cisTEM is an image processing framework.
Loading the environment
cisTEM can be used through environment modules:
By default cisTEM suggests your home directory for project setup. Since it will contain all analysis files use your BeeGFS space as project directory.
Start the user interface by calling cisTEM on the command line.
Importing TIFF files
With the K3 camera the movies are most likely in LZW compressed TIFF format to save storage space and the file suffix is *.tiff.
cisTEM expects the file pattern *.tif for the movies import. So we make an import folder, link the original files and rename the links to this convention.
Now you can import the files in the cisTEM GUI.
Submitting to the DESY maxwell cluster
Now import the DESY/CSSB cluster profile. Go to Settings → Import and choose the following file:
You should now have a run profile called Maxwell Cluster which you can choose in your Actions.
The cluster usage works in 3 steps:
- The cisTEM user interface allocates cluster resources using salloc and runs the cisTEM manager on the first node
- The manager spawns its worker tasks by using srun inside the allocated resources
- When the manager is finished the maxwell allocation will be canceled automatically.
Changing the preset submission parameters
First look for free resources with the sinfo_detailed alias:
$ sinfo_detailed NODELIST PARTITION CPUS NODES NODES(A/I) AVAIL_FEATURES max-cssb[002-010] cssb 48 9 3/5 INTEL,Gold-6126,1536G max-cssbg[001-003] cssbgpu 40 3 3/0 INTEL,V4,E5-2640,GPU,P100,GPUx2,512G : max-xxxx[101-188] all 72 88 12/70 INTEL,Gold-6140,768G max-xxxx[020-099] all 80 80 28/52 INTEL,V4,E5-2698,512G :
Now you see that 5 of the CSSB nodes with each 48 cores are idle (NODES(A/I)) and can be used.
In cisTEM navigate to Settings → Run Profiles → Maxwell Cluster and change the Manager Command like (leave the rest of the line as it is):
-n: the amount of cores e.g. 5*48 = 240
-p: the maxwell queue/partition name
-C: available features like a specific processor for correct amount of cores or a specific memory. In case of doubt just take the whole feature string.
Then edit the No. Copies of the srun command to 239 (240 - 1 manager process) and do not forget to press the Save button.
Now the updated profile will be used to start new actions.
You can use the Run Profiles → Duplicate button to create a list of your favorite submission configurations.
Running cisTEM on a dedicated cluster node
The actions Align Movie and Find CTF execute special external programs which have connections problems on when submitting the jobs to the cluster. So its best to run these steps locally on one dedicated node. Compared to the other actions they are quite fast.
The following commands allocates a 48 core machine which will be referred inside cisTEM as Run Profile: Default Local (48).
$ salloc_cssb_cpu_node salloc: Granted job allocation 2310829 salloc: Waiting for resource configuration salloc: Nodes max-cssb006 are ready for job $ ssh max-cssb006 $ module load cistem $ cisTEM :
Once you are done quit cisTEM and free the resources by exiting the shell twice (one for exiting the node, the second for exiting the allocation):
$ exit Connection to max-cssb006 closed. $ exit salloc: Relinquishing job allocation 2310829 $
Or you can cancel your allocation by:
$ scancel 2310829
salloc_cssb_cpu_node is an alias defined in the global environment
Exporting and manipulating the cisTEM database
The main cisTEM database can exported, backuped etc. via SQLite.