Merge branch 'cs/highmem' into 'master'

Add cryosparc highmem notes.

See merge request !414

content/open_ondemand/cryosparc_interactive_app.md

@@ -38,8 +38,9 @@ share a license ID will cause jobs to fail.  If you have multiple CryoSPARC sess
 - In addition to the basic fields, there are two advanced settings you can set under the _Show advanced settings..._ checkbox in the CryoSPARC OOD Form:
     - **CryoSPARC session path**: The default location of the CryoSPARC database and configuration files is `$WORK/cryosparc`. You can change this location using the *Select Path* button. You can select any of the [available file systems on Swan]({{< relref "../handling_data/data_storage/" >}}) aside from the `$HOME` filesystem.  _We do not recommend using `$HOME` for the session folder_.  Please note that each file system has its own advantages and disadvantages.
     - **Specify partition for CryoSPARC GPU jobs**: This parameter defines the GPU partition used for the GPU CryoSPARC jobs submitted to the cluster via SLURM through the interactive Desktop. If not specified, by default, these jobs are submitted to the general `gpu` partition. If you have access to a priority access partition with GPU resources, you may specify that partition here to reduce queue time.
+    - **Highmem factor**:  This parameter defines the multiplicative factor used to increase the memory (RAM) request for the `highmem` cluster lane (described below).  That is, the preset memory values within CryoSPARC for each job type will be multiplied by this factor.  Certain input sets combined with particular options may require more memory than the preset CryoSPARC values, and will otherwise fail.  Use this value in combination with using the `highmem` cluster lane to increase the requested memory on specified jobs to allow them to complete successfully.  The valid range are integer values from 1 to 10.
 
-{{< figure src="/images/OOD_CS_advanced_settings.png" width="30%" height="30%" class="img-border">}}
+{{< figure src="/images/OOD_CS_advanced_settings.png" width="40%"  class="img-border">}}
 
 After selecting the needed resources and pressing "Launch", the CryoSPARC App will start. 
 Depending on the requested resources, this process should take a few minutes.  
@@ -49,7 +50,7 @@ Once the session is ready, you will see a "Launch CryoSPARC:Swan" button.
 This button will start the CryoSPARC interactive Desktop and open the Firefox browser to the CryoSPARC login page.
 Please use the provided email and password to login to the CryoSPARC Firefox session and start using CryoSPARC.
 
-{{< figure src="/images/OOD_CS_info_card.png" width="50%" height="50%" class="img-border">}}
+{{< figure src="/images/OOD_CS_info_card.png" width="60%" height="60%" class="img-border">}}
 
 
 #### CryoSPARC SLURM jobs 
@@ -57,8 +58,9 @@ Once you create CryoSPARC Job and are ready to `Queue` it, you can select one of
 
 {{< figure src="/images/OOD_CS_job_queue.png" width="30%" height="30%" class="img-border">}}
 
-- `Lane default (node)` uses the current compute node to run the job on. This job will use the resources and partition selected in the CryoSPARC OOD Form. This will usually be a modest amount of resources (1-2 cores and 8GBs of RAM), so the `default lane` should only be used for short-running, light tasks.
-- `Lane swan (cluster)` uses SLURM to submit the CryoSPARC job to the cluster. These jobs have a maximum runtime of 7 days, use the number of CPUs or GPUs you have specified when creating the CryoSPARC job and use the partition you have selected under the _Show advanced settings..._ checkbox in the CryoSPARC OOD Form. The submitted CryoSPARC jobs will run in the background, and depending on the requested resources and partition utilization, sometimes it may take a bit before they start running. The `swan` lane should be used for the majority of the computing tasks.
+- Lane `default (node)` uses the current compute node to run the job on. This job will use the resources and partition selected in the CryoSPARC OOD Form. This will usually be a modest amount of resources (1-2 cores and 8GBs of RAM), so the `default lane` should only be used for short-running, light tasks.
+- Lane `swan (cluster)` uses SLURM to submit the CryoSPARC job to the cluster. These jobs have a maximum runtime of 7 days, use the number of CPUs or GPUs you have specified when creating the CryoSPARC job and use the partition you have selected under the _Show advanced settings..._ checkbox in the CryoSPARC OOD Form. The submitted CryoSPARC jobs will run in the background, and depending on the requested resources and partition utilization, sometimes it may take a bit before they start running. The `swan` lane should be used for the majority of the computing tasks.
+- Lane `swan-highmem (cluster)` is otherwise identical to the `swan` lane, but increases the amount of memory (RAM) requested by a constant factor.  Certain jobs may require more memory than the preset values within CryoSPARC.  This lane can be used for jobs that will otherwise fail in the standard `swan` lane due to insufficient memory.  The default is to multiply the preset CryoSPARC values by a factor of 4, but this factor may be changed when the CryoSPARC app is launched under advanced settings.  _Using this lane when it is not needed will result in longer queue times._
 
 Please note that the _"master"_ process should be running while the submitted CryoSPARC jobs are queued and running.