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Thanks to Loic for writing the majority of this. Last editted 202107.

Access

*****If you have not accessed since the IT chaos in February, or you are a new user, you must contact bmrc-help to request a token. If you are a new user of bmrc, you will need to provide your university card number and PI (cc'd in) to get a rescomp account at the same time.*****
1. Connect to VPN, either university or MSD.
2. Open a local terminal and type the following:
ssh -N -L 39000:cryosparc.hpc.in.bmrc.ox.ac.uk:39000 -f -N hmed@rescomp1.well.ox.ac.uk
If you wish to access the live version, please type 39006 instead of 39000. 
If the connection is successful, you will not get a notification/error message (basically silent consent).
3. Go to your web browser (preferable chrome) and type in the following address to access the CryoSPARC UI:
http://localhost:39000/
or, in the case of a live connection,
http://localhost:39006/
You should now be able to see the webserver.
Note that the 39000 connection hangs on a regular basis for a still unknown reason. If you are able to load 39006 fine, then please contact emsupport and either Helen or Loic will reset the webapp.

Using Cryosparc

The documentation available online is quite straightforward, and newbies are encouraged to read this.

Creating Projects

Your datasets may be grouped into 'project's, the top-level divider in cryosparc. To create a project, you click on the suitcase located on the left of project tab, and then click on the "+" button (this is, rather unhelpfully, not abundantly obvious...try to look along the same level as the suitcase, but a bit further to the right).

A window pop-up and the software ask you for a name and a directory. Choose a name and then you click on the folder icon.

Another window pop-up, and in the path tab there is "$HOME" written. Here you have to change the path to your well directory.

Importing Data

 

Every time you want to create a folder or import data it is better to provide a full path like the following example:

/gpfs2/well/strubi/user/...
You also need to change the permissions to allow CryoSPARC V2.x to be able to write into 
your well folder. You can do that by sshing into rescomp1/2, belmont or compg000.

cd /gpfs2/well/strubi/<username>

chmod 775 "new_folder_name"

(your folder should appear in green now, which signify that the permissions are ok).

This needs to be repeated for every subfolder included in the path where you want to create the cryosparc directory.

When the permissions have been given to cryosparc, you can go back to google chrome, in the project directory path you enter: /gpfs2/well/strubi/”user_name”/”folder_of_interest”/

NOTE! When you create a project in CryoSPARC V2.x, it will automatically create a folder with the corresponding project number, like "P1" and so creating subfolders for cryosparc projects is arguably not particularly useful.

Further steps

Time to get busy processing!

CryoSPARC V2.x provides software for the full processing pipeline; from raw movies to a final refined structure. For the following steps of the processing you can have a look of the official user guide: https://cryosparc.com/docs/reference/general/

Job submission process

Jobs are automagically submitted to the cluster. By default, the CPUs and the GPU located on the compG001 node will be used first and then the CPUs and the GPUs on the compG000 node will be used if the resources on the compG001 node are not available. With the current capacity of the cluster, up to 5 jobs can be run in parallel. Each node is connected to its own 1TB SSD cache drive that will automatically be used by default when you will submit jobs.

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Useful FAQs

A few things that have cropped up on the ccpem mailing list.

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1. May 2019.

After a couple of 2d and 3D steps in cryosparc, particles were imported back into relion, re-extracted, then 2d, 3d classified followed by creation of an initial model. However when running 3D refinement, relion crashed immediately. see error below.

in: /home/bio21em1/relion/src/exp_model.cpp, line 414

in: /home/bio21em1/relion/src/exp_model.cpp, line 414

in: /home/bio21em1/relion/src/exp_model.cpp, line 414
in: /home/bio21em1/relion/src/exp_model.cpp, line 414
in: /home/bio21em1/relion/src/exp_model.cpp, line 414
=== Backtrace  ===
/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]
/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]
/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]
/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]
/usr/local/bin/relion_refine_mpi() [0x42d409]
==================
ERROR:
ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.
=== Backtrace  ===
/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]
/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]
/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]
/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]
/usr/local/bin/relion_refine_mpi() [0x42d409]
==================
ERROR:
ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.
=== Backtrace  ===
/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]
/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]
/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]
/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]
/usr/local/bin/relion_refine_mpi() [0x42d409]
==================
ERROR:
ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.
=== Backtrace  ===
/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]
/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]
/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]
/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]
/usr/local/bin/relion_refine_mpi() [0x42d409]
==================
ERROR:
ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.
=== Backtrace  ===
/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]
/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]
/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]
/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]
/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]
/usr/local/bin/relion_refine_mpi() [0x42d409]
==================
ERROR:
ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.
[odin:158859] 4 more processes have sent help message help-mpi-api.txt / mpi-abort
[odin:158859] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

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SOLUTION: Delete the column ?_rlnRandomSubset #19? carried over from cryosparc.

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