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--- technical:recipes:cryosparc [2024-11-08 08:30] – created bkang
+++ technical:recipes:cryosparc [2024-11-08 13:49] (current) – [CPU job] bkang
@@ Line 1: / Line 1: @@
-====== Guide to use CryoSPARC on DARWIN ======
+====== Guide to using CryoSPARC on DARWIN ======
-Over the years the VASP build system has changed significantly.  In version 6, the use of the ''makefile.include'' to encapsulate machine-specific options has improved the portability and reproducibility of the build procedures.
+CryoSPARC is an advanced software platform designed for cryo-electron microscopy (cryo-EM), playing a crucial role in research and drug discovery processes.
-The build procedure outlined herein uses Open MPI on top of the Intel compiler suite in conjunction with CUDA 11 with the target executable destined for use on Volta- and Turing-generation NVIDIA devices.
+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|}}