[gmx-users] Runtime on 8 processors
Hi everyone, I did a simulation in an amazon cluster with 7.5 GB memory and 4 EC2 Compute Units (2 virtual cores with 2 EC2 Compute Units each) and it was done with 0.5ns/day. Now Im running a simulation in another amazon cluster of 7 GB of memory and 20 EC2 Compute Units (8 virtual cores with 2.5 EC2 Compute Units each), but still the speed is same even if i use mpirun -np 8 with the mdrun, and finally its taking the same time as 2core system, i.e. 0.5ns/day. I would like to know whether I should make any changes during compilation? I had enabled mpirun while compiling GROMACS. Do I need to make any changes, so that it will consider all the 8 processors? Thank you very much. Sumanth -- ** *Sumanth Kumar.M * On-the-Job Trainee Plant Molecular Biology Lab. Plant Breeding, Genetics and Biotechnology International Rice Research Institute DAPO-, Metro Manila Philippines Tel : +63- 9163129718 email : s.ku...@irri.org sumanthkuma...@gmail.com -- 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] Runtime on 8 processors
On 23/09/2011 4:37 PM, Sumanth M. Kumar wrote: Hi everyone, I did a simulation in an amazon cluster with 7.5 GB memory and 4 EC2 Compute Units (2 virtual cores with 2 EC2 Compute Units each) and it was done with 0.5ns/day. Now Im running a simulation in another amazon cluster of 7 GB of memory and 20 EC2 Compute Units (8 virtual cores with 2.5 EC2 Compute Units each), but still the speed is same even if i use mpirun -np 8 with the mdrun, and finally its taking the same time as 2core system, i.e. 0.5ns/day. I would like to know whether I should make any changes during compilation? I had enabled mpirun while compiling GROMACS. Do I need to make any changes, so that it will consider all the 8 processors? Virtual cores are useless for GROMACS because it saturates the processor pipelines on its own (though Intel's hyperthreading from 5-6 years ago was an exception). You need real cores, and to configure MPI to assign processes 1-to-1 to real cores. The details will be up to you and your system admins. You don't need to do anything with GROMACS other than configure with MPI. Mark Thank you very much. Sumanth -- ** *Sumanth Kumar.M * On-the-Job Trainee Plant Molecular Biology Lab. Plant Breeding, Genetics and Biotechnology International Rice Research Institute DAPO-, Metro Manila Philippines Tel : +63- 9163129718 email :s.ku...@irri.org mailto:s.ku...@irri.org sumanthkuma...@gmail.com mailto:sumanthkuma...@gmail.com -- 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] if PRODRG calculate incorrectly
Dear users, If I obtain/generate the topology file for a ligand using another program (except PRODRG); 1) How can I arrange .itp file? Because it seems very complicate. 2) Justin tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html We will make use of two files that PRODRG gives us. Save the output of the field The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens) into a text file called jz4.gro and The GROMACS topology into a file called drg.itp. Then how can I generate .gro file using another program? I was obtaining .gro and .itp files using PRODRG but PRODRG is giving improper results/output. best regards 2011/9/17 Mark Abraham mark.abra...@anu.edu.au On 17/09/2011 11:28 PM, ahmet yıldırım wrote: Dear Tsjerk and Justin, Thanks for your reply. I will contact the PRODRG developers. can you suggest anyway/anytool for generating ligand coordinates/topologies? http://www.gromacs.org/**Documentation/How-tos/Steps_** to_Perform_a_Simulationhttp://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- 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] if PRODRG calculate incorrectly
On 23/09/2011 4:48 PM, ahmet y?ld?r?m wrote: Dear users, If I obtain/generate the topology file for a ligand using another program (except PRODRG); 1) How can I arrange .itp file? Because it seems very complicate. Yes, this is not an easy thing to do. Modelling an arbitrary organic compound is a difficult task. There are links from the link I provided last time that will help you. 2) Justin tutorial:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html We will make use of two files that PRODRG gives us. Save the output of the field The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens) into a text file called jz4.gro and The GROMACS topology into a file called drg.itp. Then how can I generate .gro file using another program? Again, follow the links, please. Mark I was obtaining .gro and .itp files using PRODRG but PRODRG is giving improper results/output. best regards 2011/9/17 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 17/09/2011 11:28 PM, ahmet y?ld?r?m wrote: Dear Tsjerk and Justin, Thanks for your reply. I will contact the PRODRG developers. can you suggest anyway/anytool for generating ligand coordinates/topologies? http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation Mark -- 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/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- 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] problem in compiling GMX with MPI
thanks you,Mark the problem has been solved. I redefined the flag of openmpi, then gmx compliled successfully. -- Sincerely yours Dr Ji-Nan Niu School of Materials Science and Engineering. China University of Mining and Technology. Jiangsu Province, XuZhou 221116 P. R. China -- 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] Error mesage
Dear gmx users, Does someone know how to deal with the error mesage bellow ? With my best regards, Tanos C. C. Franca. Program mdrun, VERSION 4.5.4 Source code file: domdec_con.c, line: 693 Fatal error: DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. -- 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] Error mesage
On 23/09/2011 11:18 PM, Tanos Franca wrote: Dear gmx users, Does someone know how to deal with the error mesage bellow ? With my best regards, Tanos C. C. Franca. Program mdrun, VERSION 4.5.4 Source code file: domdec_con.c, line: 693 Fatal error: DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. Your simulation system is probably too small for the number of processors you are trying to use. However we don't know anything about what you're trying to do, and guessing is fruitless. Mark -- 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] CfP: 2nd Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim), in Symposium on Theory of Modeling and Simulation, SCS Spring Sim 2012
CALL FOR PAPERS 2nd International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 2012) # March 26-29, 2012, Orlando, FL (USA) http://www.sel.uniroma2.it/Mod4Sim12 # # Papers Due: *** November 15, 2011 *** # Accepted papers will be published in the conference proceedings and archived # in the ACM Digital Library, IEEE Xplorer and IEEE CS Digital Library. # The Symposium is co-sponsored by IEEE. # The workshop aims to bring together experts in model-based, model-driven and software engineering with experts in simulation methods and simulation practitioners, with the objective to advance the state of the art in model-driven simulation engineering. Model-driven engineering approaches provide considerable advantages to software systems engineering activities through the provision of consistent and coherent models at different abstraction levels. As these models are in a machine readable form, model-driven engineering approaches can also support the exploitation of computing capabilities for model reuse, programming code generation, and model checking, for example. The definition of a simulation model, its software implementation and its execution platform form what is known as simulation engineering. As simulation systems are mainly based on software, these systems can similarly benefit from model-driven approaches to support automatic software generation, enhance software quality, and reduce costs, development effort and time-to-market. Similarly to systems and software engineering, simulation engineering can exploit the capabilities of model-driven approaches by increasing the abstraction level in simulation model specifications and by automating the derivation of simulator code. Further advantages can be gained by using modeling languages, such as UML and SysML – but not exclusively those. For example, modeling languages can be used for descriptive modeling (to describe the system to be simulated), for analytical modeling (to specify analytically the simulation of the same system), and for implementation modeling (to define the respective simulator). A partial list of topics of interest includes: * model-driven simulation engineering processes * requirements modeling for simulation * domain specific languages for modeling and simulation * model transformations for simulation model building * model transformations for simulation model implementation * model-driven engineering of distributed simulation systems * relationship between metamodeling standards (e.g., MOF, Ecore) and distributed simulation standards (e.g., HLA, DIS) * metamodels for simulation reuse and interoperability * model-driven technologies for different simulation paradigms (discrete event simulation, multi-agent simulation, sketch-based * simulation, etc.) * model-driven methods and tools for performance engineering of simulation systems * simulation tools for model-driven software performance engineering * model-driven technologies for simulation verification and validation * model-driven technologies for data collection and analysis * model-driven technologies for simulation visualization * Executable UML * Executable Architectures * SysML / Modelica integration * Simulation Model Portability and reuse * model-based systems verification and validation * simulation for model-based systems engineering To stimulate creativity, however, the workshop maintains a wider scope and welcomes contributions offering original perspectives on model-driven engineering of simulation systems. +++ On-Line Submissions and Publication +++ We invite paper submissions in three forms: 1. Full paper (max 8 pages), describing innovative research results. These papers are eligible for the best paper award and may be invited for an extended version in a special issue of the SCS SIMULATION journal. 2. Work-in-progress paper (max 6 pages), describing novel research ideas and promising work that have not yet been fully evaluated. 3. Short paper (max 6 pages), describing industrial and hands-on experience on any relevant area (i.e. military, government, space, etc.). All the papers must be submitted through the SCS conference management systems (http://www.softconf.com/scs/DEVS12/), selecting the Mod4Sim track in the Submission Categories section. All the submitted papers must be in PDF format and must conform to the
[gmx-users] g_analyze
Hi users, I have got a data from g_mindist ie water and protein atom distance in each time frame. Now I have to find the auto correlation function using g_analyze but my output file from g_mindist has the time frame,water molecule number. How do I compute the ACF. In ACF data set the x axis is for time and what data provided in y axis. Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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
