme: second_logo: assets/images/zih_weiss.png features: - navigation.instant + - search.highlight # extends base css/js extra_css: diff --git a/doc.zih.tu-dresden.de/wordlist.aspell b/doc.zih.tu-dresden.de/wordlist.aspell index 20c9d108593a9c5ce95c74ba67f786d94278f21e..775ad216f730f61294932a87fe39d486ba26246a 100644 --- a/doc.zih.tu-dresden.de/wordlist.aspell +++ b/doc.zih.tu-dresden.de/wordlist.aspell @@ -1,6 +1,7 @@ personal_ws-1.1 en 475 aarch Abaqus +Acknowledgement ACL ACLs Addon @@ -210,6 +211,8 @@ localhost lsf lstopo Lua +lunr +lunrjs lustre mac Mac