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Commit 3dd7d919 authored by Natasha Pavlovikj's avatar Natasha Pavlovikj
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Add faq and upcate CS page

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...@@ -23,6 +23,8 @@ weight = "95" ...@@ -23,6 +23,8 @@ weight = "95"
- [I am graduating soon, what will happen with my HCC account?](#i-am-graduating-soon-what-will-happen-with-my-hcc-account) - [I am graduating soon, what will happen with my HCC account?](#i-am-graduating-soon-what-will-happen-with-my-hcc-account)
- [I need more resources than I can select with Open OnDemand Apps, can I do that?](#i-need-more-resources-than-i-can-select-with-open-ondemand-apps-can-i-do-that) - [I need more resources than I can select with Open OnDemand Apps, can I do that?](#i-need-more-resources-than-i-can-select-with-open-ondemand-apps-can-i-do-that)
- [How can I check which directories utilize the most storage on Swan?](#how-can-i-check-which-directories-utilize-the-most-storage-on-swan) - [How can I check which directories utilize the most storage on Swan?](#how-can-i-check-which-directories-utilize-the-most-storage-on-swan)
- [I want to create HCC account, but when I try to request one, I am getting the error "Your account email must match the email on record for this group". What should I do?](#i-want-to-create-hcc-account-but-when-i-try-to-request-one-i-am-getting-the-error-your-account-email-must-match-the-email-on-record-for-this-group-what-should-i-do)
- [I want to compress large directory with many files. How can I do that?](#i-want-to-compress-large-directory-with-many-files-how-can-i-do-that)
--- ---
...@@ -306,3 +308,24 @@ ncdu -f ncdu_output.txt ...@@ -306,3 +308,24 @@ ncdu -f ncdu_output.txt
Note that re-reading the filesystem to see changes in real time is not supported in this mode. After making changes (deleting/moving files), a new output file Note that re-reading the filesystem to see changes in real time is not supported in this mode. After making changes (deleting/moving files), a new output file
will need to be created and read by repeating the steps above. will need to be created and read by repeating the steps above.
#### I want to create HCC account, but when I try to request one, I am getting the error "Your account email must match the email on record for this group". What should I do?
This error message indicates that you have probably selected the *"I am the owner of this group and this account is for me."* checkbox when filling out the New User Request Form.
This checkbox should be selected only by the owner of the HCC group.
If you are not the owner of the HCC group, please do not select this checkbox and try re-submitting the form again.
#### I want to compress large directory with many files. How can I do that?
In general, we recommend using `zip` as the archive format as `zip` files keep an index of the files.
Moreover, `zip` files can be quickly indexed by the various `zip` tools, and allow extraction of all files or a subset of files.
To compress the directory named `input_folder` into `output.zip`, you can use:
{{< highlight batch >}}
zip -r output.zip input_folder/
{{< /highlight >}}
If you don't need to list and extract subsets of the archived data, we recommend using `tar` instead.
To compress the directory named `input_folder` into `output.tar.gz`, you can use:
{{< highlight batch >}}
tar zcf output.tar.gz input_folder/
{{< /highlight >}}
Depending on the size of the directory and number of files you want to compress, you can perform the compressing via an [Interactive Job]({{< relref "creating_an_interactive_job" >}}) or [SLURM job]({{< relref "submitting_jobs" >}}).
...@@ -114,6 +114,9 @@ If you want to test the CryoSPARC OOD App, you can use the [CryoSPARC Introducto ...@@ -114,6 +114,9 @@ If you want to test the CryoSPARC OOD App, you can use the [CryoSPARC Introducto
``` ```
- The *SLURM Job Name* of the CryoSPARC *"master"* process and the jobs that run on the `default` lane is always `ondemand/sys/dashboard/sys/bc_hcc_cryosparc/swan`. - The *SLURM Job Name* of the CryoSPARC *"master"* process and the jobs that run on the `default` lane is always `ondemand/sys/dashboard/sys/bc_hcc_cryosparc/swan`.
- The *SLURM Job Name* of the CryoSPARC jobs that run on the `swan` or `swan-highmem` lanes is always in the format `cryosparc_<project_uid>_<job_uid>`, where `<project_uid>` and `<job_uid>` are replaced with the CryoSPARC Project ID and CryoSPARC Job ID respectively. For example, if your CryoSPARC Project ID is 3, and your CryoSPARC Job ID is 187, the SLURM Job Name will be `cryosparc_P3_J187`. - The *SLURM Job Name* of the CryoSPARC jobs that run on the `swan` or `swan-highmem` lanes is always in the format `cryosparc_<project_uid>_<job_uid>`, where `<project_uid>` and `<job_uid>` are replaced with the CryoSPARC Project ID and CryoSPARC Job ID respectively. For example, if your CryoSPARC Project ID is 3, and your CryoSPARC Job ID is 187, the SLURM Job Name will be `cryosparc_P3_J187`.
- **I moved my CryoSPARC project directory to a different location on the cluster, and I can not access my project anymore.**
- To move CrypSPARC project directory from one location to another please archive, move and unarchive the project as explained in the [CryoSPARC documentation](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-data-management-in-cryosparc-v4.0+#use-case-moving-a-project-directory-from-one-storage-location-to-another).
- If moving the CrypSPARC project directory from one location to another as listed above is not working, you can try deleting the `cs.lock` file in the project directory of an inoperable instance as explained in the [CryoSPARC documentation](https://guide.cryosparc.com/setup-configuration-and-management/software-system-guides/guide-data-management-in-cryosparc-v4.0+#use-case-rescuing-a-project-from-an-inoperable-instance).
- **My CryoSPARC job failed and I don't know why.** - **My CryoSPARC job failed and I don't know why.**
- If your CryoSPARC job fails, it is highly likely that the requested memory was exceeded. You can check this with [seff or sacct]({{< relref "../submitting_jobs/monitoring_jobs/#monitoring-completed-jobs" >}}). - If your CryoSPARC job fails, it is highly likely that the requested memory was exceeded. You can check this with [seff or sacct]({{< relref "../submitting_jobs/monitoring_jobs/#monitoring-completed-jobs" >}}).
- If you use the `default` lane, please increase the value in the **Requested RAM in GBs** field from the CryoSPARC Open OnDemand Form. - If you use the `default` lane, please increase the value in the **Requested RAM in GBs** field from the CryoSPARC Open OnDemand Form.
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