diff --git a/doc.zih.tu-dresden.de/docs/access/jupyterhub_custom_environments.md b/doc.zih.tu-dresden.de/docs/access/jupyterhub_custom_environments.md index 9fe57b98a82ec0b1cc5a68ed42c6a115ed68b4e5..86b8486e26b8c1fdfeedb9821e36d4ce9e544d8b 100644 --- a/doc.zih.tu-dresden.de/docs/access/jupyterhub_custom_environments.md +++ b/doc.zih.tu-dresden.de/docs/access/jupyterhub_custom_environments.md @@ -1,4 +1,4 @@ -# Creating and Using a Custom Environment for JupyterHub +# Custom Environments for JupyterHub !!! info diff --git a/doc.zih.tu-dresden.de/docs/access/ssh_login.md b/doc.zih.tu-dresden.de/docs/access/ssh_login.md index c5e2c6a21fc98799ac0726a22407e1ff1193377b..760c752a2399cc8a41c5f7a921bfada5ba473465 100644 --- a/doc.zih.tu-dresden.de/docs/access/ssh_login.md +++ b/doc.zih.tu-dresden.de/docs/access/ssh_login.md @@ -1,4 +1,4 @@ -# Connecting via terminal +# Connecting via Terminal (Linux, Mac, Windows) Connecting via terminal works on every operating system. For Linux and Mac operating systems no additional software is required. For users of a Windows OS a recent version of Windows is diff --git a/doc.zih.tu-dresden.de/docs/access/ssh_mobaxterm.md b/doc.zih.tu-dresden.de/docs/access/ssh_mobaxterm.md index 791f7578956ba1848b9f8ae6650a3f93f061a849..85d5f9cfc1e55078ba9c79e881d7156dacf9ca0a 100644 --- a/doc.zih.tu-dresden.de/docs/access/ssh_mobaxterm.md +++ b/doc.zih.tu-dresden.de/docs/access/ssh_mobaxterm.md @@ -1,13 +1,11 @@ -# Connecting from Windows with MobaXterm +# Connecting with MobaXterm (Windows) -MobaXterm is an enhanced terminal for Windows with an X11 server, a tabbed SSH client, network -tools and more. - -Visit its homepage for more information (https://mobaxterm.mobatek.net). +[MobaXterm](https://mobaxterm.mobatek.net) is an enhanced terminal for Windows with an X11 server, +a tabbed SSH client, network tools and more. ## Download and install -To download go to [MobaXterm homepage](https://mobaxterm.mobatek.net/download-home-edition.html) +To download go to [MobaXterm download page](https://mobaxterm.mobatek.net/download-home-edition.html) and download a free home edition.  diff --git a/doc.zih.tu-dresden.de/docs/access/ssh_putty.md b/doc.zih.tu-dresden.de/docs/access/ssh_putty.md index f6f390868a78670d339162705ef2f79057d4ec01..28105fef81b555f6a4af28fc8fdcc128797ea65a 100644 --- a/doc.zih.tu-dresden.de/docs/access/ssh_putty.md +++ b/doc.zih.tu-dresden.de/docs/access/ssh_putty.md @@ -1,4 +1,4 @@ -# Connecting from Windows with PuTTY +# Connecting with PuTTY (Windows) PuTTY is a free and open-source terminal emulator, serial console and network file transfer application, supports several network protocols, including SCP, SSH. Visit the diff --git a/doc.zih.tu-dresden.de/docs/application/acknowledgement.md b/doc.zih.tu-dresden.de/docs/application/acknowledgement.md index 2cbb89c2b88afe5933da677f53676e600387ce1c..dfe9fd0e42bc6d97aadada80e499ac9dac2d3b50 100644 --- a/doc.zih.tu-dresden.de/docs/application/acknowledgement.md +++ b/doc.zih.tu-dresden.de/docs/application/acknowledgement.md @@ -1,4 +1,4 @@ -# Acknowledgment +# Acknowledgement To provide you with modern and powerful HPC systems in future as well, we have to show that these systems help to advance research. For that purpose we rely on your help. In most cases, the results diff --git a/doc.zih.tu-dresden.de/docs/application/terms_of_use.md b/doc.zih.tu-dresden.de/docs/application/terms_of_use.md index 45d1566ec3ca55869f7a02f83ac60f6cd8f1708a..7410198950182fe0eada76d4e02885899c803c77 100644 --- a/doc.zih.tu-dresden.de/docs/application/terms_of_use.md +++ b/doc.zih.tu-dresden.de/docs/application/terms_of_use.md @@ -1,4 +1,4 @@ -# Terms Of Use / Nutzungsbedingungen +# Terms of Use !!! attention 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 55a6e106dcc42a62050cc75759ccc943f2dd688c..9ccbb99dd41d26e69845455e88f527640d1560b8 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 @@ -1,4 +1,4 @@ -# BeeGFS Filesystem (Outdated) +# BeeGFS Filesystem on Demand (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 79fb6dcdde89c460671c1b7adb9cc7f7101973ef..8bf78779bdedf8b68d7efd60999878373da3edea 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 @@ -1,4 +1,4 @@ -# Jobs without Infiniband (Outdated) +# Jobs without InfiniBand (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 4f1319e046f05621aa155a64260fb4327942f4e1..929bcd44de2e225a4cd8c9b030c5fa90d89f7174 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 @@ -1,4 +1,4 @@ -# Hardware (Outdated) +# Switched-Off Systems (Outdated) HPC at ZIH has a quite long history and several systems have been installed and operated. Documentation on former systems for future reference can be found on the following pages: diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/mpi_issues.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/mpi_issues.md index bcabe289e3390e0ea6915ef33fb05eb1cff97fef..ccb34da378591594991ab746915fd90e9847920b 100644 --- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/mpi_issues.md +++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/mpi_issues.md @@ -1,4 +1,4 @@ -# Known MPI-Usage Issues +# Known Issues when Using MPI This pages holds known issues observed with MPI and concrete MPI implementations. diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/rome_nodes.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/rome_nodes.md index 905110c775721ded6ce280ef069b0b05e7ce146f..4347dd6b0e64005a67f4c60627a2002138a00631 100644 --- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/rome_nodes.md +++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/rome_nodes.md @@ -1,4 +1,4 @@ -# Island 7 - AMD Rome Nodes +# AMD Rome Nodes The hardware specification is documented on the page [HPC Resources](hardware_overview.md#island-7-amd-rome-cpus). diff --git a/doc.zih.tu-dresden.de/docs/software/custom_easy_build_environment.md b/doc.zih.tu-dresden.de/docs/software/custom_easy_build_environment.md index 9232e7472e8acc0254f876352310be0355d9aa4e..15063e28c0d378c0a64c3f4bf86cd85190e2605c 100644 --- a/doc.zih.tu-dresden.de/docs/software/custom_easy_build_environment.md +++ b/doc.zih.tu-dresden.de/docs/software/custom_easy_build_environment.md @@ -1,4 +1,4 @@ -# Software Install with EasyBuild +# Software Installation with EasyBuild Sometimes the [modules](modules.md) installed in the cluster are not enough for your purposes and you need some other software or a different version of a software. diff --git a/doc.zih.tu-dresden.de/docs/software/energy_measurement.md b/doc.zih.tu-dresden.de/docs/software/energy_measurement.md index ac73235a27fefc8ea6dffb934b4439391a32cfff..633d3e406d3b770d0f55220b671bab9b4b4a2bb1 100644 --- a/doc.zih.tu-dresden.de/docs/software/energy_measurement.md +++ b/doc.zih.tu-dresden.de/docs/software/energy_measurement.md @@ -1,4 +1,4 @@ -# Energy Measurement Infrastructure +# Measure Energy Consumption The Intel Haswell nodes of ZIH system are equipped with power instrumentation that allow the recording and accounting of power dissipation and energy consumption data. The data is made @@ -58,7 +58,7 @@ the node under test to start, stop, and query the measurement device. !!! note - Please always execute `clearHdeem` before `startHdeem`. + Please always execute `clearHdeem` before `startHdeem`. ## Integration in Application Performance Traces diff --git a/doc.zih.tu-dresden.de/docs/software/lo2s.md b/doc.zih.tu-dresden.de/docs/software/lo2s.md index cf34feccfca15e1e37d5278f30117aaba827e800..1183e83022396fb76b2a8c455a1c870022a06588 100644 --- a/doc.zih.tu-dresden.de/docs/software/lo2s.md +++ b/doc.zih.tu-dresden.de/docs/software/lo2s.md @@ -1,7 +1,7 @@ -# lo2s - Lightweight Node-Level Performance Monitoring +# Record Course of Events with lo2s -`lo2s` creates parallel OTF2 traces with a focus on both application and system view. -The traces can contain any of the following information: +Lightweight node-level performance monitoring tool `lo2s` creates parallel OTF2 traces with a focus +on both application and system view. The traces can contain any of the following information: * From running threads * Calling context samples based on instruction overflows diff --git a/doc.zih.tu-dresden.de/docs/software/mpi_usage_error_detection.md b/doc.zih.tu-dresden.de/docs/software/mpi_usage_error_detection.md index 66ee5b4cc26e4a646203d9911ca429ed4dba2e41..630e19e8fe6d7ca70a89175662ab8e79b9adceac 100644 --- a/doc.zih.tu-dresden.de/docs/software/mpi_usage_error_detection.md +++ b/doc.zih.tu-dresden.de/docs/software/mpi_usage_error_detection.md @@ -1,4 +1,4 @@ -# MPI Error Detection +# Check MPI Correctness with MUST MPI as the de-facto standard for parallel applications of the message passing paradigm offers more than one hundred different API calls with complex restrictions. As a result, developing diff --git a/doc.zih.tu-dresden.de/docs/software/papi.md b/doc.zih.tu-dresden.de/docs/software/papi.md index d8108bba3048da33661e0dd320a2807a0dd001aa..c5f0e7cfaf6260323a8fb572832e9f0a44f792a4 100644 --- a/doc.zih.tu-dresden.de/docs/software/papi.md +++ b/doc.zih.tu-dresden.de/docs/software/papi.md @@ -1,4 +1,4 @@ -# PAPI Library +# Read CPU Performance Counters with PAPI ## Introduction diff --git a/doc.zih.tu-dresden.de/docs/software/perf_tools.md b/doc.zih.tu-dresden.de/docs/software/perf_tools.md index 2db805a12f96e3daad253ea43e5030ad275cfb12..a32abadd94a358e3eb1f9a6c9e364313660f5b5a 100644 --- a/doc.zih.tu-dresden.de/docs/software/perf_tools.md +++ b/doc.zih.tu-dresden.de/docs/software/perf_tools.md @@ -1,4 +1,4 @@ -# Perf Tools +# Produce Performance Overview with Perf The Linux `perf` command provides support for sampling applications and reading performance counters. `perf` consists of two parts: the kernel space implementation and the userland tools. diff --git a/doc.zih.tu-dresden.de/docs/software/pika.md b/doc.zih.tu-dresden.de/docs/software/pika.md index 40202decaedd121aab6d7bf00d7958377ff19d8c..f84460f8056d8d010406dccc89a9270131cf87d5 100644 --- a/doc.zih.tu-dresden.de/docs/software/pika.md +++ b/doc.zih.tu-dresden.de/docs/software/pika.md @@ -1,4 +1,4 @@ -# PIKA +# Track Slurm Jobs with PIKA PIKA is a hardware performance monitoring stack to identify inefficient HPC jobs. Users of ZIH systems have the possibility to visualize and analyze the efficiency of their jobs via the diff --git a/doc.zih.tu-dresden.de/docs/software/scorep.md b/doc.zih.tu-dresden.de/docs/software/scorep.md index 0e2dc6c2358c95f47373a2f046f3fe4d643ae643..8966df8ed16637333299805076f0282948b0c376 100644 --- a/doc.zih.tu-dresden.de/docs/software/scorep.md +++ b/doc.zih.tu-dresden.de/docs/software/scorep.md @@ -1,4 +1,4 @@ -# Score-P +# Record Course of Events with Score-P The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. Currently, it works with the diff --git a/doc.zih.tu-dresden.de/docs/software/singularity_power9.md b/doc.zih.tu-dresden.de/docs/software/singularity_power9.md index 5daf70465d006799bc3df921dcb4698a8d648eab..080314e52f349f94caf3a1e4ca018807797fd0fa 100644 --- a/doc.zih.tu-dresden.de/docs/software/singularity_power9.md +++ b/doc.zih.tu-dresden.de/docs/software/singularity_power9.md @@ -1,4 +1,4 @@ -# Singularity for Power 9 Architecture +# Singularity for Power9 Architecture !!! note "Root privileges" diff --git a/doc.zih.tu-dresden.de/docs/software/vampir.md b/doc.zih.tu-dresden.de/docs/software/vampir.md index 64dfd00d36eb8079406ce7a47ee55324d8de32fe..ee07d2f5babebace6809e9e2c7e384326f94409d 100644 --- a/doc.zih.tu-dresden.de/docs/software/vampir.md +++ b/doc.zih.tu-dresden.de/docs/software/vampir.md @@ -1,4 +1,4 @@ -# Vampir +# Study Course of Events with Vampir ## Introduction diff --git a/doc.zih.tu-dresden.de/docs/support/support.md b/doc.zih.tu-dresden.de/docs/support/support.md index c2c9fbda8bbb70c1dddb82fb384b69a8201e6fb8..3582ae264c4ead7f41acdf14e9877af91b8c2d57 100644 --- a/doc.zih.tu-dresden.de/docs/support/support.md +++ b/doc.zih.tu-dresden.de/docs/support/support.md @@ -1,4 +1,4 @@ -# How to Ask for Support +# User Support ## Create a Ticket diff --git a/doc.zih.tu-dresden.de/mkdocs.yml b/doc.zih.tu-dresden.de/mkdocs.yml index 7c68972f5ea34a55bdd0cd8a38f0c17e2e94578a..d6d34b3c944098461ac203c11c6de728c88f414e 100644 --- a/doc.zih.tu-dresden.de/mkdocs.yml +++ b/doc.zih.tu-dresden.de/mkdocs.yml @@ -5,28 +5,28 @@ nav: - Overview: application/overview.md - Terms of Use: application/terms_of_use.md - Request for Resources: application/request_for_resources.md - - Project Request Form: application/project_request_form.md + - Project Request Form Jards: application/project_request_form.md - Project Management: application/project_management.md - Acknowledgement: application/acknowledgement.md - Access to ZIH Systems: - Overview: access/overview.md - Connecting with SSH: - - Connecting via terminal (Linux, Mac, Windows): access/ssh_login.md - - Connecting via MobaXterm (Windows): access/ssh_mobaxterm.md - - Connecting via Putty (Windows): access/ssh_putty.md + - Connecting via Terminal (Linux, Mac, Windows): access/ssh_login.md + - Connecting with MobaXterm (Windows): access/ssh_mobaxterm.md + - Connecting with PuTTY (Windows): access/ssh_putty.md - Desktop Cloud Visualization (DCV): access/desktop_cloud_visualization.md - Graphical Applications with WebVNC: access/graphical_applications_with_webvnc.md - JupyterHub: - JupyterHub: access/jupyterhub.md - - JupyterHub Custom Environments: access/jupyterhub_custom_environments.md + - Custom Environments for JupyterHub: access/jupyterhub_custom_environments.md - JupyterHub for Teaching: access/jupyterhub_for_teaching.md - JupyterHub Teaching Example: access/jupyterhub_teaching_example.md - Key Fingerprints: access/key_fingerprints.md - Security Restrictions: access/security_restrictions.md - Data Transfer: - Overview: data_transfer/overview.md - - Datamover: data_transfer/datamover.md - - Export Nodes: data_transfer/export_nodes.md + - Transfer Data Inside ZIH Systems with Datamover: data_transfer/datamover.md + - Transfer Data to/from ZIH Systems via Export Nodes: data_transfer/export_nodes.md - Data Life Cycle Management: - Overview: data_lifecycle/overview.md - Filesystems: @@ -37,7 +37,7 @@ nav: - Warm Archive: data_lifecycle/warm_archive.md - Intermediate Archive: data_lifecycle/intermediate_archive.md - Workspaces: data_lifecycle/workspaces.md - - Long-Term Preservation: data_lifecycle/longterm_preservation.md + - Long-Term Preservation of Research Data: data_lifecycle/longterm_preservation.md - Sharing Data: data_lifecycle/data_sharing.md - User Environment: - Overview: software/overview.md @@ -50,7 +50,7 @@ nav: - Containers: - Singularity: software/containers.md - Singularity Recipes and Hints: software/singularity_recipe_hints.md - - Singularity for Power9: software/singularity_power9.md + - Singularity for Power9 Architecture: software/singularity_power9.md - Virtual Machines: software/virtual_machines.md - GPU-accelerated Containers for Deep Learning (NGC Containers): software/ngc_containers.md - External Licenses: software/licenses.md @@ -81,7 +81,7 @@ nav: - Compilers and Flags: software/compilers.md - GPU Programming: software/gpu_programming.md - Mathematics Libraries: software/math_libraries.md - - MPI Usage Issues: jobs_and_resources/mpi_issues.md + - Known Issues when Using MPI: jobs_and_resources/mpi_issues.md - Debugging: software/debuggers.md - Performance Engineering Tools: - Overview: software/performance_engineering_overview.md @@ -111,21 +111,21 @@ nav: - Slurm Job File Generator: jobs_and_resources/slurm_generator.md - Checkpoint/Restart: jobs_and_resources/checkpoint_restart.md - Job Profiling: jobs_and_resources/slurm_profiling.md - - Binding And Distribution Of Tasks: jobs_and_resources/binding_and_distribution_of_tasks.md + - Binding and Distribution of Tasks: jobs_and_resources/binding_and_distribution_of_tasks.md - User Support: support/support.md - Archive: - Overview: archive/overview.md - Bio Informatics: archive/bioinformatics.md - CXFS End of Support: archive/cxfs_end_of_support.md - Load Leveler: archive/load_leveler.md - - No IB Jobs: archive/no_ib_jobs.md - - Phase2 Migration: archive/phase2_migration.md + - Jobs without InfiniBand: archive/no_ib_jobs.md + - Migration towards Phase 2: archive/phase2_migration.md - Platform LSF: archive/platform_lsf.md - - BeeGFS on Demand: archive/beegfs_on_demand.md - - Install JupyterHub: archive/install_jupyter.md + - BeeGFS Filesystem on Demand: archive/beegfs_on_demand.md + - Jupyter Installation: archive/install_jupyter.md - Switched-Off Systems: - Overview: archive/systems_switched_off.md - - From Deimos to Atlas: archive/migrate_to_atlas.md + - Migration From Deimos to Atlas: archive/migrate_to_atlas.md - System Altix: archive/system_altix.md - System Atlas: archive/system_atlas.md - System Deimos: archive/system_deimos.md diff --git a/doc.zih.tu-dresden.de/util/check-TOC-equals-page-headings.py b/doc.zih.tu-dresden.de/util/check-TOC-equals-page-headings.py new file mode 100644 index 0000000000000000000000000000000000000000..16097c70ac1aff3ab819205d7289ffb512b7f486 --- /dev/null +++ b/doc.zih.tu-dresden.de/util/check-TOC-equals-page-headings.py @@ -0,0 +1,44 @@ +""" #!/usr/bin/env python +Check for consistency between TOC and page headings. +Provide as an command line argument the path to the mkdocs.yml file. + +Author: Taras Lazariv +""" + +import os +import sys +import yaml +import pandas as pd + +def list_and_read_files(path): + "List files in a directory recursively and read the first line of each file" + files = [] + firstline = [] + for root, _, filenames in os.walk(path): + for filename in filenames: + if filename.endswith('.md'): + files.append(os.path.join(root.split('/')[-1], filename)) + firstline.append(open(os.path.join(root, filename)).readline().strip().replace('# ','')) + df = pd.DataFrame({'file': files, 'firstline': firstline}) + return df + +def main(): + "Main function" + path = os.getcwd() + df = list_and_read_files(path) + + nav_section = dict() + + with open(sys.argv[1], 'r') as file: + for line in file: + line = line.rstrip() + if line.endswith('.md'): + nav_section.update(yaml.safe_load(line)[0]) + + nav_df = pd.DataFrame(nav_section.items(), columns=['title', 'file']) + with pd.option_context('display.max_rows', None): # more options can be specified also + complete_nav_df = pd.merge(df, nav_df, on='file', how='outer') + print(complete_nav_df.loc[~(complete_nav_df['firstline'] == complete_nav_df['title'])]) + +if __name__ == '__main__': + main() \ No newline at end of file