[gmx-users] decomposition error: -rdd and -dds do not influence the number of ranks

Dear MarK Abraham and Grimaces Users, Due to the limitation of Message body. I would like to open another ticket. I have tried DD control options such as -rdd and -dds but still the same error comes out. The key is to change the number of ranks. These DD control options do not influence

Re: [gmx-users] decomposition error

Dear Mark Abraham, I am actually using gromacs with VOTCA Package in order to obtain non-bonded potentials using Iterative Boltzmann inversion (IBI). In the output file, the mdrun would be the following. gmx mdrun -v As I described in the previous email, the error message is related to

Re: [gmx-users] decomposition error

Hi, You haven't given us much information about how you're running mdrun, so I can't tell. Much useful material is in the documentation eg. http://manual.gromacs.org/documentation/5.1.3/user-guide/mdrun-performance.html Mark On Sat, 23 Jul 2016 03:34 Chang Woon Jang

Re: [gmx-users] decomposition error

Dear Mark Abraham, I am a little confused about the number of ranks. How can I choose the number of ranks? Is this mdrun option or something else? Is "number of ranks" different with "number of processors" in parallel machine? Thank you very much for your help. Best regards, Changwoon Jang

Re: [gmx-users] decomposition error

Hi, On Sat, 23 Jul 2016 03:05 Chang Woon Jang wrote: > Dear Mark Abraham, > >Thank you for the details. Do 27, 18, or 12 mean -dds option or > something else? No, the number of ranks. -dds pertains to how much margin DD requires to make sure the largest

Re: [gmx-users] decomposition error

Dear Mark Abraham, Thank you for the details. Do 27, 18, or 12 mean -dds option or something else? How can I set up proper DD option? Thank you for your advice. Best regards, Changwoon Jang On Fri, Jul 22, 2016 at 8:58 PM, Mark Abraham wrote: > Hi, > > Well, is

Re: [gmx-users] decomposition error

Hi, Well, is it reasonable that your system has a dihedral where the furthest particles are 1.4nm apart? If so, then your system is quite small with respect to the range of interactions within it, and as that output notes mdrun is limited to three ranks in each direction. So 27, 18 or 12 can give

Re: [gmx-users] decomposition error

Dear Justin Lemkul, I have looked at the log file as below. Initializing Domain Decomposition on 16 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.668 nm,

Re: [gmx-users] decomposition error

On 7/22/16 7:03 PM, Chang Woon Jang wrote: Dear Justin A. Lumkul, Thank you for your answer. I am sorry for asking what is DD. My topology topol.top file is below. Would you please tell me about what is DD? How can I set up in topology file? DD = domain decomposition. Please look in

Re: [gmx-users] decomposition error

Dear Justin A. Lumkul, Thank you for your answer. I am sorry for asking what is DD. My topology topol.top file is below. Would you please tell me about what is DD? How can I set up in topology file? Thank you. Best regards, Changwoon Jang [ defaults ] ; nbfunccomb-rule

[gmx-users] decomposition error

Dear Grimaces Users, I have the decomposition error. I have tried to reduce the number of cores but still have the same problem. In my conf.gro, the cell size is about 5.5x5.5x5.5 but I do not know what the minimum cell size of 1.875nm. Would you please give me some comments or relevant topics