[gmx-users] (no) superlinear Scaling on Opterons
As a little update I want to share the following numbers. Maybe they are useful for somebody, who wants to configure his next cluster. :-) Davids suggestion with the -shuffle hit exactly the crucial point. Thanks. cores ns/day (speedup) - -shuffle-shuffle -sort 010.289 0.285 0.286 020.487 (1.69) 0.567 (1.99) 0.667 (2.33) 040.768 (2.66) 1.122 (3.94) 1.313 (4.59) 081.330 (4.60) 2.087 (7.32) 2.504 (8.76) 121.776 (6.15) 2.861 (10.04) 3.429 (11.99) 162.137 (7.39) 3.600 (12.63) 4.320 (15.10) 202.550 (8.82) 3.982 (13.97) 4.881 (17.07) Gromacs-3.3.1 compiled with gcc mvapich2-9.8-13 rockscluststers-4.3 dual AMD Opteron 2218 (2.6 GHz) (4 cores per node) Mellanox IB adapter -- Dr. Jens Krueger Institute of Biophotonics School of Biomedical Science and Engineering National Yang-Ming University 155, Li-Non St., Sec. 2 Taipei, 112, Taiwan (R.O.C.) mobile: 0921452940 http://www.ym.edu.tw/~wfischer begin:vcard fn;quoted-printable:=E5=8F=A4=E7=A0=94=E6=80=9D n;quoted-printable:Kr=C3=BCger;Jens x-mozilla-html:FALSE version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no) superlinear Scaling on Opterons
Jens Krueger wrote: > Hello, > > there have been multiple reports on the list of superlinear scaling on > AMD Opterons of the 200 series. > > We have recently purchased a small cluster with the following > configuration for each compute node: > - 2x Opteron 2218 (4 cores per node) > - 2 GB RAM > - Supermicro H8DM8 mainboard > - Mellanox PCI-E x8 Infiniband (running with OFED-1.2 and mvapich2) > - Rockscluster 4.3 > - Gromacs-3.3.1 try grompp -shuffle > > > For the DPPC benchmark we achieve the following numbers: > > cores ns/day speedup > > 01 0.289 1.00 > 02 0.487 1.69 > 04 0.768 2.66 > 08 1.330 4.60 > 12 1.776 6.15 > 16 2.137 7.39 > 20 2.550 8.82 > > > Compared to the benchmark section > (http://www.gromacs.org/content/view/25/38/) and other published data > (e.g. http://biowulf.nih.gov/apps/gromacs/bench-3.3.1.html) the > performance drops to soon when using more cpu's. In fact we are far away > from superlinear scaling and the performance on 20 cores is only half as > good as on the biowulf cluster. > We systematically checked the hardware and tried different compiler and > MPI, all giving no or only minor improvement. > > Has anybody hands on an Opteron cluster with cpu's from the 2000 series? > It would be of immense value for us to get reference data from a similar > machine. > > > Thanks, > > Jens > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no) superlinear Scaling on Opterons
Hello, there have been multiple reports on the list of superlinear scaling on AMD Opterons of the 200 series. We have recently purchased a small cluster with the following configuration for each compute node: - 2x Opteron 2218 (4 cores per node) - 2 GB RAM - Supermicro H8DM8 mainboard - Mellanox PCI-E x8 Infiniband (running with OFED-1.2 and mvapich2) - Rockscluster 4.3 - Gromacs-3.3.1 For the DPPC benchmark we achieve the following numbers: cores ns/day speedup 01 0.289 1.00 02 0.487 1.69 04 0.768 2.66 08 1.330 4.60 12 1.776 6.15 16 2.137 7.39 20 2.550 8.82 Compared to the benchmark section (http://www.gromacs.org/content/view/25/38/) and other published data (e.g. http://biowulf.nih.gov/apps/gromacs/bench-3.3.1.html) the performance drops to soon when using more cpu's. In fact we are far away from superlinear scaling and the performance on 20 cores is only half as good as on the biowulf cluster. We systematically checked the hardware and tried different compiler and MPI, all giving no or only minor improvement. Has anybody hands on an Opteron cluster with cpu's from the 2000 series? It would be of immense value for us to get reference data from a similar machine. Thanks, Jens -- Dr. Jens Krueger Institute of Biophotonics School of Biomedical Science and Engineering National Yang-Ming University 155, Li-Non St., Sec. 2 Taipei, 112, Taiwan (R.O.C.) mobile: 0921452940 http://www.ym.edu.tw/~wfischer begin:vcard fn;quoted-printable:=E5=8F=A4=E7=A0=94=E6=80=9D n;quoted-printable:Kr=C3=BCger;Jens x-mozilla-html:FALSE version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
