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Hi James,
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<div class="">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?<br class="">
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Thanks,<br class="Apple-interchange-newline">
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<b class="">Dr. T.J. Ragan</b><br class="">
<br class="">
Senior Research Computation Officer<br class="">
Leicester Institute of Structural and Chemical Biology<br class="">
University of Leicester, University Road, Leicester LE1 7RH, UK<br class="">
<br class="">
<span style="font-weight: bold; color: rgb(187, 0, 0);" class="">t:</span><span class="Apple-converted-space"> </span>+44 (0)116 223 1287<br class="">
<span style="font-weight: bold; color: rgb(187, 0, 0);" class="">e:</span><span class="Apple-converted-space"> </span><a href="mailto:tjr22@leicester.ac.uk" class="">TJ.Ragan@leicester.ac.uk</a><br class="">
<span style="font-weight: bold; color: rgb(187, 0, 0);" class="">w:</span><a href="http://www.le.ac.uk/liscb" class=""><span class="Apple-converted-space"> </span>www.le.ac.uk/liscb</a><br class="">
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<img src="https://www2.le.ac.uk/++resource++leicester.plonetheme.images/uollogo.png" alt="University of Leicester Logo" hspace="20" style="float: left; margin: 10px 0px;" class=""><img src="https://le.ac.uk/~/media/uol/images/graphics/logos/athena-swan-silver-award.jpg" alt="Athena Swan Silver Award" height="60" hspace="20" style="float: left;" class=""><br class="">
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<blockquote type="cite" class="">
<div class="">On 4 Mar 2019, at 17:36, James Montantes <<a href="mailto:james.montantes@exxactcorp.com" class="">james.montantes@exxactcorp.com</a>> wrote:</div>
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Dear Relion users,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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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. <o:p class=""></o:p></div>
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<b class=""><o:p class=""> </o:p></b></div>
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<b class="">Version:</b><span class="Apple-converted-space"> </span>Relion 3.0 Git version as of Oct 21<sup class="">st</sup>, 2018<o:p class=""></o:p></div>
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<b class="">System:</b><span class="Apple-converted-space"> </span><a href="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" originalsrc="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" shash="KOYCUwy+9NW+I/PKOcSn8idAJBZ0g83EoFrk7hi7Vjml1D2ToQOP8yWeBLDf3HXsyltQ6yzymeSgzIQtHJsguMa4bL8b94KontMV/zj3WQj5i8izO7HZeU4xHnVu+I/bwf+r3yXcHy+DWqzzUuluffs4U15dgP3Gn9esIFjZNSs=" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">Exxact
Relion Cryo-em Workstation</a><span class="Apple-converted-space"> </span>2 x Intel Xeon Scalable Silver 4114 CPUs, 4 x RTX2080, 2 x 2TB SSD Raid 0, NVIDIA Driver Version: 410.57 <o:p class=""></o:p></div>
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<b class="">Benchmark Set 1</b><span class="Apple-converted-space"> </span>- from<span class="Apple-converted-space"> </span><a href="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" originalsrc="https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Benchmarks_%26_computer_hardware" shash="hrjyVJ4dqaioCYxcZ05W6bLLyqA8UE3iGZ93cXgyLdmcq+xmPnibEzcwkYJi1HI1EXTyYi87tvms3Aw8kX0Qg5Qbjz9XUxoJAewIPvG98bvFvZ0kyC5FLQQje9Pg05vgBPgssU6D57wzqep/Iq0O77g6TlySawHcr9N0Y7g+CE8=" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Benchmarks_%26_computer_hardware</a><o:p class=""></o:p></div>
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wget<span class="Apple-converted-space"> </span><a href="ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion_benchmark.tar.gz" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion_benchmark.tar.gz</a><span class="Apple-converted-space"> </span>.<o:p class=""></o:p></div>
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tar -zxf relion_benchmark.tar.gz<o:p class=""></o:p></div>
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<b class="">SUMMARY CUDA 9.2 sm6.1(hrs) CUDA 10.0 sm7.5(hrs)<o:p class=""></o:p></b></div>
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1 x RTX2080 5.24 5.79<o:p class=""></o:p></div>
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1 x RTX2080 Preread 5.10 5.22<o:p class=""></o:p></div>
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2 x RTX2080 3.00 3.04<o:p class=""></o:p></div>
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2 x RTX2080 Preread 2.68 2.69<o:p class=""></o:p></div>
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4 x RTX2080 2.00 2.05<o:p class=""></o:p></div>
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<span id="cid:image001.png@01D4D26C.12DF9310"><image001.png></span><o:p class=""></o:p></div>
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<b class="">COMMANDS<o:p class=""></o:p></b></div>
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<b class="">3D Classification<o:p class=""></o:p></b></div>
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Base Command<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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<b class="">CUDA 9.2, sm6.1 (Default Relion 3.0beta2 build)<o:p class=""></o:p></b></div>
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### 1 x RTX2080 ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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5.24 HOURS<o:p class=""></o:p></div>
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### 1 x 2080 pre-read ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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5.10 HOURS<o:p class=""></o:p></div>
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### 2 x RTX2080 ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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3.00 HOURS<o:p class=""></o:p></div>
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### 2 x 2080 pre-read ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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2.68 HOURS<o:p class=""></o:p></div>
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### 4 x 2080 ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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2.00 HOURS<o:p class=""></o:p></div>
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<b class="">CUDA 10.0, sm7.5<o:p class=""></o:p></b></div>
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### 1 x 2080 ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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5.79 HOURS<o:p class=""></o:p></div>
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### 1 x 2080 pre-read ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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5.22 HOURS<o:p class=""></o:p></div>
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### 2 x 2080 ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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3.04 HOURS<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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### 2 x 2080 pre-read ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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2.69 HOURS<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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### 4 x 2080 ###<o:p class=""></o:p></div>
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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<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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2.05 HOURS<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<o:p class=""> </o:p></div>
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Best Regards,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<b class=""><span style="color: rgb(1, 89, 145);" class="">James Montantes<span class="Apple-converted-space"> </span></span></b><span style="" class=""><o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 10pt; color: rgb(64, 64, 64);" class="">Ph<span class="Apple-converted-space"> </span></span></b><span style="font-size: 10pt; color: rgb(64, 64, 64);" class=""><a href="tel:510.226.7366;319" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">510.226.7366
x319</a><span class="Apple-converted-space"> </span>|<b class=""><span class="Apple-converted-space"> </span>M<span class="Apple-converted-space"> </span></b><a href="tel:408.761.3071" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">408.761.3071</a><b class=""><span class="Apple-converted-space"> </span></b>|<b class=""><span class="Apple-converted-space"> </span>Fax</b> <a href="tel:510.226.7367" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">510.226.7367</a></span><span style="" class=""><o:p class=""></o:p></span></div>
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