[3dem] Relion Benchmarks for NVIDIA RTX 2080

Ragan, Tj (Dr.) tj.ragan at leicester.ac.uk
Thu Mar 21 02:48:25 PDT 2019 

Hi James,

Thanks for the information.  We’ve noticed that for GTX1080 and above (1080, 1080Ti, etc,…) CPU performance can have a significant impact on benchmark time.  Can you give any sense of the cpu utilisation during the runs?

Thanks,

Dr. T.J. Ragan

Senior Research Computation Officer
Leicester Institute of Structural and Chemical Biology
University of Leicester, University Road, Leicester LE1 7RH, UK

t: +44 (0)116 223 1287
e: TJ.Ragan at leicester.ac.uk<mailto:tjr22 at leicester.ac.uk>
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On 4 Mar 2019, at 17:36, James Montantes <james.montantes at exxactcorp.com<mailto:james.montantes at exxactcorp.com>> wrote:

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://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.exxactcorp.com%2FRelion-for-Cryo-EM-Solutions%3Futm_source%3Dweb%2520referral%26utm_medium%3Dbacklink%26utm_campaign%3DRelion%2520User%2520Mailing%2520List%26utm_term%3D3dem%26utm_content%3Drtx%25202080%2520benchmark&data=02%7C01%7Ctj.ragan%40leicester.ac.uk%7Cb4dc00a320a9446e1d9908d6a0cbf1ac%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636873195136060015&sdata=R1oUu54qzot%2FS%2FQM0f2zP56WcuNGyJPUJRAsSzSPeXM%3D&reserved=0> 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<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww2.mrc-lmb.cam.ac.uk%2Frelion%2Findex.php%3Ftitle%3DBenchmarks_%2526_computer_hardware&data=02%7C01%7Ctj.ragan%40leicester.ac.uk%7Cb4dc00a320a9446e1d9908d6a0cbf1ac%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636873195136060015&sdata=7nUlfiJAPcVGn0QUaiBPM4M710sD3xbFP5arz3%2Fj%2BYY%3D&reserved=0>
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<tel:510.226.7366;319> | M 408.761.3071<tel:408.761.3071> | Fax 510.226.7367<tel:510.226.7367>
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