====== 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. [(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. 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|}}