[gmx-users] g_mindist for hydrophobic interactions
Dear All, I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a cross talk for receptor's transactivation. Is g_mindist a good tool for this purpose? Do you have more suggestions? Moreover, should I use trjconv for pbc treatment before running g_mindist? Thank you in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Dear gmx users I am performing a simulation by gromacs. for building the ligand itp file by Prodrg, I get an error thet boron atom is not supported by this program. Do you have any propose for solute this problem? regards -- Somayeh Alimohammadi Ph.D Student of Medical Nanotechnology Shahid Beheshti University of Medical Sciences Tehran-Iran -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_mindist for hydrophobic interactions
Another option is g_hbond -contact. On 8 Sep 2014, at 09:25, Ca C. devi...@hotmail.com wrote: Dear All, I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a cross talk for receptor's transactivation. Is g_mindist a good tool for this purpose? Do you have more suggestions? Moreover, should I use trjconv for pbc treatment before running g_mindist? Thank you in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GPU job failed
Hello: I am trying to use the following command in Gromacs-5.0.1: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 10 but it always failed with messages: 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 1 PP rank in this node: #0, #1 --- Program mdrun_mpi, VERSION 5.0.1 Source code file: /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, line: 359 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors However, this command works fine in Gromacs-4.6.5, and I don't know why it failed in 5.0.1. Does anybody have any idea? thx a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g-select failed
Hello: I am trying to make two groups for my lipids sytem by g_select with command line: g_select_mpi -sf select.dat -f em.gro here is the content of select.dat: up=z80; down=z80; but it failed with messages: Program: gmx select, VERSION 5.0.1 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 232) Function:void gmx::CommandLineParser::parse(int*, char**) Error in user input: Invalid command-line options In command-line option -sf Error in adding selections from file 'select.dat' Too few selections provided thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Status of MD simulation
hi I am running a 5ns simulation using mdrun command. So this will take a day to complete. So I want to know that how to check the status of simulation in between the run whether it is going in right direction or not? thanks regards ankit -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g-select failed
Hi, On Mon, Sep 8, 2014 at 4:47 PM, Albert mailmd2...@gmail.com wrote: I am trying to make two groups for my lipids sytem by g_select with command line: g_select_mpi -sf select.dat -f em.gro here is the content of select.dat: up=z80; down=z80; but it failed with messages: ... Your selection file only declares two selection variables (up and down), but no actual selections. Since g_select expects to get some selections, it gives the error message. You can specify your selections like this if you want to give them names: up z80; down z80; Best regards, Teemu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Integrator problem
Hi everyoneI want to ask one question...In my .mdp file if I use md intergrator for energy minimisation .then system is fine...but if I use steep integrator...my system got error of more force on one atomI not clear why this is happeingcan any body guide me please.. Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Status of MD simulation
Make a temporary copy of the files (generally not necessary, but might help) and observe whatever suits you. Mark On Sep 8, 2014 3:50 PM, ankit agrawal aka...@gmail.com wrote: hi I am running a 5ns simulation using mdrun command. So this will take a day to complete. So I want to know that how to check the status of simulation in between the run whether it is going in right direction or not? thanks regards ankit -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Status of MD simulation
Hi...I think the best way is to check log file If I m wrong please do correct me!! Regards Lovika On 8 Sep 2014 19:21, ankit agrawal aka...@gmail.com wrote: hi I am running a 5ns simulation using mdrun command. So this will take a day to complete. So I want to know that how to check the status of simulation in between the run whether it is going in right direction or not? thanks regards ankit -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Integrator problem
The md integrator does MD, not EM... Mark On Sep 8, 2014 4:11 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyoneI want to ask one question...In my .mdp file if I use md intergrator for energy minimisation .then system is fine...but if I use steep integrator...my system got error of more force on one atomI not clear why this is happeingcan any body guide me please.. Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g-select failed
Hello Teemu: thanks a lot for such helpful advices. It works now. If I would like to select protein and z80, I use following select.dat file: up protein and z80; down protein and z80; but it failed with messages: In command-line option -sf Error in parsing selections from file 'select.dat' syntax error invalid selection 'up protein and z80' do you have any idea how to add additional options? thx again Albert On 09/08/2014 03:59 PM, Teemu Murtola wrote: Your selection file only declares two selection variables (up and down), but no actual selections. Since g_select expects to get some selections, it gives the error message. You can specify your selections like this if you want to give them names: up z80; down z80; Best regards, Teemu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU and MPI
I have found my mistake and hopefully this information is useful. This is caused by pinning of OPENMP threads by MPI. By default, all OPENMP threads belongs to each MPI rank will run on one core only in our cluster. I didn't realize this partially because Gromacs's thread MPI (this is employed when I run Gromacs on one node only) doesn't have this problem. best, dawei On Tue, Sep 2, 2014 at 9:23 AM, Da-Wei Li lida...@gmail.com wrote: I did a little more test. It is unexpected that mixed use of MPI and OPENMP on 2 nodes will cause dramatic efficiency lose. That is, my previous slowdown is not caused by GPU. BTW, each node on our cluster has two X5650 XEON cpu (6 cores each) and two Nvidia M2070 GPU (not K40 as I thought before). Test 1: 12 core on one node, 12 MPI rank, 50ns/day Test 2: 12 core on one node, 2 MPI rank, 6 OPENMP threads per rank, 41 ns/day Test 3: 24 core on two nodes, 24 MPI rank, 80ns./day Test 4: 24 core on two nodes, 4 MPI rank, 6 OPENMP threads per rank, 15 ns/day dawei On Tue, Sep 2, 2014 at 6:20 AM, Szilárd Páll pall.szil...@gmail.com wrote: You may want to try other settings between 4x6 and 24x1 too, e.g. 12x2 or 6x4 - especially if you have a dual-socket 6-core machine with HyperThreading. In my experience, using as many ranks as hardware threads with HT in GPU runs results in big slowdown compared to either not using HT (i.e. 12x1) or using 2 threads/rank (12x2). Cheers, -- Szilárd On Mon, Sep 1, 2014 at 5:13 PM, Carsten Kutzner ckut...@gwdg.de wrote: On 01 Sep 2014, at 15:58, Da-Wei Li lida...@gmail.com wrote: No. With GPU, both domain and PME domain are decomposited by 4X1X1, because I use 4 MPI ranks, in line with 4 GPUs. W/o GPU, domain decomposition is 20X1X1 and PME is 4X1X1. So the difference in performance could be due to the different DD and PME/PP settings. I would try to use exactly the same settings with and without GPU. With GPUs, you then would need to specify something like mpirun -n 24 mdrun -dd 20 1 1 -npme 4 -gpu_id 01 So you get 10 DD plus 2 PME ranks per node and map the first 5 DD ranks to GPU id 0, and the last 5 DD ranks to GPU id 1. Carsten dawei On Mon, Sep 1, 2014 at 8:39 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Dawei, on two nodes, regarding the cases with and without GPUs, do you use the same domain decomposition in both cases? Carsten On 01 Sep 2014, at 14:30, Da-Wei Li lida...@gmail.com wrote: I have added -resethway but still the same result. Use two GPU and 12 cores distributed in 2 nodes will result 33 ns/day, that is, it is about 3 time slower than MD run on one node (2GPU+12core). I have no idea what is wrong. dawei On Mon, Sep 1, 2014 at 5:34 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, take a look at mdrun’s hidden but sometimes useful options: mdrun -h -hiddden Carsten On 01 Sep 2014, at 11:07, Oliver Schillinger o.schillin...@fz-juelich.de wrote: Hi, I did not know about the -resethway command line switch to mdrun. Why is it nowhere documented? Or am I blind/stupid? Cheers, Oliver On 08/29/2014 05:15 PM, Carsten Kutzner wrote: Hi Dawei, On 29 Aug 2014, at 16:52, Da-Wei Li lida...@gmail.com wrote: Dear Carsten Thanks for the clarification. Here it is my benchmark for a small protein system (18k atoms). (1) 1 node (12 cores/node, no GPU): 50 ns/day (2) 2 nodes (12 cores/node, no GPU): 80 ns/day (3) 1 node (12 cores/node, 2 K40 GPUs/node): 100 ns/day (4) 2 nodes (12 cores/node, 2 K40 GPUs/node): 40 ns/day I send out this question because the benchmark 4 above is very suspicious. Indeed, if you get 80 ns/day without GPUs, then it should not be less with GPUs. For how many time steps do you run each of the benchmarks? Do you use the -resethway command line switch to mdrun to disregard the first half of the run (where initialization and balancing is done, you don’t want to count that in a benchmark)? Carsten But I agree size of my system may play a role. best, dawei On Fri, Aug 29, 2014 at 10:36 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Dawei, the mapping of GPUs to PP ranks is printed for the Master node only, but if this node reports two GPUs, then all other PP ranks will also use two GPUs (or an error is reported). The scaling will depend also on your system size, if this is too small, then you might be better off by using a single node. Carsten On 29 Aug 2014, at 16:24, Da-Wei Li lida...@gmail.com wrote: Dear users, I recently try to run Gromacs on two nodes, each of them has 12 cores and 2 GPUs. The nodes are connected with infiniband and scaling is pretty good when no GPU is evolved. My command is like this: mpiexec -npernode 2 -np 4 mdrun_mpi -ntomp 6 However, it looks like Gromacs only
Re: [gmx-users] Integrator problem
Oo.thanks for guiding Mark !!! Regards Lovika On 8 Sep 2014 19:45, Mark Abraham mark.j.abra...@gmail.com wrote: The md integrator does MD, not EM... Mark On Sep 8, 2014 4:11 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyoneI want to ask one question...In my .mdp file if I use md intergrator for energy minimisation .then system is fine...but if I use steep integrator...my system got error of more force on one atomI not clear why this is happeingcan any body guide me please.. Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU and MPI
Now the question is how can we solve the problem in GPU workstaton and make two GPU work together for one task? thx Albert On 09/08/2014 04:18 PM, Da-Wei Li wrote: I have found my mistake and hopefully this information is useful. This is caused by pinning of OPENMP threads by MPI. By default, all OPENMP threads belongs to each MPI rank will run on one core only in our cluster. I didn't realize this partially because Gromacs's thread MPI (this is employed when I run Gromacs on one node only) doesn't have this problem. best, dawei -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Performing MD simulations in presence of trivalent cations.
Hello gmx users, I am currently working on the ion dependent persistence length calculations of RNA strands.I want to calculate it in presence of multivalent cations like Al3+ and Co3+. I guess in order to do that we have to include the specifications of these ions (either one) in the ions.itp file mentioned in the force field directory. My question is whether mentioning the charge +3 and giving a name (say Al) and mass of the ion would be sufficient enough for it or some other protocols are required.Also, is there any force field which will be suitable for such cations? I am not a professional in this field and any sort of help will be highly appreciated. Regards, Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] protein-ligand complex by gromacs
hi GMX users i have simulated the protein-ligand complex by gromacs. I've repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box. I've checked all of the input files and the steps , but I did not understand why this happened. Please help me . Thank you for your kindness -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Performing MD simulations in presence of trivalent cations.
On 2014-09-08 18:28, soumadwip ghosh wrote: Hello gmx users, I am currently working on the ion dependent persistence length calculations of RNA strands.I want to calculate it in presence of multivalent cations like Al3+ and Co3+. I guess in order to do that we have to include the specifications of these ions (either one) in the ions.itp file mentioned in the force field directory. My question is whether mentioning the charge +3 and giving a name (say Al) and mass of the ion would be sufficient enough for it or some other protocols are required.Also, is there any force field which will be suitable for such cations? I am not a professional in this field and any sort of help will be highly appreciated. That's going to be really difficult. Present force fields have a lot of problems even with Mg2+ and Ca2+. In any way do you need to search the literature for Van der Waals (Lennard-Jones) parameters for such ions. Regards, Soumadwip -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no data read from file pdo.gz
On 9/8/14 12:36 AM, Lyna Luo wrote: Hi Justin, The blank between lines are just from email format. I used only one window to see if g_wham can readin my data, but I actually have 64 window. Please see the error message below. Thanks again! -Lyna GROMACS: gmx wham, VERSION 5.0 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: g_wham -ip pdo.dat -bins 400 -temp 300 -tol 0.1 -auto Found 64 pdo files in pdo.dat Automatic determination of boundaries from 64 pdo files... Using gunzig executable /bin/gunzip Opening disa_job13_pdo/job.job13.63.sort.colvars.traj,temp.bb.pdo.gz ... [100%] Determined boundaries to 10002004087734272.00 and -10002004087734272.00 Opening disa_job13_pdo/job.job13.0.sort.colvars.traj,temp.bb.pdo.gz ... [ 2%] WARNING, no data points read from file disa_job13_pdo/job.job13.0.sort.colvars.traj,temp.bb.pdo.gz (check -b option) Opening disa_job13_pdo/job.job13.1.sort.colvars.traj,temp.bb.pdo.gz ... [ 3%] WARNING, no data points read from file disa_job13_pdo/job.job13.1.sort.colvars.traj,temp.bb.pdo.gz (check -b option) Opening disa_job13_pdo/job.job13.2.sort.colvars.traj,temp.bb.pdo.gz ... [ 5%] WARNING, no data points read from file disa_job13_pdo/job.job13.2.sort.colvars.traj,temp.bb.pdo.gz (check -b option) My pdo file looks like below. Is there something wrong with component selection or nskip or the two column data format? # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group TestAtom # Nr. of pull groups 1 # Group 1 GR1 Umb. Pos. 57.6 Umb. Cons. 2.0 # 5054910 5.76202567601903e+01 5054920 5.76153109776819e+01 5054930 5.76057280906502e+01 5054940 5.76000707360825e+01 5054950 5.75956747536078e+01 5054960 5.75863624004517e+01 5054970 5.75807826101227e+01 5054980 5.75752353578918e+01 5054990 5.75700050629966e+01 5055000 5.75644906348954e+01 5055010 5.75599694771144e+01 5055020 5.75577873701180e+01 5055030 5.75528304157033e+01 Any number of things could be wrong here. Realize that .pdo files have been obsolete since about 2008, so the code referring to them is not routinely used or maintained. So something could be going on there, and I suspect that is at least part of the problem, given the fact that the maximum and minimum can't be calculated properly. Another possibility is that the contents of the files are misinterpreted; a quick look at the code suggests that the first field should be float (time in ps, not timestep) so something may be off. You may want to consider using Alan Grossfield's WHAM program so you don't have to deal with all this .pdo-specific stuff; most people use that program for analyzing NAMD output. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] protein-ligand complex by gromacs
On 9/8/14 12:30 PM, Mahboobeh Eslami wrote: hi GMX users i have simulated the protein-ligand complex by gromacs. I've repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box. I've checked all of the input files and the steps , but I did not understand why this happened. This sounds like a simple periodicity issue. Check your use of trjconv. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Limitation on the maximum number of OpenMPI threads
Hello, I was trying to run a simulation on Gromacs-4.6.3 which has been compiled without thread MPI on a BlueGene/Q system. The configurations per node are as follows: PowerPC A2, 64-bit, 1.6 GHz, 16 cores SMP, 4 threads per core For running on 8 nodes I tried: srun mdrun_mpi -ntomp 64 But, this gave me an error: Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/staff/sheed/apps/gromacs-4.6.3/src/mdlib/nbnxn_search.c, line: 2520 Fatal error: 64 OpenMP threads were requested. Since the non-bonded force buffer reduction is prohibitively slow with more than 32 threads, we do not allow this. Use 32 or less OpenMP threads. So, I tried using 32 and it works fine. The problem is the performance seems to be too low; for 1 ns run it shows an estimated time of more than a day. The same run on a workstation with 6 cores and 2 GPU gives a performance of 17 ns/day. I am now at loss. Any ideas what is happening ?? Regards, Abhishek Acharya -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU and MPI
Helo Yunlong: thx a lot for the reply. It works in Gromacs-4.6.5, but it does NOT in Gromacs-5.0.1. I used the following command: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 10 but it always failed with messages: 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 1 PP rank in this node: #0, #1 --- Program mdrun_mpi, VERSION 5.0.1 Source code file: /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, line: 359 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors However, this command works fine in Gromacs-4.6.5, and I don't know why it failed in 5.0.1. best Albert On 09/08/2014 05:33 PM, Yunlong Liu wrote: For using two GPU, just add option -gpu_id 01 to specify each gpu for each MPI process. Yunlong -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] electric filed
Hello: I am simulating a protein in lipids bilyaer and I am going to apply 50mV voltage across the bilayer. I noticed this paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056342 The author did in Gromacs. I noticed that there is a Electric fieldselectric field option for mdp file, So I am just wondering will the following setting would be enough for my purpose: E_z= 1 0.08 1 All the other settings would be the same as normal membrane protein simulation as indicated in Gromacs tutorial. Thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU and MPI
Hi, Albert I think the error message is very clear. You have one MPI rank per node, but provide 2 GPUs per node. The gpuid argument is applied on each of the node. dawei On Mon, Sep 8, 2014 at 2:38 PM, Albert mailmd2...@gmail.com wrote: Helo Yunlong: thx a lot for the reply. It works in Gromacs-4.6.5, but it does NOT in Gromacs-5.0.1. I used the following command: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 10 but it always failed with messages: 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 1 PP rank in this node: #0, #1 --- Program mdrun_mpi, VERSION 5.0.1 Source code file: /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, line: 359 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors However, this command works fine in Gromacs-4.6.5, and I don't know why it failed in 5.0.1. best Albert On 09/08/2014 05:33 PM, Yunlong Liu wrote: For using two GPU, just add option -gpu_id 01 to specify each gpu for each MPI process. Yunlong -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU and MPI
HI Dawei: Yes, it is. I am running it in a workstation which have 1 CPU (20 cores) plus 2 GPU. It is not a server. That's why I use additional option: -ntomp 10 So that each MPI rank can use 10 core CPU. This works fine in Gromacs-4.6.5, but it doesn't work in 5.0.1 thx Albertt On 09/08/2014 09:08 PM, Da-Wei Li wrote: Hi, Albert I think the error message is very clear. You have one MPI rank per node, but provide 2 GPUs per node. The gpuid argument is applied on each of the node. dawei -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU and MPI
Hi, Albertt It is quite strange. Your log file should provide how many MPI ranks and how many OPENMP threads per rank. Can you check that part to find how many MPI ranks are there? best, dawei On Mon, Sep 8, 2014 at 3:18 PM, Albert mailmd2...@gmail.com wrote: HI Dawei: Yes, it is. I am running it in a workstation which have 1 CPU (20 cores) plus 2 GPU. It is not a server. That's why I use additional option: -ntomp 10 So that each MPI rank can use 10 core CPU. This works fine in Gromacs-4.6.5, but it doesn't work in 5.0.1 thx Albertt On 09/08/2014 09:08 PM, Da-Wei Li wrote: Hi, Albert I think the error message is very clear. You have one MPI rank per node, but provide 2 GPUs per node. The gpuid argument is applied on each of the node. dawei -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PME
Dear GMX Users I have a question about PME loading When executing mdrun. All my MD simulations (DNA-ligand interaction in triclinic box) are computed on in-house Linux 64-bit Intel Core-i7. According to gromacs tutorial in Justin web site (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html), For a cubic box, the optimal setup will have a PME load of 0.25 and for a dodecahedral box, the optimal PME load is 0.33. Is this result should be obtained with my computer (with np=8)? or these PME load will be obtained only with np8? Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] [ANN] MDTraj 1.0: Trajectory Analysis in Python
Hello, We are happy to announce the 1.0 release of MDTraj. MDTraj is a modern, lightweight and efficient software package for analyzing molecular dynamics trajectories. It reads and writes trajectory data from a wide variety of formats, including those used by AMBER, GROMACS, CHARMM, NAMD and TINKER. The package has a strong focus on interoperability with the wider scientific Python ecosystem. The 1.0 release indicates substantial stabilization of the package, and a strong commitment to backward compatibility. New features since the 0.9 release include and interactive WebGL-based protein visualization in IPython notebook and a full implementation of DSSP secondary structure assignment. More information, detailed release notes, downloads and a large number of example analysis notebooks can be found at http://mdtraj.org. Cheers, Robert T. McGibbon and the MDTraj Development Team -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU job failed
Hi, It looks like you're starting two ranks and passing two GPU IDs so it should work. The only think I can think of is that you are either getting the two MPI ranks placed on different nodes or that for some reason mpirun -np 2 is only starting one rank (MPI installation broken?). Does the same setup work with thread-MPI? Cheers, -- Szilárd On Mon, Sep 8, 2014 at 2:50 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to use the following command in Gromacs-5.0.1: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 10 but it always failed with messages: 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 1 PP rank in this node: #0, #1 --- Program mdrun_mpi, VERSION 5.0.1 Source code file: /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, line: 359 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors However, this command works fine in Gromacs-4.6.5, and I don't know why it failed in 5.0.1. Does anybody have any idea? thx a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PME
Hi, By default, there will be no separate PME ranks used with less than AFAIR 12 ranks (i.e. the default with small number of ranks is -npme 0). Without separate PME ranks (and without GPUs) there is no PP-PME load balance to tweak, so the PME load is not very relevant from performance optimization point of view. Cheers, -- Szilárd On Mon, Sep 8, 2014 at 9:06 PM, kiana moghaddam ki_moghad...@yahoo.com wrote: Dear GMX Users I have a question about PME loading When executing mdrun. All my MD simulations (DNA-ligand interaction in triclinic box) are computed on in-house Linux 64-bit Intel Core-i7. According to gromacs tutorial in Justin web site (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html), For a cubic box, the optimal setup will have a PME load of 0.25 and for a dodecahedral box, the optimal PME load is 0.33. Is this result should be obtained with my computer (with np=8)? or these PME load will be obtained only with np8? Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU job failed
Same idea with Szilard. How many nodes are you using? On one nodes, how many MPI ranks do you have? The error is complaining about you assigned two GPUs to only one MPI process on one node. If you spread your two MPI ranks on two nodes, that means you only have one at each. Then you can't assign two GPU for only one MPI rank. How many GPU do you have on one node? If there are two, you can either launch two PPMPI processes on one node and assign two GPU for them. If you only want to launch one MPI rank on each node, you can assign only one GPU for each node ( by -gpu_id 0 ) Yunlong Try to run Sent from my iPhone On Sep 8, 2014, at 5:35 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi, It looks like you're starting two ranks and passing two GPU IDs so it should work. The only think I can think of is that you are either getting the two MPI ranks placed on different nodes or that for some reason mpirun -np 2 is only starting one rank (MPI installation broken?). Does the same setup work with thread-MPI? Cheers, -- Szilárd On Mon, Sep 8, 2014 at 2:50 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to use the following command in Gromacs-5.0.1: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 10 but it always failed with messages: 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no, stat: compatible 2 GPUs user-selected for this run. Mapping of GPUs to the 1 PP rank in this node: #0, #1 --- Program mdrun_mpi, VERSION 5.0.1 Source code file: /soft2/plumed-2.2/gromacs-5.0.1/src/gromacs/gmxlib/gmx_detect_hardware.c, line: 359 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 1 PP MPI process per node, but you provided 2 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors However, this command works fine in Gromacs-4.6.5, and I don't know why it failed in 5.0.1. Does anybody have any idea? thx a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] [CfP] 5th International Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim)
# 5th International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 2015) CALL FOR PAPERS # April 12-15, 2015, Alexandria, VA (USA) http://www.sel.uniroma2.it/Mod4Sim15 # # Papers Due: *** November 10, 2014 *** Accepted papers will be # published in the conference proceedings and archived in the ACM # Digital Library. # 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. +++ Important Dates +++ * Abstract Submission Deadline (optional): September 12, 2014 * Paper Submission Deadline: November 10, 2014 * Decision to paper authors: January 9, 2015 * Camera ready due: February 10, 2015 * Conference dates: April 12-15, 2015 Organizing Committee * Andrea DÕAmbrogio - University of Rome Tor Vergata, Italy * Paolo Bocciarelli - University of Rome Tor Vergata, Italy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Limitation on the maximum number of OpenMPI threads
Hi, Generally speaking, in the absence of accelerators, OpenMP as used in GROMACS 4.6/5.0 is only useful as you get down to around a few hundred atoms per core (details vary, but since you often can't get fewer than 512 cores of BG/Q the point is often moot there), and only at fairly low OpenMP thread counts (hence the error). BG/Q has 4 hardware threads per core, but because of the way the processor issues instructions to them, you will observe benefit with mdrun only if you use either 2 or 3 of them. You should start by setting an MPI rank per core, and vary -ntomp to observe that (probably) 2 is best. You can then increase the number of nodes=ranks until mdrun starts complaining that it can't find a suitable domain decomposition (because they're getting too small). Then you can get some value from splitting an MPI rank over two cores (and thus doubling -ntomp to try 4 or 6), etc. Under such conditions, and with a good PP-PME load balance, I have seen mdrun (admittedly NVE, and not writing a trajectory) continue getting faster until about 30 atoms/core, but that's an unrealistic scenario. Your mileage will be worse in the real world. Mark On Mon, Sep 8, 2014 at 8:15 PM, Abhi Acharya abhi117acha...@gmail.com wrote: Hello, I was trying to run a simulation on Gromacs-4.6.3 which has been compiled without thread MPI on a BlueGene/Q system. The configurations per node are as follows: PowerPC A2, 64-bit, 1.6 GHz, 16 cores SMP, 4 threads per core For running on 8 nodes I tried: srun mdrun_mpi -ntomp 64 But, this gave me an error: Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/staff/sheed/apps/gromacs-4.6.3/src/mdlib/nbnxn_search.c, line: 2520 Fatal error: 64 OpenMP threads were requested. Since the non-bonded force buffer reduction is prohibitively slow with more than 32 threads, we do not allow this. Use 32 or less OpenMP threads. So, I tried using 32 and it works fine. The problem is the performance seems to be too low; for 1 ns run it shows an estimated time of more than a day. The same run on a workstation with 6 cores and 2 GPU gives a performance of 17 ns/day. I am now at loss. Any ideas what is happening ?? Regards, Abhishek Acharya -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU job failed
thanks a lot for reply both Yunlong and Szilard. I don't set up PBS system and nodes in the workstation. In the GPU workstation, it contains 1 CPU with 20 cores, and two GPUs. So it is similar to 1 nodes with 2 GPUs. But I don't know why 4.6.5 works, but 5.0.1 doesn't ... Thx again for reply. Albert On 09/08/2014 11:59 PM, Yunlong Liu wrote: Same idea with Szilard. How many nodes are you using? On one nodes, how many MPI ranks do you have? The error is complaining about you assigned two GPUs to only one MPI process on one node. If you spread your two MPI ranks on two nodes, that means you only have one at each. Then you can't assign two GPU for only one MPI rank. How many GPU do you have on one node? If there are two, you can either launch two PPMPI processes on one node and assign two GPU for them. If you only want to launch one MPI rank on each node, you can assign only one GPU for each node ( by -gpu_id 0 ) Yunlong -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Query regarding the addition of solvent molecule
Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 7:10 AM, Christina Florina wrote: Hi, I have included the chx.itp file in the protein.top file already. Checked with the molecule name (CHX) in the .itp file and also in the topology file variable name which matches CHX. But still I am getting the same error. Kindly need help to resolve it. Something doesn't add up. You will need to provide all of your files for download via a file-sharing service to diagnose. A simple #include statement and correct updating of [molecules] is all that is needed. -Justin On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 2:50 AM, Christina Florina wrote: Hi, I have just started my work in MD and using Gromacs 5.0. I need to use cyclohexane as my solvent instead of water. I generated the topology file, .itp and .gro using PRODRG. I have successfully incorporated the .gro file using solvate command and generated the solvent box. But I am facing problem with grompp (ions.mdp) step before the addition of ions. gmx grompp -f ions.mdp -c protein_solv.gro -p protein.top -o ions.tpr I am getting the FATAL ERROR: NO SUCH MOLECULETYPE CHX though I have checked with the molecule name (CHX) in the cyclohexane .itp file. I have tired changing the name of the molecule also. Do I need to add this cyclohexane solvent molecule in the forcefield file or .atp file, .rtp file? I tried adding them but still not able to run this. I might be incorrect while adding it in the .rtp file. So, I kindly need help regarding the addition of new solvent molecule in gromacs since I have other organic solvents also for my md work and having the same problem. You need to #include the CHX .itp file in the system .top, and update [molecules] accordingly. Please note as well that PRODRG topologies are of low quality in my experience and need to be corrected. CHX is simple, a ring of CH2 atom types, all with zero charge. Other results are less trivial to fix. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
