Re: [gmx-users] GROMACS-4.5-beta1 is out!
Hello I tried the Gromacs 4.5 beta. However, my MPI mdrun died. Here it is the output. The Gromacs-4.0.7 work fine for the same system. It is protein in water system. There are about 22000 atoms. *** Will use 9 particle-particle and 7 PME only nodes This is a guess, check the performance at the end of the log file Making 1D domain decomposition 9 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 rank 9 in job 1 hpc-8-16.local_53455 caused collective abort of all ranks exit status of rank 9: killed by signal 9 dawei On Fri, Jul 30, 2010 at 3:20 PM, Rossen Apostolov rossen.aposto...@cbr.su.se wrote: After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is out! It is full of many new and exciting features, please try them out! If something is not working as expected, please send a mail or file a bugzilla report. For developers: there is a new branch for stable releases called release-4-5-patches. Bugfixes should be applied there *first*, and if needed, merged from that branch into the master after the fix. See http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more information. New features: 2D decomposition support for PME: improved load balancing with up to 40% overall performance improvement for large systems. Memory usage is improved for very large systems, allowing simulations of 100 million atoms. Running on multi-core nodes now automatically uses threads for domain decomposition through the built-in threaded MPI library GPU computing support Check-pointing is made more secure:MD5sum are used to verify that all files are correctly in-place before a simulation is appended. Output file appending at continuation is turned on by default Full Cmake support. Autoconf/automake will be deprecated after the final 4.5 release! Full support for 7 AMBER force fields Support for CHARMM27, including cmap for dihedrals Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. Support for nucleic acid simulations Support for Velocity-Verlet integrators for reversible T- and P-coupling; MTTK pressure control integrators; Nose-Hoover chains Support for Bennett acceptance ratio (BAR) free energy calculations Decoupling group setup for free energy File formats: All GROMACS tools can now read any VMD supported trajectory format, without converting trajectory first. (VMD is required) g_rdf was a little bit enhanced that structure factors can be calculated for any system, by supplying the necessary data via sfactor.dat. Most of the common atomtypes are already contained, but everybody who needs more freedom can enhance the table Library support for dynamic index groups based on textual selections (experimental feature). See the tool g_select, the included template.c, or Doxygen documentation for information on how to write analysis tools using the library. Existing tools have not (yet) been converted. g_tune_pme: For a given number of processes or threads this tool systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It also checks whether performance can be enhanced by shifting load between the real and the reciprocal space part of the Ewald sum. g_membed: a very convenient utility for embedding membrane proteins into equilibrated lipid bilayers Big thanks to all developers, contributors and users! -- gmx-users mailing list gmx-us...@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS-4.5-beta1 is out!
Hi, what is the error message? Look at stdout/stderr and log file. Roland On Tue, Aug 3, 2010 at 11:21 AM, Da-Wei Li lida...@gmail.com wrote: Hello I tried the Gromacs 4.5 beta. However, my MPI mdrun died. Here it is the output. The Gromacs-4.0.7 work fine for the same system. It is protein in water system. There are about 22000 atoms. *** Will use 9 particle-particle and 7 PME only nodes This is a guess, check the performance at the end of the log file Making 1D domain decomposition 9 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 rank 9 in job 1 hpc-8-16.local_53455 caused collective abort of all ranks exit status of rank 9: killed by signal 9 dawei On Fri, Jul 30, 2010 at 3:20 PM, Rossen Apostolov rossen.aposto...@cbr.su.se wrote: After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is out! It is full of many new and exciting features, please try them out! If something is not working as expected, please send a mail or file a bugzilla report. For developers: there is a new branch for stable releases called release-4-5-patches. Bugfixes should be applied there *first*, and if needed, merged from that branch into the master after the fix. See http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more information. New features: 2D decomposition support for PME: improved load balancing with up to 40% overall performance improvement for large systems. Memory usage is improved for very large systems, allowing simulations of 100 million atoms. Running on multi-core nodes now automatically uses threads for domain decomposition through the built-in threaded MPI library GPU computing support Check-pointing is made more secure:MD5sum are used to verify that all files are correctly in-place before a simulation is appended. Output file appending at continuation is turned on by default Full Cmake support. Autoconf/automake will be deprecated after the final 4.5 release! Full support for 7 AMBER force fields Support for CHARMM27, including cmap for dihedrals Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. Support for nucleic acid simulations Support for Velocity-Verlet integrators for reversible T- and P-coupling; MTTK pressure control integrators; Nose-Hoover chains Support for Bennett acceptance ratio (BAR) free energy calculations Decoupling group setup for free energy File formats: All GROMACS tools can now read any VMD supported trajectory format, without converting trajectory first. (VMD is required) g_rdf was a little bit enhanced that structure factors can be calculated for any system, by supplying the necessary data via sfactor.dat. Most of the common atomtypes are already contained, but everybody who needs more freedom can enhance the table Library support for dynamic index groups based on textual selections (experimental feature). See the tool g_select, the included template.c, or Doxygen documentation for information on how to write analysis tools using the library. Existing tools have not (yet) been converted. g_tune_pme: For a given number of processes or threads this tool systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It also checks whether performance can be enhanced by shifting load between the real and the reciprocal space part of the Ewald sum. g_membed: a very convenient utility for embedding membrane proteins into equilibrated lipid bilayers Big thanks to all developers, contributors and users! -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] GROMACS-4.5-beta1 is out!
On 01/08/10 22:03, Rossen Apostolov wrote: On 07/31/2010 10:17 PM, ms wrote: As a young GROMACS user, thank you a lot! I just want to ask: On 30/07/10 20:20, Rossen Apostolov wrote: * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. - Is there a 4.5 version of the manual which documents the implicit solvent feature? - It is already tested enough that one can be comfortable (albeit cautious) using it for real work, or does it require a lot of testing, in your opinion? thanks again! m. As far as I know it's production ready code, but still - this is a beta release so I would do some local testing first. I've put an updated version on the website: http://www.gromacs.org/Documentation/Manual Here is the direct link: http://www.gromacs.org/@api/deki/files/101/=manual-4.5-beta1.pdf thank you very much! m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS-4.5-beta1 is out!
On 07/31/2010 10:17 PM, ms wrote: As a young GROMACS user, thank you a lot! I just want to ask: On 30/07/10 20:20, Rossen Apostolov wrote: * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. - Is there a 4.5 version of the manual which documents the implicit solvent feature? - It is already tested enough that one can be comfortable (albeit cautious) using it for real work, or does it require a lot of testing, in your opinion? thanks again! m. As far as I know it's production ready code, but still - this is a beta release so I would do some local testing first. I've put an updated version on the website: http://www.gromacs.org/Documentation/Manual Here is the direct link: http://www.gromacs.org/@api/deki/files/101/=manual-4.5-beta1.pdf Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS-4.5-beta1 is out!
Hi Rossen, Could you send me a documentation of memory usage by gromacs-4.5-beta1. I would like to know the maximum no. of atoms that we can simulate on our university supercomputer. amit On Fri, Jul 30, 2010 at 12:20 PM, Rossen Apostolov rossen.aposto...@cbr.su.se wrote: After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is out! It is full of many new and exciting features, please try them out! If something is not working as expected, please send a mail or file a bugzilla report. For developers: there is a new branch for stable releases called release-4-5-patches. Bugfixes should be applied there **first**, and if needed, merged from that branch into the master after the fix. See http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more information. New features: - 2D decomposition support for PME: improved load balancing with up to 40% overall performance improvement for large systems. - Memory usage is improved for very large systems, allowing simulations of 100 million atoms. - Running on multi-core nodes now automatically uses threads for domain decomposition through the built-in threaded MPI library - GPU computing support - Check-pointing is made more secure:MD5sum are used to verify that all files are correctly in-place before a simulation is appended. Output file appending at continuation is turned on by default - Full Cmake support. Autoconf/automake will be deprecated after the final 4.5 release! - Full support for 7 AMBER force fields - Support for CHARMM27, including cmap for dihedrals - Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. - Support for nucleic acid simulations - Support for Velocity-Verlet integrators for reversible T- and P-coupling; MTTK pressure control integrators; Nose-Hoover chains - Support for Bennett acceptance ratio (BAR) free energy calculations - Decoupling group setup for free energy - File formats: All GROMACS tools can now read any VMD supported trajectory format, without converting trajectory first. (VMD is required) - g_rdf was a little bit enhanced that structure factors can be calculated for any system, by supplying the necessary data via sfactor.dat. Most of the common atomtypes are already contained, but everybody who needs more freedom can enhance the table - Library support for dynamic index groups based on textual selections (experimental feature). See the tool g_select, the included template.c, or Doxygen documentation for information on how to write analysis tools using the library. Existing tools have not (yet) been converted. - g_tune_pme: For a given number of processes or threads this tool systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It also checks whether performance can be enhanced by shifting load between the real and the reciprocal space part of the Ewald sum. - g_membed: a very convenient utility for embedding membrane proteins into equilibrated lipid bilayers Big thanks to all developers, contributors and users! -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS-4.5-beta1 is out!
On 2010-07-31 21.34, Amit Choubey wrote: Hi Rossen, Could you send me a documentation of memory usage by gromacs-4.5-beta1. I would like to know the maximum no. of atoms that we can simulate on our university supercomputer. It is roughly linear with the number of atoms. Just try it. amit On Fri, Jul 30, 2010 at 12:20 PM, Rossen Apostolov rossen.aposto...@cbr.su.se mailto:rossen.aposto...@cbr.su.se wrote: After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is out! It is full of many new and exciting features, please try them out! If something is not working as expected, please send a mail or file a bugzilla report. For developers: there is a new branch for stable releases called release-4-5-patches. Bugfixes should be applied there **first**, and if needed, merged from that branch into the master after the fix. See http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more information. New features: * 2D decomposition support for PME: improved load balancing with up to 40% overall performance improvement for large systems. * Memory usage is improved for very large systems, allowing simulations of 100 million atoms. * Running on multi-core nodes now automatically uses threads for domain decomposition through the built-in threaded MPI library * GPU computing support * Check-pointing is made more secure:MD5sum are used to verify that all files are correctly in-place before a simulation is appended. Output file appending at continuation is turned on by default * Full Cmake support. Autoconf/automake will be deprecated after the final 4.5 release! * Full support for 7 AMBER force fields * Support for CHARMM27, including cmap for dihedrals * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. * Support for nucleic acid simulations * Support for Velocity-Verlet integrators for reversible T- and P-coupling; MTTK pressure control integrators; Nose-Hoover chains * Support for Bennett acceptance ratio (BAR) free energy calculations * Decoupling group setup for free energy * File formats: All GROMACS tools can now read any VMD supported trajectory format, without converting trajectory first. (VMD is required) * g_rdf was a little bit enhanced that structure factors can be calculated for any system, by supplying the necessary data via sfactor.dat. Most of the common atomtypes are already contained, but everybody who needs more freedom can enhance the table * Library support for dynamic index groups based on textual selections (experimental feature). See the tool g_select, the included template.c, or Doxygen documentation for information on how to write analysis tools using the library. Existing tools have not (yet) been converted. * g_tune_pme: For a given number of processes or threads this tool systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It also checks whether performance can be enhanced by shifting load between the real and the reciprocal space part of the Ewald sum. * g_membed: a very convenient utility for embedding membrane proteins into equilibrated lipid bilayers Big thanks to all developers, contributors and users! -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS-4.5-beta1 is out!
As a young GROMACS user, thank you a lot! I just want to ask: On 30/07/10 20:20, Rossen Apostolov wrote: * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. - Is there a 4.5 version of the manual which documents the implicit solvent feature? - It is already tested enough that one can be comfortable (albeit cautious) using it for real work, or does it require a lot of testing, in your opinion? thanks again! m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS-4.5-beta1 is out!
After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is out! It is full of many new and exciting features, please try them out! If something is not working as expected, please send a mail or file a bugzilla report. For developers: there is a new branch for stable releases called release-4-5-patches. Bugfixes should be applied there **first**, and if needed, merged from that branch into the master after the fix. See http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more information. New features: * 2D decomposition support for PME: improved load balancing with up to 40% overall performance improvement for large systems. * Memory usage is improved for very large systems, allowing simulations of 100 million atoms. * Running on multi-core nodes now automatically uses threads for domain decomposition through the built-in threaded MPI library * GPU computing support * Check-pointing is made more secure:MD5sum are used to verify that all files are correctly in-place before a simulation is appended. Output file appending at continuation is turned on by default * Full Cmake support. Autoconf/automake will be deprecated after the final 4.5 release! * Full support for 7 AMBER force fields * Support for CHARMM27, including cmap for dihedrals * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines for both cut-off and all-vs-all simulations. * Support for nucleic acid simulations * Support for Velocity-Verlet integrators for reversible T- and P-coupling; MTTK pressure control integrators; Nose-Hoover chains * Support for Bennett acceptance ratio (BAR) free energy calculations * Decoupling group setup for free energy * File formats: All GROMACS tools can now read any VMD supported trajectory format, without converting trajectory first. (VMD is required) * g_rdf was a little bit enhanced that structure factors can be calculated for any system, by supplying the necessary data via sfactor.dat. Most of the common atomtypes are already contained, but everybody who needs more freedom can enhance the table * Library support for dynamic index groups based on textual selections (experimental feature). See the tool g_select, the included template.c, or Doxygen documentation for information on how to write analysis tools using the library. Existing tools have not (yet) been converted. * g_tune_pme: For a given number of processes or threads this tool systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It also checks whether performance can be enhanced by shifting load between the real and the reciprocal space part of the Ewald sum. * g_membed: a very convenient utility for embedding membrane proteins into equilibrated lipid bilayers Big thanks to all developers, contributors and users! -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
