[3dem] Relion Benchmarks for NVIDIA RTX 2080

James Montantes james.montantes at exxactcorp.com
Mon Mar 4 09:36:42 PST 2019 

Dear Relion users,

Exxact Corporation has performed a series of Relion 3.0 benchmarks utilizing NVIDIA RTX 2080 GPUs. These were ran using CUDA9.2 and CUDA 10.0 See below for our results.  We plan to release more benchmarks in the future.

Version: Relion 3.0 Git version as of Oct 21st, 2018
System: Exxact Relion Cryo-em Workstation<https://www.exxactcorp.com/Relion-for-Cryo-EM-Solutions?utm_source=web%20referral&utm_medium=backlink&utm_campaign=Relion%20User%20Mailing%20List&utm_term=3dem&utm_content=rtx%202080%20benchmark> 2 x Intel Xeon Scalable Silver 4114 CPUs,  4 x RTX2080, 2 x 2TB SSD Raid 0, NVIDIA Driver Version: 410.57

Benchmark Set 1 - from https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Benchmarks_%26_computer_hardware
wget ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion_benchmark.tar.gz .
tar -zxf relion_benchmark.tar.gz


SUMMARY         CUDA 9.2 sm6.1(hrs)      CUDA 10.0 sm7.5(hrs)
1 x RTX2080                        5.24                                        5.79
1 x RTX2080 Preread        5.10                                         5.22
2 x RTX2080                        3.00                                        3.04
2 x RTX2080 Preread        2.68                                        2.69
4 x RTX2080                        2.00                                        2.05


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COMMANDS

3D Classification
Base Command
mpirun -n XXX `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d


CUDA 9.2, sm6.1  (Default Relion 3.0beta2 build)
### 1 x RTX2080 ###
mpirun -n 2 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --scratch_dir /scr --gpu 0 --pool 100 --dont_combine_weights_via_disc --j 6

5.24 HOURS

### 1 x 2080 pre-read ###
mpirun -n 2 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --preread_images --gpu 0 --pool 100 --dont_combine_weights_via_disc --j 6

5.10 HOURS

### 2 x RTX2080 ###
mpirun -n 3 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --scratch_dir /scr --gpu 0:1 --pool 100 --dont_combine_weights_via_disc --j 6

3.00 HOURS

### 2 x 2080 pre-read ###
mpirun -n 3 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --preread_images --gpu 0:1 --pool 100 --dont_combine_weights_via_disc --j 6

2.68 HOURS

### 4 x 2080 ###
mpirun -n 5 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --scratch_dir /scr --gpu 0:1:2:3 --pool 100 --dont_combine_weights_via_disc --j 6

2.00 HOURS


CUDA 10.0, sm7.5
### 1 x 2080 ###
mpirun -n 2 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --scratch_dir /scr --gpu 0 --pool 100 --dont_combine_weights_via_disc --j 6

5.79 HOURS


### 1 x 2080 pre-read ###
mpirun -n 2 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --preread_images --gpu 0 --pool 100 --dont_combine_weights_via_disc --j 6

5.22 HOURS


### 2 x 2080 ###
mpirun -n 3 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --scratch_dir /scr --gpu 0:1 --pool 100 --dont_combine_weights_via_disc --j 6

3.04 HOURS

### 2 x 2080 pre-read ###
mpirun -n 3 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --preread_images --gpu 0:1 --pool 100 --dont_combine_weights_via_disc --j 6

2.69 HOURS

### 4 x 2080 ###
mpirun -n 5 `which relion_refine_mpi` --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --scratch_dir /scr --gpu 0:1:2:3 --pool 100 --dont_combine_weights_via_disc --j 6

2.05 HOURS


Best Regards,


James Montantes
Ph 510.226.7366 x319 | M 408.761.3071 | Fax 510.226.7367
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Exxact Corporation | www.exxactcorp.com<https://www.exxactcorp.com/Relion-for-Cryo-EM-Solutions?utm_source=web%20referral&utm_medium=backlink&utm_campaign=Relion%20User%20Mailing%20List&utm_term=3dem&utm_content=rtx%202080%20benchmark>
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