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====== Guide to using CryoSPARC on DARWIN ======

CryoSPARC is an advanced software platform designed for cryo-electron microscopy (cryo-EM), playing a crucial role in research and drug discovery processes.

This document provides the user manual for CryoSPARC v4.3.1, which has been installed on DARWIN.

====== Start CryoSPARC master ======

CryoSPARC will be run in a screen mode at one of GPU node ( r1t00 with tesla_t4:1 in this example ).
You need to remember which login node you are.

<code bash>
[(workgroup:user)@login01 ~]$ screen
[(workgroup:user)@login01 ~]$ salloc -p idle --gpus=tesla_t4:1 -N1 -n1 --cpus-per-task=4 --mem=200G --time=01:00:00
[(workgroup:user)@r1t00 ~]$ export CRYOSPARC_INSTANCE_DIR=$TMPDIR
[(workgroup:user)@r1t00 ~]$ vpkg_require cryosparc/4.3.1
[(workgroup:user)@r1t00 ~]$ cryosparcm start  # this start cryosparc_master and set up environment.
</code>

You will see below if cryoSPARC runs successfully. Please remember your username, password, and port name, as they are printed out.

{{:technical:recipes:fig1.jpg?600|}}


====== Start CryoSPARC workstation and access web interface ======

{{:technical:recipes:fig2.jpg?800|}}

====== Start new project or attach previous project ======

{{:technical:recipes:fig3.jpg?800|}}

====== Attach previous project ======

{{:technical:recipes:fig4.jpg?800|}}

====== Set number of GPU ======

{{:technical:recipes:fig5.jpg?800|}}


====== Queue the job ======
Clicking the "Queue" button will load this job, and Slurm will queue the job on the GPU node.

{{:technical:recipes:fig6.jpg?800|}}

====== Monitor job status ======

{{:technical:recipes:fig7.jpg?800|}}

====== CPU job ======

You can also run CPU jobs in current setting.

{{:technical:recipes:fig8.jpg?800|}}