From a0bf0276abded314aa7eaea5dbdeb07ea44098b7 Mon Sep 17 00:00:00 2001 From: Adam Caprez <acaprez2@unl.edu> Date: Sat, 19 Oct 2019 00:35:43 +0000 Subject: [PATCH] Fix references enough so the site will build. --- content/Applications/Application_Specific_Guides/Jupyter.md | 2 +- .../blast_with_allinea_performance_reports.md | 2 +- .../ray_with_allinea_performance_reports.md | 2 +- .../alignment_tools/blast/running_blast_alignment.md | 2 +- .../Application_Specific_Guides/dmtcp_checkpointing.md | 2 +- content/_index.md | 2 +- content/connecting/_index.md | 2 +- content/faq/_index.md | 2 +- content/guides/submitting_jobs/_index.md | 3 +-- content/guides/submitting_jobs/submitting_an_openmp_job.md | 2 +- content/quickstarts/connecting/for_maclinux_users.md | 2 +- content/quickstarts/connecting/for_windows_users.md | 2 +- content/quickstarts/connecting/mobaxterm_windows.md | 4 ++-- content/quickstarts/submitting_jobs.md | 3 +-- 14 files changed, 15 insertions(+), 17 deletions(-) diff --git a/content/Applications/Application_Specific_Guides/Jupyter.md b/content/Applications/Application_Specific_Guides/Jupyter.md index 44213395..b3f5de58 100644 --- a/content/Applications/Application_Specific_Guides/Jupyter.md +++ b/content/Applications/Application_Specific_Guides/Jupyter.md @@ -51,7 +51,7 @@ Select the other options based on your computing needs. Note that a SLURM Job wi Many popular `python` and `R` packages are already installed and available within Jupyter Notebooks. However, it is possible to install custom packages to be used in notebooks by creating a custom Anaconda Environment. Detailed information on how to create such an environment can be found at - [Using an Anaconda Environment in a Jupyter Notebook on Crane]({{< relref "using_anaconda_package_manager/#using-an-anaconda-environment-in-a-jupyter-notebook-on-crane" >}}). + [Using an Anaconda Environment in a Jupyter Notebook on Crane]({{< relref "/Applications/Using_Your_Own_Software/using_anaconda_package_manager#using-an-anaconda-environment-in-a-jupyter-notebook-on-crane" >}}). --- diff --git a/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md index ae01912e..5fd9443a 100644 --- a/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md +++ b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/blast_with_allinea_performance_reports.md @@ -4,7 +4,7 @@ description = "Example of how to profile BLAST using Allinea Performance Reports +++ Simple example of using -[BLAST]({{< relref "/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment" >}}) +[BLAST]({{< relref "/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment" >}}) with Allinea Performance Reports (`perf-report`) on Crane is shown below: {{% panel theme="info" header="blastn_perf_report.submit" %}} diff --git a/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md index 09fab74b..de4dc0d5 100644 --- a/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md +++ b/content/Applications/Application_Specific_Guides/allinea_profiling_and_debugging/allinea_performance_reports/ray_with_allinea_performance_reports.md @@ -3,7 +3,7 @@ title = "Ray with Allinea Performance Reports" description = "Example of how to profile Ray using Allinea Performance Reports" +++ -Simple example of using [Ray]({{< relref "/guides/running_applications/bioinformatics_tools/de_novo_assembly_tools/ray" >}}) +Simple example of using [Ray]({{< relref "/Applications/Application_Specific_Guides/bioinformatics_tools/de_novo_assembly_tools/ray" >}}) with Allinea PerformanceReports (`perf-report`) on Tusker is shown below: {{% panel theme="info" header="ray_perf_report.submit" %}} diff --git a/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md index 4024fe76..e9345267 100644 --- a/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md +++ b/content/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md @@ -28,7 +28,7 @@ $ blastn -help These BLAST alignment commands are multi-threaded, and therefore using the BLAST option **-num_threads <number_of_CPUs>** is recommended. -HCC hosts multiple BLAST databases and indices on Crane. In order to use these resources, the ["biodata" module] ({{<relref "/guides/running_applications/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases: +HCC hosts multiple BLAST databases and indices on Crane. In order to use these resources, the ["biodata" module] ({{<relref "/Applications/Application_Specific_Guides/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases: - **16SMicrobial** - **env_nt** diff --git a/content/Applications/Application_Specific_Guides/dmtcp_checkpointing.md b/content/Applications/Application_Specific_Guides/dmtcp_checkpointing.md index 5fca1a4c..66985673 100644 --- a/content/Applications/Application_Specific_Guides/dmtcp_checkpointing.md +++ b/content/Applications/Application_Specific_Guides/dmtcp_checkpointing.md @@ -61,7 +61,7 @@ will keep running with the options defined in the initial Simple example of using DMTCP with -[BLAST]({{< relref "/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment" >}}) +[BLAST]({{< relref "/Applications/Application_Specific_Guides/bioinformatics_tools/alignment_tools/blast/running_blast_alignment" >}}) on crane is shown below: {{% panel theme="info" header="dmtcp_blastx.submit" %}} diff --git a/content/_index.md b/content/_index.md index bc6b11c4..7aa654ad 100644 --- a/content/_index.md +++ b/content/_index.md @@ -59,7 +59,7 @@ Duo Security Duo two-factor authentication is **required** for access to HCC resources. Registration and usage of Duo security can be found in this -section: [Setting up and using Duo]({{< relref "setting_up_and_using_duo">}}) +section: [Setting up and using Duo]({{< relref "/Accounts/setting_up_and_using_duo">}}) **Important Notes** diff --git a/content/connecting/_index.md b/content/connecting/_index.md index bc6b11c4..7aa654ad 100644 --- a/content/connecting/_index.md +++ b/content/connecting/_index.md @@ -59,7 +59,7 @@ Duo Security Duo two-factor authentication is **required** for access to HCC resources. Registration and usage of Duo security can be found in this -section: [Setting up and using Duo]({{< relref "setting_up_and_using_duo">}}) +section: [Setting up and using Duo]({{< relref "/Accounts/setting_up_and_using_duo">}}) **Important Notes** diff --git a/content/faq/_index.md b/content/faq/_index.md index 1090e762..75240bf5 100644 --- a/content/faq/_index.md +++ b/content/faq/_index.md @@ -36,7 +36,7 @@ how to install the necessary software for your operating system Information on how to change or retrieve your password can be found on the documentation page: [How to change your -password]({{< relref "how_to_change_your_password" >}}) +password]({{< relref "/Accounts/how_to_change_your_password" >}}) All passwords must be at least 8 characters in length and must contain diff --git a/content/guides/submitting_jobs/_index.md b/content/guides/submitting_jobs/_index.md index 73e0272e..ad8002d6 100644 --- a/content/guides/submitting_jobs/_index.md +++ b/content/guides/submitting_jobs/_index.md @@ -11,8 +11,7 @@ must create a SLURM script that will run your processing. After submitting the job, SLURM will schedule your processing on an available worker node. -Before writing a submit file, you may need to -[compile your application]({{< relref "/guides/running_applications/compiling_source_code" >}}). +Before writing a submit file, you may need to compile your application. - [Ensure proper working directory for job output](#ensure-proper-working-directory-for-job-output) - [Creating a SLURM Submit File](#creating-a-slurm-submit-file) diff --git a/content/guides/submitting_jobs/submitting_an_openmp_job.md b/content/guides/submitting_jobs/submitting_an_openmp_job.md index 7c04168c..837f2c15 100644 --- a/content/guides/submitting_jobs/submitting_an_openmp_job.md +++ b/content/guides/submitting_jobs/submitting_an_openmp_job.md @@ -34,7 +34,7 @@ automatically match the `ntasks-per-node` value (in this example 16). Directions to compile OpenMP can be found on [Compiling an OpenMP Application] -({{< relref "/guides/running_applications/compiling_source_code/compiling_an_openmp_application" >}}). +({{< relref "/Applications/Using_Your_Own_Software/compiling_an_openmp_application" >}}). ### Further Documentation diff --git a/content/quickstarts/connecting/for_maclinux_users.md b/content/quickstarts/connecting/for_maclinux_users.md index f5fef28b..d50f41e9 100644 --- a/content/quickstarts/connecting/for_maclinux_users.md +++ b/content/quickstarts/connecting/for_maclinux_users.md @@ -5,7 +5,7 @@ weight = "22" +++ ##### Use of Duo two-factor authentication is **required** to access HCC resources. -##### Please see [Setting up and Using Duo]({{< relref "setting_up_and_using_duo" >}}). +##### Please see [Setting up and Using Duo]({{< relref "/Accounts/setting_up_and_using_duo" >}}). --- - [Access to HCC Supercomputers] (#access-to-hcc-supercomputers) - [File Transferring with HCC Supercomputers] (#file-transfering) diff --git a/content/quickstarts/connecting/for_windows_users.md b/content/quickstarts/connecting/for_windows_users.md index fb3f1a78..09494e91 100644 --- a/content/quickstarts/connecting/for_windows_users.md +++ b/content/quickstarts/connecting/for_windows_users.md @@ -5,7 +5,7 @@ weight = "20" +++ ##### Use of Duo two-factor authentication is **required** to access HCC resources. -##### Please see [Setting up and Using Duo]({{< relref "setting_up_and_using_duo" >}}). +##### Please see [Setting up and Using Duo]({{< relref "/Accounts/setting_up_and_using_duo" >}}). --- diff --git a/content/quickstarts/connecting/mobaxterm_windows.md b/content/quickstarts/connecting/mobaxterm_windows.md index 4e64a449..6a7c000a 100644 --- a/content/quickstarts/connecting/mobaxterm_windows.md +++ b/content/quickstarts/connecting/mobaxterm_windows.md @@ -5,7 +5,7 @@ weight = "22" +++ ##### Use of Duo two-factor authentication is **required** to access HCC resources. -##### Please see [Setting up and Using Duo]({{< relref "setting_up_and_using_duo" >}}). +##### Please see [Setting up and Using Duo]({{< relref "/Accounts/setting_up_and_using_duo" >}}). --- This quick start will help you configure your MobaXterm installation to work with HCC resources. @@ -76,4 +76,4 @@ In the Generator window, click `Generate` and move your mouse around in the `Key After the key is generated, go to the `Conversions` tab and select `Export OpenSSH key` and save it to your local machine. {{< figure src="/images/moba/exportssh.png" height="450" >}} -**Treat the private key file the same as you would a password. Keep your private key in a secure location and do not share it with anyone.** \ No newline at end of file +**Treat the private key file the same as you would a password. Keep your private key in a secure location and do not share it with anyone.** diff --git a/content/quickstarts/submitting_jobs.md b/content/quickstarts/submitting_jobs.md index e2ab2fa2..60f5f28c 100644 --- a/content/quickstarts/submitting_jobs.md +++ b/content/quickstarts/submitting_jobs.md @@ -11,8 +11,7 @@ must create a SLURM script that will run your processing. After submitting the job, SLURM will schedule your processing on an available worker node. -Before writing a submit file, you may need to -[compile your application]({{< relref "/guides/running_applications/compiling_source_code" >}}). +Before writing a submit file, you may need to compile your application. - [Ensure proper working directory for job output](#ensure-proper-working-directory-for-job-output) - [Creating a SLURM Submit File](#creating-a-slurm-submit-file) -- GitLab