Re: [gmx-users] About system requirement to gromacs
Both are probably using 4 cores, the first one as threads, the second via mpi. However, in the second one you are using 16 threads to run 4 copies of the same simulation, 4 threads each, thus getting performance similar (or less) to using only one core. When using mpi, you should use mdrun_mpi instead, ie: mpirun -np 4 mdrun_mpi -v -deffnm topol1 / Linus On Wed, Aug 1, 2012 at 12:36 PM, rama david ramadavidgr...@gmail.com wrote: Thank you Mark for reply.. I run mdrun and mpirun with following command. I pasted output also.. Please help me to parse it.. 1. mdrun -v -deffnm topol1 2. mpirun -np 4 mdrun -v -deffnm topol1 1.mdrun -v -deffnm topol1 step 30, will finish Wed Aug 1 16:49:28 2012 Average load imbalance: 12.3 % Part of the total run time spent waiting due to load imbalance: 5.1 % NOTE: 5.1 % performance was lost due to load imbalance in the domain decomposition. You might want to use dynamic load balancing (option -dlb.) Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 2.035 2.035100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:109.127 5.744 2.632 9.117 gcq#98: You're About to Hurt Somebody (Jazzy Jeff) 2. mpirun -np 4 mdrun -v -deffnm topol1 Getting Loaded... Reading file topol1.tpr, VERSION 4.5.5 (single precision) Starting 4 threads Starting 4 threads Starting 4 threads Starting 4 threads Loaded with Money Loaded with Money Loaded with Money Loaded with Money Making 1D domain decomposition 4 x 1 x 1 Making 1D domain decomposition 4 x 1 x 1 Making 1D domain decomposition 4 x 1 x 1 Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Protein in water' 5 steps,100.0 ps. starting mdrun 'Protein in water' 5 steps,100.0 ps. starting mdrun 'Protein in water' 5 steps,100.0 ps. starting mdrun 'Protein in water' 5 steps,100.0 ps. NOTE: Turning on dynamic load balancing NOTE: Turning on dynamic load balancing step 0 NOTE: Turning on dynamic load balancing step 100, will finish Wed Aug 1 19:36:10 2012vol 0.83 imb F 2% vol 0.84 imb step 200, will finish Wed Aug 1 19:32:37 2012vol 0.87 imb F 16% vol 0.86 imb step 300, will finish Wed Aug 1 19:34:59 2012vol 0.88 imb F 4% vol 0.85 imb step 400, will finish Wed Aug 1 19:36:27 2012^Cmpirun: killing job... -- mpirun noticed that process rank 0 with PID 4257 on node VPCEB34EN exited on signal 0 (Unknown signal 0). -- 4 total processes killed (some possibly by mpirun during cleanup) mpirun: clean termination accomplished As you can also see the mdun command estimate to complete Aug 1 16:49:28 2012 while mpirun taking the time Wed Aug 1 19:36:10 2012vol Mpirun command taking more time... so from above output I can guess In mpirun 4 processor are used Sorry if I take any wrong meaning from output.. Thank you for giving your valuable time.. With best wishes and regards Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Gromacs installation
If you install package 1 on your list, the second one will be installed as well (ie you need both of them). // Linus On Mon, Jul 30, 2012 at 10:56 AM, rama david ramadavidgr...@gmail.com wrote: Hi GROMACS FRIENDS, I have dell T3500 precision, 64 bits, 6C workstation with fedora operating system. I want to install gromacs in parallel mode with mpi... I am planning to performed Replica Exchange Molecular Dynamics ( REMD ). As per REMD instruction http://www.gromacs.org/Documentation/How-tos/REMD?highlight=remd, GROMACS should not compile in threading. I install open mpi with command line yum -y install openmpi. I found that fedora add/remove software package has gromacs 4.5.5 version that can be easily installed by command yum .. It enlisted with total 15 different packages : eg.. two packages.. 1. GROMACS Open MPI binaries and libraries 2 . GROMACS OPEN MPI shared libraries and a more.. Please can you tell me which packages I have to install so that I can run GROMACS 4.5.5 in parallel to do REMD. Thank you in advance Have a nice day.. With Best Wishes and regards. Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: question about minimisation
Quite sure it's just different syntax in topology and mdp file. Compare to C; #define POSRES // expressed as -DPOSRES in the mdp file #ifdef POSRES // when working in the topology file // Linus On Thu, Jul 26, 2012 at 1:52 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ho, first I minimize my structure. This is the corresponding mdp file: define = -DPOSRES integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz and then I run a md run. This is the corresponding mdp file: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no In my topology file I include the restraint files like this: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif #ifdef POSRES #include posre_memb.itp #endif This won't work for multiple [moleculetype] entries. See http://www.gromacs.org/Documentation/How-tos/Position_Restraints I just recognize that there is a DPOSRES in the mdp files and a POSRES in my topology file. Is this the problem. Do I have to write it the same way in the several files? http://www.gromacs.org/Documentation/Include_File_Mechanism Mark I just see that the [ position_restraints ] part is included under the [dihedral] and not between the [moleculetype] and the [atom] part. And according to the site you wrote me this is a problem, right? But this was done by gromacs itself. Shell I write it to the [moleculetype] part? A [position_restraints] directive belongs to the [moleculetype] in which it is declared. The original location of the #include statement produced by Gromacs is correct; it follows sequentially within the protein [moleculetype]. Your inclusion of the membrane restraint file within the protein [moleculetype] is, however, incorrect. But I can not see why it can not work that I have 2 restriction files? Can you please explain it to me? You can have two restraint files for different [moleculetypes] but they must be organized as such. okey. So the whole thing with [atoms], [bonds], [dihedral] all contains to the entry in [moleculetype] , right? Any directive belongs to the [moleculetype] that immediately precedes it. Once a new [moleculetype] is declared (either directly or indirectly via #include mechanism), you're working with a different molecule. But directly before I include the membrane restriction file I include the membrane definition: #include amber03.ff/dum.itp #ifdef POSRES #include posre_memb.itp #endif So I thought that it is directly after the atomtype it belongs to. I thought that it is the same in the case with the water, where first the water definition is included and after that the restriction of the water. Or am I wrong? Well the #include statement shown here is different than the one you showed previously, which was wrong. Please always be sure you're providing accurate information - it wastes less time and avoids confusion. I include the dummy atoms definition right after the ions. Or is this the wrong position? The position of #include statements in this context is irrelevant. You can list the [moleculetypes] in any order you like, but the relevant dependent directives must be contained appropriately and the order of the listing in [molecules] must match the coordinate file. Otherwise, it's fairly flexible. -Justin 4935 4952 4950 4951 4 4950 4954 4952 4953 4 4954 4973 4972 4974 4 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include amber03.ff/tip3p.itp #ifdef
Re: [gmx-users] MPIRUN on Ubontu
In order to use MPI on Ubuntu with the distribution-supplied package, you need to use a combination of mpirun and mdrun_mpi, e.g. mpirun -np 2 mdrun_mpi -deffnm md to run on two cores. On Mon, Dec 27, 2010 at 7:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: גדעון לפידות wrote: Hi all, I have recently installed Ubonto on my computer (i5 processor) and installed gromacs 4.0.7. I have installed openmpi and fftw but when using mpirun command instead of getting parallel processes it simply runs the same job four times simultaneously. How do I make the necessary adjustments. Properly compile an MPI-enabled mdrun. Since you've provided no detail on how you did the installation, the only thing to suggest is that you've done something wrong. Follow the installation guide: http://www.gromacs.org/Downloads/Installation_Instructions Alternatively, use the newest version of Gromacs (4.5.3), which uses threading for parallelization instead of requiring external MPI support. -Justin Thanks, Gideon -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] what is the nicelevel ?
The nicelevel is simply the priority of the process, where 19 is the lowest priority (ie most other programs will use the cpu before the gromacs process does) and -20 the highest. See man nice. // Linus On Tue, Dec 7, 2010 at 10:13 PM, GZ Zhang zgz...@gmail.com wrote: Hi, ALL I'm using genbox to create a water box. There is a flag called -nice which is described to be used to set the nicelevel. What is nicelevel ? What does the default value 19 mean ? What if I would like to increase the decimal places (the default is 3) of all numbers. Thanks. Regards, Guozhen -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dssp
What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] (no subject)
Use grompp normally, without the -np flag. Then run mdrun_mpi with your normal parameters as mpirun -np x mdrun_mpi -deffnm xx On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri amin_a...@yahoo.comwrote: Hi all, I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package manager. I want to run a simulation in parallel on a multi processor, single PC, but to compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun, it still runs as a single job. Thanks a lot for any instruction. Bests, Amin -- 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
