[gmx-users] intel grompp with pathscale mdrun
Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask because I can only compile mdrun with the pathscale compiler because make install hangs while make install-mdrun works fine. make install is hanging on making g_rms.o as previously posted: http://lists.gromacs.org/pipermail/gmx-users/2011-December/066682.html . I tried this again with the 4.0.12.1 version of the compiler and have the same result. Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] intel grompp with pathscale mdrun
Should work just fine. As far as compilation hanging...maybe hand-compile that .o with less aggressive optimization flags, then try make again? MZ On Tue, Dec 6, 2011 at 2:20 PM, Chris Neale chris.ne...@utoronto.ca wrote: Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask because I can only compile mdrun with the pathscale compiler because make install hangs while make install-mdrun works fine. make install is hanging on making g_rms.o as previously posted: http://lists.gromacs.org/pipermail/gmx-users/2011-December/066682.html . I tried this again with the 4.0.12.1 version of the compiler and have the same result. Thank you, Chris. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] intel grompp with pathscale mdrun
Thank you Matthew. your suggestion for the hanging .o compilation sounds good. I didn't try it because in the end the intel compiler produced the fastest executables in any event. For those interested, here are my benchmarking speeds for one of my simulation systems (270,000 atoms) on 48 cores of an AMD magny-cours cluster at 2.1 GHz. I have no idea why the intel icc compiler outperforms the pathscale and pgi compilers on AMD computers, but that seems to be the case. intel icc 12.0.5.220 = 3.733 ns/day intel icc 12.0.5.220 with -msse3 = 3.765 ns/day pathscale 4.0.12.1 = 3.467 ns/day pgi 11.8 = 3.092 ns/day pgi 11.8 with -tp istanbul -fast = 3.156 ns/day Again, thank you, Chris. -- original message -- As far as compilation hanging...maybe hand-compile that .o with less aggressive optimization flags, then try make again? MZ On Tue, Dec 6, 2011 at 2:20 PM, Chris Neale chris.neale at utoronto.ca wrote: Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask because I can only compile mdrun with the pathscale compiler because make install hangs while make install-mdrun works fine. make install is hanging on making g_rms.o as previously posted: http://lists.gromacs.org/pipermail/gmx-users/2011-December/066682.html . I tried this again with the 4.0.12.1 version of the compiler and have the same result. Thank you, Chris. -- gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Previous message: [gmx-users] intel grompp with pathscale mdrun Next message: [gmx-users] dihedral format in top file? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] intel grompp with pathscale mdrun
Hi Chris, You can also try with open64. Let us know in case you face any issues in compiling and running. We will be glad to help you. Thanks Anupama -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca Sent: Wednesday, December 07, 2011 8:15 AM To: gmx-users@gromacs.org Subject: [gmx-users] intel grompp with pathscale mdrun Thank you Matthew. your suggestion for the hanging .o compilation sounds good. I didn't try it because in the end the intel compiler produced the fastest executables in any event. For those interested, here are my benchmarking speeds for one of my simulation systems (270,000 atoms) on 48 cores of an AMD magny-cours cluster at 2.1 GHz. I have no idea why the intel icc compiler outperforms the pathscale and pgi compilers on AMD computers, but that seems to be the case. intel icc 12.0.5.220 = 3.733 ns/day intel icc 12.0.5.220 with -msse3 = 3.765 ns/day pathscale 4.0.12.1 = 3.467 ns/day pgi 11.8 = 3.092 ns/day pgi 11.8 with -tp istanbul -fast = 3.156 ns/day Again, thank you, Chris. -- original message -- As far as compilation hanging...maybe hand-compile that .o with less aggressive optimization flags, then try make again? MZ On Tue, Dec 6, 2011 at 2:20 PM, Chris Neale chris.neale at utoronto.ca wrote: Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask because I can only compile mdrun with the pathscale compiler because make install hangs while make install-mdrun works fine. make install is hanging on making g_rms.o as previously posted: http://lists.gromacs.org/pipermail/gmx-users/2011-December/066682.html . I tried this again with the 4.0.12.1 version of the compiler and have the same result. Thank you, Chris. -- gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Previous message: [gmx-users] intel grompp with pathscale mdrun Next message: [gmx-users] dihedral format in top file? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
