Re: [gmx-users] GPU-gromacs
On Oct 25, 2013, at 4:07 PM, aixintiankong aixintiank...@126.com wrote: Dear prof., i want install gromacs on a multi-core workstation with a GPU(tesla c2075), should i install the openmpi or mpich2? If you want to run Gromacs on just one workstation with a single GPU, you do not need to install an MPI library at all! Carsten -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Output pinning for mdrun
Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- 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] Output pinning for mdrun
On Oct 24, 2013, at 4:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, No. mdrun reports the stride with which it moves over the logical cores reported by the OS, setting the affinity of GROMACS threads to logical cores, and warnings are written for various wrong-looking cases, but we haven't taken the time to write a sane report of how GROMACS logical threads and ranks are actually mapped to CPU cores. Where supported by the processor, the CPUID information is available and used in gmx_thread_affinity.c. It's just not much fun to try to report that in a way that will make sense on all possible hardware that supports CPUID - and then people will ask why it doesn't map to what their mpirun reports, get confused by hyper-threading, etc. Yes, I see. What question were you seeking to answer? Well, I just wanted to check whether my process placement is correct and that I am not getting decreased performance due to a suboptimal placement. In many cases the performance is really bad (like 50% of the expected values) if the pinning is wrong or does not work, but you never know. On some clusters there are of course tools that check and output the process placement for a dummy parallel job, or environment variables like MP_INFOLEVEL for loadleveler. Thanks! Carsten Mark On Thu, Oct 24, 2013 at 11:44 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- 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 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 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] parallelization
Hi, On Oct 17, 2013, at 2:25 PM, pratibha kapoor kapoorpratib...@gmail.com wrote: Dear gromacs users I would like to run my simulations on all nodes(8) with full utilisation of all cores(2 each). I have compiled gromacs version 4.6.3 using both thread mpi and open mpi. I am using following command: mpirun -np 8 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro But I am getting following error: Setting the total number of threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI . Although during compilation I have used: cmake .. -DGMX_MPI=ON -DGMX_THREAD_MPI=ON you can either use MPI or thread_mpi. But you can use MPI and OpenMP with -DGMX_MPI=ON -DGMX_OPENMP=ON If I dont use -nt option, I could see that all the processors(8) are utilised but I am not sure whether all cores are being utilised. For You can run with mpirun -np 16 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro to use all 16 available cores. version 4.6.3 without mpi, I Know by default gromacs uses all the threads but not sure if mpi version uses all threads or not. Take a look at the md.log output file, there it should be written what Groamcs did use! Best, Carsten Any help is appreciated. -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] MPI runs on a local computer
Hi Jianqing, On Sep 19, 2013, at 2:48 PM, Xu, Jianqing x...@medimmune.com wrote: Say I have a local desktop having 16 cores. If I just want to run jobs on one computer or a single node (but multiple cores), I understand that I don't have to install and use OpenMPI, as Gromacs has its own thread-MPI included already and it should be good enough to run jobs on one machine. However, for some reasons, OpenMPI has already been installed on my machine, and I compiled Gromacs with it by using the flag: -DGMX_MPI=ON. My questions are: 1. Can I still use this executable (mdrun_mpi, built with OpenMPI library) to run multi-core jobs on my local desktop? Or the default Thread-MPI is actually a better option for a single computer or single node (but multi-cores) for whatever reasons? You can either use OpenMPI or Gromacs build-in thread MPI library. If you only want to run on a single machine, I would recommend recompiling with thread-MPI, because this is in many cases a bit faster. 2. Assuming I can still use this executable, let's say I want to use half of the cores (8 cores) on my machine to run a job, mpirun -np 8 mdrun_mpi -v -deffnm md a). Since I am not using all the cores, do I still need to lock the physical cores to use for better performance? Something like -nt for Thread-MPI? Or it is not necessary? Depends on whether you get good scaling or not. Compare to a run on 1 core, for large systems the 4 or 8 core parallel runs should be (nearly) 4 or 8 times as fast. If that is the case, you do not need to worry about pinning. b). For running jobs on a local desktop, or single node having ... say 16 cores, or even 64 cores, should I turn off the separate PME nodes (-npme 0)? Or it is better to leave as is? You may want to check with g_tune_pme. Note that the optimum will depend on your system, and for each MD system you should find that out. 3. If I want to run two different projects on my local desktop, say one project takes 8 cores, the other takes 4 cores (assuming I have enough memory), I just submit the jobs twice on my desktop: nohup mpirun -np 8 mdrun_mpi -v -deffnm md1 log1 nohup mpirun -np 4 mdrun_mpi -v -deffnm md2 log2 Will this be acceptable ? Will two jobs be competing the resource and eventually affect the performance? Make some quick test runs (over a couple of minutes). Then you can check the performance of your 8 core run with and without another simulation running. Best, Carsten Sorry for so many detailed questions, but your help on this will be highly appreciated! Thanks a lot, Jianqing To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] performance issue with the parallel implementation of gromacs
16 166.5700.3941.0381.239 8 6 3 3 00 435.3893.3990.397 - 10 8 2 4 0 -1( 20) 237.6236.2980.7291.406 5 4 7 5 1 25 286.9901.6620.6031.813 5 9 3 6 1 20 235.8180.7540.7341.495 5 4 7 7 1 16 167.8883.0281.0301.256 8 6 3 8 10 284.2643.7750.609 - 8 5 4 9 1 -1( 16) 167.8581.9241.0301.303 8 6 3 10 2 25 298.6371.6600.5791.696 5 9 3 11 2 20 281.6471.0740.6141.296 5 4 7 12 2 16 184.0124.0220.9411.244 8 6 3 13 20 304.6580.7930.568 - 8 5 4 14 2 -1( 16) 183.0842.2030.9451.188 8 6 3 Best performance was achieved with 16 PME nodes (see line 2) and original PME settings. Please use this command line to launch the simulation: mpirun -np 160 /data1/shashi/localbin/gromacs/bin/mdrun_mpi -npme 16 -s 4icl.tpr -pin on Both of these outcomes(1.110ns/day and 1.038ns/day) are lower than what I get on my workstation with Xeon W3550 3.07 GHz using 8 thread (1.431ns/day) for a similar system. The bench.log file generated by g_tune PME shows very high load imbalance (60% -100 %). I have tried several combinations of np and npme but the perfomance is always in this range only. Can someone please tell me what is it that I am doing wrong or how can I decrease the simulation time. -- Regards Ashutosh Srivastava -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] question about installation parameters
Hi, On Sep 16, 2013, at 11:23 AM, mjyang mjy...@hku.hk wrote: Dear GMX users, I have a question about the combination of the installation parameters. I compiled the fftw lib with --enable-sse2 and configured the gromacs with cmake .. -DGMX_CPU_ACCELERATION=SSE4.1. I'd like to know if it is ok to use such a combination? yes, for Gromacs the FFTW should always be compiled with SSE2. You can combine that with any -DGMX_CPU_ACCELERATION setting you want, typically the best that is supported on your platform. Best, Carsten Many thanks. Mingjun-- 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 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] Umbrella sampling simulations using make_edi with -restrain and -harmonic
Hi Po-chia, On Sep 10, 2013, at 9:53 AM, Chen, Po-chia pc...@gwdg.de wrote: Hi all, I can't seem to find the correct combination of EDI parameters impose a harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2, and I'd like to confirm that the inputs I have are actually correct. Here is the make_edi command I used to generate the .edi file fed to mdrun: echo C-alpha System | make_edi -restrain -harmonic \ -f ../ca-evec.trr \ -eig ../ca-eval.xvg \ -s ../analysis.tpr \ -ori ./init.gro \ -outfrq 2500 -deltaF0 150 -Eflnull 100 -flood 1 \ -o constrain.edi I think you should add -tau 0 when using flooding as harmonic restraint (since you do not want the flooding potential to change). Where the eigenvectors and eigenvalues are previously derived by g_covar for a set of unrestrained trajectories. The origin file init.gro is the same as the starting coordinates of this constrained run, extracted from a previous EDI run to start at an appropriate location on the eigenvector space. The 1st eigenvalue is ~ 66, and the eigenvector looked fine in VMD when plotted by g_anaeig -extr. So mdrun -ei constrain.edi runs normally, but the flooding potential drops to zero so the protein diffuses freely along the 1st eigenvector. e.g. the first/last line in edsam.xvg looks like: # time RMSD EV1projFLOOD EV1-Ef1 EV1-Vf1 EV1-deltaF 0.0 0.43 9.99 -9.4e+1 9.5e-8 3.8e-9 -5.3e-4 10.0 0.40 9.49 0.0 -0.0 1.6e-44-0.0 ... 1.00 0.94 -2.2 0.0 -0.0 1.6e-44-0.0 When c(0) is supposed to be according 9.99 as I set init.gro to be the -ori. Do I need to change -alpha as well? What parameters am I missing/added by mistake? The manual gives no indication as to which ones to do. Can you check whether make_edi -ori wrote the correct position on the 1st eigenvector in your .edi file? Scroll down to a line called # NUMBER OF EIGENVECTORS + COMPONENTS GROUP 7 (Group 7 means the flooding vectors), if you have a single flooding vector, the next line should read 1 and in the following line you will find three entries that describe nr spring constant reference projection ref. proj. change per time step which I guess read in your case 1 19.99 no 4th entry so the reference projection should be 9.99, as calculated from your .ori structure. If there is no 3rd entry, you can simply put it there manually (and leave away the -ori option to make_edi). Best, Carsten = = = P.S. the relevant constrain.edi lines contain: ... #DELTA_F0 150.00 #INIT_DELTA_F 0.0 #TAU 0.10 #EFL_NULL -100.00 #ALPHA2 -1.0 #KT 2.50 #HARMONIC 1 #CONST_FORCE_FLOODING 0 ... -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Rotation Constraints - PMF - external potential
by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it. A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Rotation Constraints - PMF - external potential
On Jul 24, 2013, at 5:53 PM, battis...@libero.it wrote: Dear Carsten could you give me more information about your suggestions? I tried but probably I did not understand well what you meant. Hi Anna, I suggested to use the enforced rotation module of Gromacs 4.6 to restrain the orientation of your molecule(s). If you want to use the orientation restraints module instead, I am afraid I can not help you much with that, maybe someone else on this list? In order to avoid the rotation of the structure A and of the structure B, I have defined into the index file a group A_B that contains A+B and I have setted in the mdp file the following parameters: ; Orientation restraints: No or Yes orire= yes ; Orientation restraints force constant and tau for time averaging orire-fc = 500 orire-tau= 100 orire-fitgrp = A_B ; Output frequency for trace(SD) and S to energy file nstorireout = 100 As I have synthetically described in the first post , the structures A and B (characterized by a cylindrical shape) are defined by a number of 32 unit- structures that I call s. Into the itp is defined the topology for the s structure, and so in order to put an orientation restraints between atoms that are not included into the same itp file, I cannot put into the topology a section like that described into the manual 4.6.2 pag. 92 namely, [ orientation_restraints ], could I ? Could you tell me How I can fix the orientation of the systems A and B? Using the enforced rotation module you would choose an index group and an axis for each group that you want to fix the orientation, set the rotation angle to zero and choose an appropriate force constant. Appropriate potential functions would be the pivot-free ones if I understand your setting correctly. I don't understand the manual's explanation about the orire-fitgrp: (fit group for orientation restraining. This group of atoms is used to determine the rotation R of the system with respect to the reference orientation. The reference orientation is the starting conformation of the first subsystem. For a protein, backbone is a reasonable choice) How one have to give the group? using an index file or defining the group in the topology? This is the orire-fitgrp = A_B mdp file setting that you made. Best, Carsten Messaggio originale Da: ckut...@gwdg.de Data: 23/07/2013 13.09 A: battis...@libero.itbattis...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: [gmx-users] Rotation Constraints - PMF Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it. A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49
Re: [gmx-users] Rotation Constraints - PMF + rerun
On Jul 24, 2013, at 12:30 PM, battis...@libero.it wrote: Dear Carsten, Thank you very much for your very useful help! I'm making some tries to test the orire options that probably will solve my problem. In order to do not waste resource, I thought using the rerun option of mdrun I can use the trajectories generated before, where my mistake was to allow the rotation of my structure. So I generated a new topol.tpr file changing the orire options in the mdp and I made: 1. mdrun -rerun ../traj.xtc -s topol.tpr -o trj.trr 2. trjcat -f traj.trr -o trajout.xtc but in the trajout.xtc there is only one point as I can check for example Hm, I am not sure, maybe you need to use -x trj.xtc instead of -o trj.trr to trigger output of all .xtc frames. How many frames are in ../traj.xtc? Carsten with: 3. g_gyrate -f trajout.xtc -s topol.tpr -n index.ndx Could you confirm me that it is not possible follow this idea? In fact I suppose that this method it is not applicable; but it is necessary to generate a new trajectory, because the angular restraints modify completely the trajectory. Or, just to be sure, did I not made the things in the right way? Thank you very much! Anna Messaggio originale Da: ckut...@gwdg.de Data: 23/07/2013 13.09 A: battis...@libero.itbattis...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: [gmx-users] Rotation Constraints - PMF Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it. A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Rotation Constraints - PMF
Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it.A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Intel compiling failed
Hi Albert, one reason for the error you see could be that you are using a non-Intel MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. Carsten On Apr 5, 2013, at 12:25 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to compile gromacs with intel compiler. However, it failed when I compile FFTW3 with command: ./configure --enable-sse --enable-float --with-pic --enable-single --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 CC=icc CXX=icc F77=ifort here is the log file: mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset' ../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined references to `_intel_fast_memset' follow collect2: ld returned 1 exit status make[3]: *** [mpi-bench] Error 1 make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3' make: *** [all] Error 2 thank you very much best Albert -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Intel compiling failed
On Apr 5, 2013, at 12:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/5/13 6:38 AM, Carsten Kutzner wrote: Hi Albert, one reason for the error you see could be that you are using a non-Intel MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. Is there any point in compiling FFTW in parallel? I have never once done it nor found it necessary. Hi, you are absolutely right, sorry I did not express that clearly. The thing is, if you compile the FFTW using the Intel compiler and then compile Gromacs using Intels mpicc or mpigcc compiler wrapper, you will get these undefined references to _intel* at link time. To make it work, you need to use the mpiicc (two i's here) compiler wrapper for Gromacs. Carsten -Justin On Apr 5, 2013, at 12:25 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to compile gromacs with intel compiler. However, it failed when I compile FFTW3 with command: ./configure --enable-sse --enable-float --with-pic --enable-single --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 CC=icc CXX=icc F77=ifort here is the log file: mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset' ../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined references to `_intel_fast_memset' follow collect2: ld returned 1 exit status make[3]: *** [mpi-bench] Error 1 make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3' make: *** [all] Error 2 thank you very much best Albert -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Justin A. Lemkul, Ph.D. Research Scientist 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 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Intel compiling failed
On Apr 5, 2013, at 4:21 PM, Albert mailmd2...@gmail.com wrote: On 04/05/2013 12:38 PM, Carsten Kutzner wrote: Hi Albert, one reason for the error you see could be that you are using a non-Intel MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. Carsten thanks a lot both Carsten and Justin. I've compiled both fftw and openmpi with intel icc and ifort well. However, when I try to compile gromacs, it failed?: Hm, this is another issue now. What version of the Intel compiler are you using? With icc 13.0 it works for me, but I remember having problems with older versions as well. Carsten cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1 -DCMAKE_PREFIX_PATH=/home/albert/install/fftw-3.3.3 -DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpiCC -DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpicc [ 0%] [ 0%] [ 0%] [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o cc1plus: error: unrecognized command line option '-ip' cc1plus: error: unrecognized command line option '-ip' CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message): Error generating /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o cc1plus: error: unrecognized command line option '-ip'make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 cc1plus: error: unrecognized command line option '-ip' make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs CMake Error at cuda_tools_generated_copyrite_gpu.cu.o.cmake:198 (message): Error generating /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_copyrite_gpu.cu.o] Error 1 make[2]: *** Waiting for unfinished jobs CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:198 (message): Error generating /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 best Albert -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] 4.6.1 support double precision GPU now?
On Apr 2, 2013, at 5:47 PM, Albert mailmd2...@gmail.com wrote: Hello: I am wondering is double precision supported in current 4.6.1 GPU version? Otherwise it would be very slow to use CPU version running free energy calculations…. Hi Albert, no, GPU calculations can be done only in single precision. Best, Carsten thank you very much best Albert -- 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 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] g_tune_pme can't be executed
Hi Daniel, are you using the newest version of 4.6? There was an issue with g_tune_pme, which I already fixed. I guess it could be responsible for the error that you see. Best, Carsten On Mar 21, 2013, at 2:26 PM, Daniel Wang iwnk...@gmail.com wrote: Hi everyone~ When I run g_tune_pme_mpi, it prompts: Fatal error: Need an MPI-enabled version of mdrun. This one (mdrun_mpi) seems to have been compiled without MPI support. I'm sure my gromacs is compiled WITH MPI support and mpiexec -n xx mdrun_mpi -s yy.tpr works normally. How to fix it? I'm using gromacs4.6 and Intel MPI 4.1.0. Thanks. -- Daniel Wang / npbool Computer Science Technology, Tsinghua University -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Mismatching number of PP MPI processes and GPUs per node
Hi, On Mar 11, 2013, at 10:50 AM, George Patargias g...@bioacademy.gr wrote: Hello Sorry for posting this again. I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration (CUDA 5.0 lib) using the following SGE batch script. #!/bin/sh #$ -V #$ -S /bin/sh #$ -N test-gpus #$ -l h=xgrid-node02 #$ -pe mpi_fill_up 12 #$ -cwd source /opt/NetUsers/pgkeka/gromacs-4.6_gpu_mpi/bin/GMXRC export DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-5.0/lib:$DYLD_LIBRARY_PATH mpirun -np 12 mdrun_mpi -s test.tpr -deffnm test_out -nb gpu After detection of the installed GPU card 1 GPU detected on host xgrid-node02.xgrid: #0: NVIDIA Quadro 4000, compute cap.: 2.0, ECC: no, stat: compatible GROMACS issues the following error Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 12 PP MPI processes per node, but only 1 GPU were detected. It can't be that we need to run GROMACS only on a single core so that it matches the single GPU card. Have you compiled mdrun_mpi with OpenMP threads support? Then, if you do mpirun -np 1 mdrun_mpi … it should start one MPI process with 12 OpenMP threads, which should give you what you want. You can also manually specify the number of OpenMP threads by adding -ntomp 12 Carsten Do you have any idea what has to be done? Many thanks. Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] compiling on different architecture than the compute nodes architecture
Hi, On Feb 6, 2013, at 6:03 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: Dear All, I would like to compile gromacs 4.6 to run with the correct acceleration on the compute nodes on our local cluster. Some of the nodes have intel sandy-bridge whilst others only have sse4.1 and some (including the login and single core job nodes) are still stuck on ssse3 (gmx would use sse2 acceleration here). Installing several versions is not a problem however, I'm not sure how to make cmake build a version of the code that is not using the acceleration for the system on which the code is being compiled. Restrictions on job sizes makes running the compilation on the sandy-bridge nodes almost impossible. Can anyone let me know which flags cmake needs to enable avx-256 acceleration? Use -DGMX_CPU_ACCELERATION=AVX_256 Try ccmake to have a look at the variables you can define and what values they can be set to. Carsten my standard cmake line is: $ CC=mpiicc CXX=mpiicpc ; cmake -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/include -DMKL_LIBRARIES=$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/libmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so -DCMAKE_INSTALL_PREFIX=$HOME/libs/gromacs ../ Thanks, Richard -- 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 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] voltage for membrane?
On Dec 23, 2012, at 11:23 PM, Martin Hoefling martin.hoefl...@gmail.com wrote: You can have a look at http://www.ncbi.nlm.nih.gov/pubmed/21843471 , maybe that does what you want. On http://www.mpibpc.mpg.de/grubmueller/compel you will find installation instructions for the special gromacs version that support the above mentioned protocol. Best, Carsten -- 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] Essential dynamics (ED) sampling using make_edi
Hi Bipin Singh, the parameters -deltaF0, -deltaF, -tau, -alpha, and -T are used only for flooding and have no effect in pure essential dynamics. Which coordinates appear in the output trajectory (*.trr, *.xtc) is exclusively controlled by .mdp options (i.e. the group you select there), not by the content of the .edi file. Best, Carsten On Dec 11, 2012, at 6:27 PM, bipin singh bipinel...@gmail.com wrote: Hello All, I want to use the essential dynamics (ED) sampling method to simulate the unfolding to folding process using make_edi option of GROMACS. For this task I am using -radcon option (acceptance radius contraction along the first two eigenvectors towards the folded structure (b4md.gro)) of make_edi as below: *make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -tar b4md.gro -radcon 1-2 -o sam.edi * *b4md.gro:* folded structure (C-alpha only) *topol.tpr: *all atom * eigenvec.trr*:from g_covar (C-alpha only) Is this is the correct way of doing the ED sampling... Also I am not sure about the following: *1)* How to judge the correct/appropriate value for the: -maxedsteps *2)* How to judge the appropriate values for the following parameters for an Essential dynamics sampling input *(or it is neglected for ED sampling and used only for flooding input ) * -deltaF0 -deltaF -tau -alpha -T *3) *Will the output trajectory (produced using mdrun -ei sam.edi ) contain all atoms or only the C-alpha atoms (using the above make_edi command). -- *--- Thanks and Regards, Bipin Singh* -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] g_tune_pme for multiple nodes
Hi Chandan, the number of separate PME nodes in Gromacs must be larger than two and smaller or equal to half the number of MPI processes (=np). Thus, g_tune_pme checks only up to npme = np/2 PME nodes. Best, Carsten On Dec 4, 2012, at 1:54 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear Carsten and Florian, Thanks for you useful suggestions. It did work. I still have a doubt regarding the execution : export MPIRUN=`which mpirun` export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes the no. of pme nodes. As I am executing it on a single node, mdrun never checks pme for greater than 12 ppn. So, how do I understand that the pme is tuned for 24 ppn spanning across the two nodes. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it just spawns the mdrun's. Carsten Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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 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
Re: [gmx-users] g_tune_pme for multiple nodes
On Dec 4, 2012, at 2:45 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for the reply. If PME nodes for the g_tune is half of np, then if it exceeds the ppn of of a node, how would g_tune perform. What I mean if $NPROCS=36, the its half is 18 ppn, but 18 ppns are not present in a single node (max. ppn = 12 per node). How would g_tune function in such scenario? Typically mdrun allocates the PME and PP nodes in an interleaved way, meaning you would end up with 9 PME nodes on each of your two nodes. Check the -ddorder of mdrun. Interleaving is normally fastest unless you could have all PME processes exclusively on a single node. Carsten Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Dec 4, 2012 at 6:39 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, the number of separate PME nodes in Gromacs must be larger than two and smaller or equal to half the number of MPI processes (=np). Thus, g_tune_pme checks only up to npme = np/2 PME nodes. Best, Carsten On Dec 4, 2012, at 1:54 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear Carsten and Florian, Thanks for you useful suggestions. It did work. I still have a doubt regarding the execution : export MPIRUN=`which mpirun` export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes the no. of pme nodes. As I am executing it on a single node, mdrun never checks pme for greater than 12 ppn. So, how do I understand that the pme is tuned for 24 ppn spanning across the two nodes. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it just spawns the mdrun's. Carsten Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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] g_tune_pme for multiple nodes
Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Carsten, Thanks for your suggestion. I did try to pass to total number of cores with the np flag to the g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I have pasted the snippet of the PBS script. #!/bin/csh #PBS -l nodes=2:ppn=12:twelve #PBS -N bilayer_tune cd $PBS_O_WORKDIR export MDRUN=/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5 from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it just spawns the mdrun's. Carsten Then I submit the script using qsub. When I login to the compute nodes there I donot find and mdrun executable running. I also tried using nodes=1 and np 12. It didnot work through qsub. Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 It worked. Also, if I just use $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 g_tune_pme executes on the head node and writes various files. Kindly let me know what am I missing when I submit through qsub. Thanks Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] Re: Question about scaling
in 2 or 4 smaller sets, the number of interactions shouldn't change and so the calculation time shouldn't change? Or is something fancy in the algorithm, which reducces the time spent for calling up the arrays if the calculation is for a smaller set of interactions? -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] Question about scaling
Hi Thomas, On Nov 12, 2012, at 5:18 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Dear all, i did some scaling tests for a cluster and i'm a little bit clueless about the results. So first the setup: Cluster: Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR GROMACS version: 4.0.7 and 4.5.5 Compiler: GCC 4.7.0 MPI: Intel MPI 4.0.3.008 FFT-library: ACML 5.1.0 fma4 System: 895 spce water molecules this is a somewhat small system I would say. Simulation time: 750 ps (0.002 fs timestep) Cut-off: 1.0 nm but with long-range correction ( DispCorr = EnerPres ; PME (standard settings) - but in each case no extra CPU solely for PME) V-rescale thermostat and Parrinello-Rahman barostat I get the following timings (seconds), whereas is calculated as the time which would be needed for 1 CPU (so if a job on 2 CPUs took X s the time would be 2 * X s). These timings were taken from the *.log file, at the end of the 'real cycle and time accounting' - section. Timings: gmx-version 1cpu2cpu4cpu 4.0.7 422333843540 4.5.5 378032552878 Do you mean CPUs or CPU cores? Are you using the IB network or are you running single-node? I'm a little bit clueless about the results. I always thought, that if i have a non-interacting system and double the amount of CPUs, i You do use PME, which means a global interaction of all charges. would get a simulation which takes only half the time (so the times as defined above would be equal). If the system does have interactions, i would lose some performance due to communication. Due to node imbalance there could be a further loss of performance. Keeping this in mind, i can only explain the timings for version 4.0.7 2cpu - 4cpu (2cpu a little bit faster, since going to 4cpu leads to more communication - loss of performance). All the other timings, especially that 1cpu takes in each case longer than the other cases, i do not understand. Probalby the system is too small and / or the simulation time is too short for a scaling test. But i would assume that the amount of time to setup the simulation would be equal for all three cases of one GROMACS-version. Only other explaination, which comes to my mind, would be that something went wrong during the installation of the programs… You might want to take a closer look at the timings in the md.log output files, this will give you a clue where the bottleneck is, and also tell you about the communication-computation ratio. Best, Carsten Please, can somebody enlighten me? Greetings Thomas -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] GROMACS with different gcc and FFT versions but one unique *tpr file
Hi Thomas, the .tpr files you prepare should be identical if you prepare them with the same Gromacs version - regardless of the compiler. You can check that with gmxdump and a diff if you like. If you run these .tpr files using different machines or different compilers they will not be numerically identical. Even if you run them twice on the same machine but with dynamic load balancing on, they will not be numerically identical any more. Carsten On Nov 8, 2012, at 3:43 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Dear all, i have access to a cluster on which GROMACS is compiled with a different version of GCC and a different FFT libary (compared to the local machine). Will this affect simulationns if i prepare the *.tpr on the local machine and run the simulation on the cluster and the local machine? Sorry if this is a dumb question. I could imagine that the two simulations will be not numerical identical due to the different FFT libaries, but how strong this effect is and what else could happen i have no idea... Greetings Thomas -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] Regarding g_tune_pme optimization
Hi, On Nov 1, 2012, at 4:13 PM, Venkat Reddy venkat...@gmail.com wrote: Dear all Gromacs users, I have *two *questions: 1) I have been doing my simulation on a computer having 24 processors. I issued *g_tune_pme -s *.tpr -launch *command to directly launch my *mdrun *with the optimized settings. At the end of optimization, g_tune_pme has given -npme as *'0'*. My doubt is, how could it be possible to get best performance without dedicated PME nodes? This is normal, it just means that 24 PME nodes are optimal and thus no *separate* PME nodes are needed. Carsten 2) What could be the optimum value for *-rcom *to get the best performance on a super cluster (*i.e., 256 nodes*)? Thanks in advance With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] too much warnings and notes
Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly. You can also override the warnings with the -maxwarn number option in grompp. Carsten On Oct 29, 2012, at 3:52 PM, Albert mailmd2...@gmail.com wrote: hello: I am generating a .tpr file for proten/ligand system, but it has so much warnings: NOTE 1 [file md.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 23436 of the 23436 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 20254 of the 23436 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'LIG' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'POPC' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Setting gen_seed to 6947582 Velocities were taken from a Maxwell distribution at 300 K NOTE 3 [file complex.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Number of degrees of freedom in T-Coupling group Protein_LIG is 9475.34 Number of degrees of freedom in T-Coupling group POPC is 33353.66 Number of degrees of freedom in T-Coupling group Water_and_ions is 53973.00 Largest charge group radii for Van der Waals: 0.299, 0.299 nm Largest charge group radii for Coulomb: 0.299, 0.299 nm NOTE 4 [file md.mdp]: The sum of the two largest charge group radii (0.597592) is larger than rlist (1.00) - rvdw (1.20) -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] too much warnings and notes
Hi, On Oct 29, 2012, at 3:57 PM, Albert mailmd2...@gmail.com wrote: On 10/29/2012 03:56 PM, Carsten Kutzner wrote: Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly. You can also override the warnings with the -maxwarn number option in grompp. Carsten Hello Carsten: thanks for kind reply. the only thing I confused is the last one: NOTE 4 [file md.mdp]: The sum of the two largest charge group radii (0.597592) is larger than rlist (1.00) - rvdw (1.20) this is explained here: http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb Carsten -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] Ion conduction through a protein-membrane system
Hi Shima, there is also a patch for Gromacs available to study ion conduction through membrane channels that you might find useful. Please take a look at this page: http://www.mpibpc.mpg.de/grubmueller/compel Best, Carsten On Oct 2, 2012, at 8:16 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear users, I want to study ion conduction through a protein-memrane system. First of all, I tried to simulate a usual protein-membrane system. I'd like to know if it is possible to add asymmetrical number of ions to leaflets of membrane? Secondly, is it possible to apply an external electrical field to study ion conduction in a system? Thanks in advance. Sincerely, Shima -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] g_tune_pme cannot be executed
Hi Zifeng, have you tried to use g_tune_pme -npstring none … Carsten On Aug 20, 2012, at 5:07 PM, zifeng li lizife...@gmail.com wrote: Dear Gromacs users, Morning! I am using Gromacs 4.5.4 version and tries to use the magic power of g_tune_pme. However, it cannot be executed with the error in benchtest.log file: mpirun error: do not specify a -np argument. it is set for you. The cluster I use needs to submit mpirun job though PBS script, which looks like following: #PBS -l nodes=8 #PBS -l walltime=2:00:00 #PBS -l pmem=2gb cd $PBS_O_WORKDIR # echo echo echo Job started on `hostname` at `date` g_tune_pme -s npt echo echo Job Ended at `date` echo ~ I can run the command mpirun mdrun_mpi -deffnm npt using this PBS script before and as you notice, -np for g_tune_mpe is not used. Any suggestions about this issue? What I have tried for your reference: 1. to delete the first line. well...it won't help. 2. to set the environmental variable as Manual suggests curiously: export MPIRUN=/usr/local/mpirun -machinefile hostsuse my account name as the hosts here. Thanks in advance! Good day :) -Zifeng -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] g_tune_pme for multiple nodes
Hi Chandan, g_tune_pme also finds the optimal number of PME cores if the cores are distributed on multiple nodes. Simply pass the total number of cores to the -np option. Depending on the MPI and queue environment that you use, the distribution of the cores over the nodes may have to be specified in a hostfile / machinefile. Check g_tune_pme -h on how to set that. Best, Carsten On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I am using 4.5.5 of gromacs. I was trying to use g_tune_pme for a simulation. I intend to execute mdrun at multiple nodes with 12 cores each. Therefore, I would like to optimize the number of pme nodes. I could execute g_tune_pme -np 12 md.tpr. But this will only find the optimal PME nodes for single nodes run. How do I find the optimal PME nodes for multiple nodes. Any suggestion would be helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] how to optimize performance of IBM Power 775?
Hi Albert, On Aug 25, 2012, at 7:37 AM, Albert mailmd2...@gmail.com wrote: Dear: Our institute got a IBM Power 775 cluster and it claimed to be very good. However, it doesn't support g_tune_pme. Are you shure that it is not supported? Maybe you just need the right syntax. I use the following script for job submission: #@ job_name = gromacs_job #@ output = gromacs.out #@ error = gromacs.err #@ class = kdm #@ node = 4 #@ tasks_per_node = 32 #@ wall_clock_limit = 01:00:00 #@ network.MPI = sn_all,not_shared,US,HIGH #@ notification = never #@ environment = COPY_ALL #@ job_type = parallel #@ queue mpiexec -n 128 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s md.tpr it is only 7 ns/day. However, in another cluster with the same system, Core number and parameters, I can get up to 30 ns/day. Does anybody have any advices for this issue? On a Power6 machine, I have successfully used the following job file: # @ shell=/bin/ksh # # Sample script for LoadLeveler # # @ error = run_1.err.$(jobid) # @ output = run_1.out.$(jobid) # @ job_type = parallel # @ environment= COPY_ALL # @ node_usage= not_shared # @ node = 1 # @ tasks_per_node = 4 # @ resources = ConsumableCpus(1) # @ network.MPI = sn_all,not_shared,us # @ wall_clock_limit = 0:05:00 # @ notification = complete # @ queue # # run the program # export MDRUN=/path/to/gromacs-4.5.1/bin/mdrun_mpi export MPIRUN=poe #no poe here! /path/to/g_tune_pme -np 4 \ -npstring none -s ./ap.tpr -resetstep 1 -steps 10 Hope that helps, Carsten thank you very much Albert -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] how to run g_tune_pme in cluster?
On Apr 26, 2012, at 11:37 AM, Albert wrote: hello: it can find mdrun correctly. and it is only give me the log file as I mentioned in previous thread. What files are produced by g_tune_pme? Is there a benchtest.log? Can you cat its contents? Carsten thank you very much On 04/26/2012 09:53 AM, Carsten Kutzner wrote: Hi, what output does g_tune_pme provide? What is in log and in perf.out? Can it find the correct mdrun / mpirun executables? Carsten On Apr 26, 2012, at 9:28 AM, Albert wrote: Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I tried many times with following command: g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt 24 log but it always failed. Option Type Value Description -- -[no]h bool no Print help info and quit -[[CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105 [CUDANodeA:03384] [[60523,1],22] could not get route to [[INVALID],INVALID] [CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 86 -- 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 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 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: 4095 characters, fgets2 has size 4095
Hi Steven, you might have to remove files with weird names (such as ._name) in the directory where you run grompp or in your forcefield directory. Carsten On Apr 10, 2012, at 11:52 AM, Steven Neumann wrote: Dear Gmx Users, It is 1st time I came across such problem. While preparing my NPT simulation before umbrella samping: grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' Its not about the files in bad format as I have never had this problem - I am using Gromacs 4.5.4 installed on the cluster, I am using PuTTy shell. I always use dos2gmx ibefore processing. Can you advise? Steven -- 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 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] another g_tune_pme problem
On Apr 1, 2012, at 8:01 PM, Albert wrote: Hello: I am trying to test g_tune_pme in workstation by command: g_tune_pme_d -v -s md.tpr -o bm.trr -cpi md.cpt -cpo bm.cpt -g bm.log -launch -nt 16 but it stopped immediately with following logs. I complied gromacs with a -d in each module such as mdrun_d and I aliased mdrun_d to mdrun in the shell. However, my g_tune_pme still claimed that it cannot execute md_run.. Hi, so what does benchtest.log say? Carsten thank you very much --log-- back Off! I just backed up perf.out to ./#perf.out.5# Will test 3 tpr files. Will try runs with 4 - 8 PME-only nodes. Note that the automatic number of PME-only nodes and no separate PME nodes are always tested. Back Off! I just backed up benchtest.log to ./#benchtest.log.5# --- Program g_tune_pme_d, VERSION 4.5.5 Source code file: gmx_tune_pme.c, line: 631 Fatal error: Cannot execute mdrun. Please check benchtest.log for problems! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Once Again Let Me Do This (Urban Dance Squad) -- 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 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] Scaling/performance on Gromacs 4
Hi Sara, my guess is that 1500 steps are not at all sufficient for a benchmark on 64 cores. The dynamic load balancing will need more time to adapt the domain sizes for optimal balance. It is also important that you reset the timers when the load is balanced (to get clean performance numbers); you might want to use the -resethway switch for that. g_tune_pme will help you find the performance optimum on any number of nodes, from 4.5 on it is included in Gromacs. Carsten Am Feb 20, 2012 um 5:12 PM schrieb Sara Campos: Dear GROMACS users My group has had access to a quad processor, 64 core machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores) and I made some performance tests, using the following specifications: System size: 299787 atoms Number of MD steps: 1500 Electrostatics treatment: PME Gromacs version: 4.0.4 MPI: LAM Command ran: mpirun -ssi rpi tcp C mdrun_mpi ... #CPUS Time (s) Steps/s 64 195.000 7.69 32 192.000 7.81 16 275.000 5.45 8 381.000 3.94 4 751.000 2.00 2 1001.000 1.50 1 2352.000 0.64 The scaling is not good. But the weirdest is the 64 processors performing the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on JCTC and I do not understand why this is happening. Can anyone help? Thanks in advance, Sara -- 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 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] Is there a way to omit particles with, q=0, from Coulomb-/PME-calculations?
Hi Thomas, Am Jan 17, 2012 um 10:29 AM schrieb Thomas Schlesier: But would there be a way to optimize it further? In my real simulation i would have a charged solute and the uncharged solvent (both have nearly the same number of particles). If i could omit the uncharged solvent from the long-ranged coulomb-calculation (PME) it would save much time. Or is there a reason that some of the PME stuff is also calculated for uncharged particles? For PME you need the Fourier-transformed charge grid and you get back the potential grid from which you interpolate the forces on the charged atoms. The charges are spread each on typically 4x4x4 (=PME order) grid points, and in this spreading only charged atoms will take part. So the spreading part (and also the force interpolation part) will become faster with less charges. However, the rest of PME (the Fourier transforms and calculations in reciprocal space) are unaffected by the number of charges. For this only the size of the whole PME grid matters. You could try to lower the number of PME grid points (enlarge fourierspacing) and at the same time enhance the PME order (to 6 for example) to keep a comparable force accuracy. You could also try to shift more load to real space, which will also lower the number of PME grid points (g_tune_pme can do that for you). But I am not shure that you can get large performance benefits from that. Best, Carsten (Ok, i know that this is a rather specical system, in so far that in most md-simulations the number of uncharged particles is negligible.) Would it be probably better to move the question to the developer-list? Greetings Thomas On 17/01/2012 7:32 PM, Thomas Schlesier wrote: On 17/01/2012 4:55 AM, Thomas Schlesier wrote: Dear all, Is there a way to omit particles with zero charge from calculations for Coulomb-interactions or PME? In my calculations i want to coarse-grain my solvent, but the solute should be still represented by atoms. In doing so the solvent-molecules have a zero charge. I noticed that for a simulation with only the CG-solvent significant time was spent for the PME-part of the simulation. If i would simulate the complete system (atomic solute + coarse-grained solvent), i would save only time for the reduced number of particles (compared to atomistic solvent). But if i could omit the zero-charge solvent from the Coulomb-/PME-part, it would save much additional time. Is there an easy way for the omission, or would one have to hack the code? If the latter is true, how hard would it be and where do i have to look? (First idea would be to create an index-file group with all non-zero-charged particles and then run in the loops needed for Coulomb/PME only over this subset of particles.) I have only experience with Fortran and not with C++. Only other solution which comes to my mind would be to use plain cut-offs for the Coulomb-part. This would save time required for doing PME but will in turn cost time for the calculations of zeros (Coulomb-interaction for the CG-solvent). But more importantly would introduce artifacts from the plain cut-off :( Particles with zero charge are not included in neighbour lists used for calculating Coulomb interactions. The statistics in the M E G A -F L O P S A C C O U N T I N G section of the .log file will show that there is significant use of loops that do not have Coul component. So already these have no effect on half of the PME calculation. I don't know whether the grid part is similarly optimized, but you can test this yourself by comparing timing of runs with and without charged solvent. Mark Ok, i will test this. But here is the data i obtained for two simulations, one with plain cut-off and the other with PME. As one sees the simulation with plain cut-offs is much faster (by a factor of 6). Yes. I think I have seen this before for PME when (some grid cells) are lacking (many) charged particles. You will see that the nonbonded loops are always VdW(T) for tabulated VdW - you have no charges at all in this system and GROMACS has already optimized its choice of nonbonded loops accordingly. You would see Coul(T) + VdW(T) if your solvent had charge. It's not a meaningful test of the performance of PME vs cut-off, either, because there are no charges. Mark --- With PME: M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops --- VdW(T) 1132.029152 61129.574 0.1 Outer nonbonded loop1020.997718 10209.977 0.0 Calc Weights
Re: [gmx-users] modify the gromacs4.5.5 code: using cout
Use fprintf(stdout, …); Carsten On Nov 30, 2011, at 12:27 PM, 杜波 wrote: dear teacher, i want to modify the gromacs4.5.5 code ,can i use function cout which is introuduce in c++. i add the code #include string.h #include iostream at the head of the md.c but when i make , there is a error md.c:103:20: error: iostream: No such file or directory thanks regards, Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 ; +8613820062885 E-mail: 2008d...@gmail.com ; dubo2...@tju.edu.cn -- 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 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] do_dssp segmentation fault
Hi, On Nov 23, 2011, at 8:24 AM, Alex Jemulin wrote: Thanks for your reply Could you tell me the name of the file to download and how to install it? Please follow the instructions at http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage and http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial. In short: git clone git://git.gromacs.org/gromacs.git git checkout --track -b release-4-5-patches origin/release-4-5-patches If you are using CMake, you can then just install this like the normal .tar.gz distributions from the gromacs home page. If you are using autotools, do a ./bootstrap before the configure step. Best, Carsten Bests Da: Carsten Kutzner ckut...@gwdg.de A: Alex Jemulin alexbioi...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Inviato: Martedì 22 Novembre 2011 13:25 Oggetto: Re: [gmx-users] do_dssp segmentation fault Dear Alex, On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? I removed a segmentation fault in do_dssp a couple of weeks ago but this is post version 4.5.5. So you need to check out the current release-4-5-patches from the git server. I believe this will fix your problem. Carsten Thank in ad -- 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 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] do_dssp segmentation fault
Dear Alex, On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? I removed a segmentation fault in do_dssp a couple of weeks ago but this is post version 4.5.5. So you need to check out the current release-4-5-patches from the git server. I believe this will fix your problem. Carsten Thank in ad -- 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 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] suggestion that mdrun should ensure npme the numberof processes
Hi, On Aug 17, 2011, at 1:24 AM, chris.ne...@utoronto.ca chris.ne...@utoronto.ca wrote: Currently, gromacs4.5.4 gives a segfault if one runs mpirun -np 8 mdrun_mpi -npme 120 with no warning of the source of the problem. Obviously npmennodes is a bad setup, but a check would be nice. cr-npmenodes is set in mdrun.c right after the command line args are passed, and in the code there is also a comment that npmennodes should not cause a problem at that point. However, if npmennodes, in init_domain_decomposition / dd_choose_grid / optimize_ncells the number of pp nodes = nnodes-npme turns out to be negative such that in factorize the memory allocation does not work. I would have filed a bug report, however the web page seems to be down at the moment. Best, Carsten Thank you, Chris. -- 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 thewww 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] g_tune_pme
Hi Carla,
On Jul 28, 2011, at 9:38 AM, Carla Jamous wrote:
Hi everyone, please I was running simulations with gromacs version 4.0.3 ,but
I got the following error:
Average load imbalance: 12.1 %
Part of the total run time spent waiting due to load imbalance: 6.9 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 %
Y 9 %
Average PME mesh/force load: 0.807
Part of the total run time spent waiting due to PP/PME imbalance: 5.3 %
This is not an error but just a hint how you could optimize your performance.
NOTE: 6.9 % performance was lost due to load imbalance
in the domain decomposition.
NOTE: 5.3 % performance was lost because the PME nodes
had less work to do than the PP nodes.
You might want to decrease the number of PME nodes
or decrease the cut-off and the grid spacing.
After searching the archive mailing list and reading the manual , I decided
to use g_tune_pme so I switched to gromacs 4.5.4. Here's my script:
Note that there is also a g_tune_pme version for 4.0.7:
http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/index.html
As another possibility, you can use the tpr file you created with 4.0.x as
input for
Gromcas 4.5.x, also for g_tune_pme, this is probably the easiest solution.
#PBS -S /bin/bash
#PBS -N job_md6ns
#PBS -e job_md6ns.err
#PBS -o job_md6ns.log
#PBS -m ae -M carlajam...@gmail.com
#PBS -l select=2:ncpus=8:mpiprocs=8
#PBS -l walltime=024:00:00
cd $PBS_O_WORKDIR
export GMXLIB=$GMXLIB:/scratch/carla/top:.
module load gromacs
chem=/opt/software/SGI/gromacs/4.5.4/bin/
mdrunmpi=mpiexec /opt/software/SGI/gromacs/4.5.4/bin/
${chem}grompp -v -f md6ns.mdp -c 1rlu_apo_mdeq.gro -o 1rlu_apo_md6ns.tpr -p
1rlu_apo.top
${mdrunmpi}g_tune_pme -v -s 1rlu_apo_md6ns.tpr -o 1rlu_apo_md6ns.trr -cpo
state_6ns.cpt -c 1rlu_apo_md6ns.gro -x 1rlu_apo_md6ns.xtc -e md6ns.edr -g
md6ns.log -np 4 -ntpr 1 -launch
But now, I have the following error message:
Fatal error:
Library file residuetypes.dat not found in current dir nor in your GMXLIB
path.
Why don't you build your tpr file on your workstation and then switch over
to the cluster? I guess this will make life easier for you.
Also note that you must not call g_tune_pme in parallel (which you do by
${mdrunmpi}g_tune_pme. g_tune_pme will spawn its own MPI processes with the
help of the MPIRUN and MDRUN environment variables. See g_tune_pme -h,
probably you need do set
export MDRUN=/opt/software/SGI/gromacs/4.5.4/bin/mdrun
export MPIRUN=`which mpiexec`
Hope that helps,
Carsten
Except that I'm using amber94 force-field and that my topology files are in a
special directory called top where I modified certain things. With gromacs
4.0.3, it always worked so I don't know what is happening here.
Please does anyone have an idea of what it might be?
Do I have to run pdb2gmx, editconf, etc... with the gromacs 4.5.4 for it to
work?
Thank you,
Carla
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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Re: [gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI
Hi, you could try a make clean, and then configure again with --enable-threads. It seems for some reason you only build the serial mdrun version. Carsten On Mar 24, 2011, at 1:51 PM, Adam Herbst wrote: Dear GROMACS users, I successfully installed GROMACS 4.5.1 several months ago on a Mac Pro with 12 CPUs, and the mdrun command (not mpirun mdrun_mpi) allows parallel simulations--it automatically uses multiple processors, while the number of processors can be manually specified as N with the flag mdrun -nt N. I understand that this is a feature of GROMACS 4 and later. Now I am making minor changes to the mdrun source code, and I want to recompile such that the parallel version of mdrun is updated with my changes. But when I run: make mdrun (or just make) make install-mdrun (or just make install) from the top-level source directory, the only executables that are updated are the ones with the _mpi suffix, such as mdrun_mpi. The version of mdrun in src/kernel/ is updated, but this one has no -nt flag and cannot seem to run on multiple processors. And when I run mpirun -np N mdrun_mpi [options], the same simulation is started separately on each processor, leading to a crash. If I use mpirun -np 1 -cpus-per-proc N mdrun_mpi [options], I get an error message that this is not supported on my computer (An attempt to set processor affinity has failed). I can't configure the input .tpr file for parallel because grompp doesn't have the -np flag in GROMACS 4. How can I update the parallel-capable mdrun executable with my changes? Thanks in advance, Adam -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] New maintenance release: gromacs-4.5.4
Hi, try to add the --disable-shared flag to your invocation of .configure. Carsten On Mar 22, 2011, at 3:26 PM, Ye MEI wrote: Thank you for the new version of gromacs. But the compilation of gromacs failed on my computer. The commands are as follows: make distclean export CC=icc export F77=ifort export CXX=icc export CFLAGS=-xS -I/apps/fftw3/include export FFLAGS=-xS -I/apps/fftw3/include export CXXFLAGS=-I/apps/fftw3/include export LDFLAGS=-L/apps/fftw3/lib -lfftw3f ./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x --with-qmmm-gaussian make and the error message is icc -shared .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o .libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o .libs/domdec_network.o .libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o .libs/ewald.o .libs/force.o .libs/forcerec.o .libs/ghat.o .libs/init.o .libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o .libs/nsgrid.o .libs/perf_est.o .libs/genborn.o .libs/genborn_sse2_single.o .libs/genborn_sse2_double.o .libs/genborn_allvsall.o .libs/genborn_allvsall_sse2_single.o .libs/genborn_allvsall_sse2_double.o .libs/gmx_qhop_parm.o .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o .libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o .libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o .libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o .libs/vcm.o .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o .libs/fft5d.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o .libs/qm_gamess.o .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o .libs/gmx_fft_fftpack.o .libs/gmx_fft_mkl.o .libs/qm_orca.o .libs/mdebin_bar.o -Wl,--rpath -Wl,/home/ymei/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath -Wl,/apps/gromacs4.5/lib -lxml2 -L/apps/fftw3/lib /apps/fftw3/lib/libfftw3f.a ../gmxlib/.libs/libgmx.so -lnsl -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0 ld: /apps/fftw3/lib/libfftw3f.a(problem.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value However, it works fine for gromacs 4.5.3. Can anyone help? Ye MEI 2011-03-22 From： Rossen Apostolov Date： 2011-03-22 03:24:55 To： Discussion list for GROMACS development; Discussion list for GROMACS users; gmx-announce CC： Subject： [gmx-users] New maintenance release: gromacs-4.5.4 Dear Gromacs community, A new maintenance release of Gromacs is available for download at ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz. Some notable updates in this release: * Fixed pdb2gmx picking up force field from local instead of library directory * Made pdb2gmx vsite generation work again for certain His namings. * Fixed incorrect virial and pressure averages with certain nst... values (instantaneous values correct) * Fixed incorrect cosine viscosity output * New -multidir alternative for mdrun -multi option * Several minor fixes in analysis tools * Several updates to the program documentation Big thanks to all developers and users! Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- 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] Performance in ia64 and x86_64
Hello Ignacio, On Feb 25, 2011, at 10:25 AM, Ignacio Fernández Galván wrote: Well, I've compiled mdrun with MPI (with fortran kernels in the ia64), and run my test system in both machines, with a single processor. The results are still worrying (to me). This is a 50 time step (0.5 ns) simulation with 1500 water molecules, not a big system, but it still takes some hours: x86_64: 3.147 ns/day ia64: 0.507 ns/day Is this difference normal? Am I doing anything wrong? what further data should I Some time ago I compared Itanium and x86 performances, see the fifth slide of this PDF: http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/Talks/PDFs/kutzner07talk-optimizing.pdf With Fortran kernels I got a performance of 0.31 ns/day for an 80,000 atom system (with PME) on an Altix 4700, so your 0.5 ns/day for 1,500 waters seems too slow to me. What processor is this? Are you shure you are using the Fortran and not the C kernels? Carsten-- 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] GROMACS installation query
On Feb 23, 2011, at 6:16 AM, Tom Dupree wrote: Greetings all, I am new to Linux and wish to confirm some facts before I press on with the installation. In the installation guide, http://www.gromacs.org/Downloads/Installation_Instructions There is a line saying “...Where assembly loops are in use, GROMACS performance is largely independent of the compiler used. However the GCC 4.1.x series of compilers are broken for GROMACS, and these are provided with some commodity Linux clusters. Do not use these compilers!...” Firstly I assume this still applies to GROMACS version 4.5 and not just to earlier ones. (Confirm/deny?) To my knowledge there are no workarounds for gcc 4.1.x compiler bugs in the newer Gromacs versions. Secondly I read this as GCC 4.2.x and greater should be fine. (confirm/deny?) Yes. You could also use the Intel compiler which will typically give you one or two percent extra performance. But do not expect too much. Carsten -- 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] configure: error: cannot compute sizeof (off_t)
On Feb 20, 2011, at 9:30 PM, Justin Kat wrote: Dear experts, I am still unable to overcome this error during the configuration: configure: error: cannot compute sizeof (off_t) See `config.log' for more details. So what does config.log say about cannot compute sizeof (off_t) ? Carsten I came across this thread with the exact same setup as I have: http://lists.gromacs.org/pipermail/gmx-users/2011-February/058369.html I have tried uninstalling openmpi 1.4.4 and installing the more stable openmpi1.4.3 but I am still experiencing the same error. ./configure --enable-mpi --program-suffix=_mpi MPICC=/usr/local/bin/mpicc --with-fft=fftw3 I have also tried to explicitly provide the path to mpicc as above but it still gives me the same error. This may or may not be relevant but at the end of the config.log there is also this line: configure: exit 77 Does that mean anything? Any help at all is appreciated! Thanks, Justin-- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Performance in ia64 and x86_64
Hi Ignacio, On Feb 11, 2011, at 1:33 PM, Ignacio Fernández Galván wrote: Hi all, I'm compiling and testing gromacs 4.5.3 in different machines, and I'm wondering if it's normal that the ia64 is much slower than the x86_64 I don't know full details of the machines, because I'm not the administrator or owner, but /proc/cpuinfo says: ia64 (128 cores): Dual-Core Intel(R) Itanium(R) Processor 9140N x86_64 (16 cores): Intel(R) Xeon(R) CPU E5540 @ 2.53GHz Just looking at the GHz, one is 2.5 and the other is 1.4, so I'd expect some difference, but not a tenfold one: with 8 threads (mdrun -nt 8) I get 0.727 hours/ns on the x86_64, but 7.607 hours/ns on the ia64. (With 4 threads, it's 1.3 and 13.7). I compiled both cases with gcc, although different versions, and default options. I had read assembly or fortran kernels could help with ia64, but fortran is apparently incompatible with threads, and when I tried with assembly the mdrun seemed stuck (no timestep output was written). Is this normal? Is Yes, there is a problem with the ia64 assembly loops and this is exactly how it manifests. I did run into that problem several times. What you can do is to use the fortran kernels and compile with MPI. The performance of the threaded and MPI versions should be the same, and the fortran kernels are nearly as fast as the ia64 assembly. Probably you can speed things up a few percent by using the Intel compiler. Cheers, Carsten there something else I'm missing? Also, in the x86_64 system I get much lower performance with 12 or 16 threads, I guess that could be because of the cores/processors, but I don't know what's the exact configuration of the machine. Again: is this normal? Thanks, Ignacio -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] General MD question
Hi Stephan, On Jan 31, 2011, at 5:18 PM, lloyd riggs wrote: Dear All, A quick question as I have not really delved into code for gromacs ever, nor know anyone close whom has worked on it. If I set up an MD simulation using a 4 protein complex, and 1 small peptide, plus waters, etc...and run the whole thing the proteins never move, only the amino acids within(constant temp RT and pressure 1 bar). Two domains make one complex, and another two the other. Basically, if I seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will drift (the chains) towards each other, but the two large (global) protein units never move their center (I know I can make it work with Pull vectors, but why not in the simple system with a generated initial randomized velocities), I woundered why they are fixed in a normal run with minimal parameters? Is there a reason (specific to developers), historical reason, or other? As waters move around fine, and anything else added (salt, small molecules of 20-30 atoms, water) except the central molecule(s) of interest. In a 'normal' run they should not be fixed. Could it be that you did accidentally fix them by specifying center of mass removal (comm-grps in .mdp)? Carsten Grüsse Stephan Watkins -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] segmentation fault: g_velacc
Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] segmentation fault: g_velacc
Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I don't use the -m option, I have no problem. Upon searching the userslist, I found this thread: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054813.html and a patch, but I don't find any related bugs reported elsewhere. So, I am just wondering if I sould go ahead and use the patch or if there could be something else that is wrong. Will appreciate any kind of pointers. Either apply the patch or upgrade to a newer version of Gromacs that contains this bug fix. -Justin Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Re: Gromacs + GPU: Problems running dppc example in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz
Hi Camilo, On Jan 27, 2011, at 7:19 AM, Camilo Andrés Jimenez Cruz wrote: Sorry, abrupt sending, the coulombtype is the same coulombtype = cut-off Is your cut-off actually 0.0 then? Carsten and constraints = all-bonds is the same. Any idea? 2011/1/27 Camilo Andrés Jimenez Cruz camilo.jimen...@gmail.com Hi all! I am trying to run the dppc example located in ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz, with the gpu version of gromacs, when I run it I get WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. --- Program mdrun_sg, VERSION 4.5.3 Source code file: /usr/src/redhat/BUILD/gromacs-4.5.3/src/kernel/openmm_wrapper.cpp, line: 555 Fatal error: OpenMM supports only the following methods for electrostatics: NoCutoff (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- but when I compare the mdp file with the examples in http://www.gromacs.org/Downloads/Installation_Instructions/Gromacs_on_GPUs (impl_1nm, for example), the integrator is the same integrator = md -- Camilo Andrés Jiménez Cruz -- Camilo Andrés Jiménez Cruz -- 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 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] 4 x Opteron 12-core or 4 x Xeon 8-core ?
Hi David, On Jan 20, 2011, at 1:21 PM, David McGiven wrote: Dear Gromacs Users, We're going to buy a new server for HPC. It is going to run mainly Gromacs calculations. Regarding Gromacs performance, I'm wondering which one, you Gromacs users and developers, think will be faster. AMD Server : 4 x AMD Opteron 6176 12-core 2.3 Ghz + 96GB Memory (2GB / core) Intel Server : 4 x Intel Xeon 8-core 2.66 Ghz + 64 GB RAM (2GB / core) We normally run ~100k atom systems with PME and explicit water. Which one would you recommend ? Also, of course, AMD Server is cheaper. But we are mainly interested on performance. If you have a fixed amount of money, you will get the most ns/day if you buy the AMD Magny Cours machines. Each one will be slower compared to the Intel server but you will get more servers altogether, thus more total performance. If you can only buy a single server and you do not care about what it costs, the Intel will be faster for shure. Note that you do not need 2 GB/core for 100k atoms MD systems if you run Gromacs. Half of it will be more than enough. Carsten Thanks. Best Regards, David -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] gromacs 4.5.3 with threads instead of MPI
Hi, On Jan 17, 2011, at 4:11 PM, Arnau Cordomi wrote: Dear Gromacs Users, We normally run gromacs 4.0.x mdrun with OpenMPI in a 24 core shared-memory server (SunFire X4450). i. e. the command we use for a 12 core run is : mpirun -np 12 mdrun -v -c output_md.gro This is working great so far. Now we are trying to use gromacs 4.5.x and I found this on the release notes (http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x) : “Running on a multi-core node now uses thread-based parallelization to automatically spawn the optimum number of threads in the default build. MPI is now only required for parallelization over the network.” So, I guess now instead of “mpirun -np 12 mdrun -v -c output_md.gro” we should use “mdrun -nt 12 -v -c output_md.gro” and expect the same performance. Am I right? Right. Also, is this “automatically spawn the optimum number of threads” reliable ? Does that mean that if the recommended number is 4 cores (threads) there’s no way to make it run faster even if specifying -nt 12 or 24 ? You should use the number of logical cores you have. This is normally the number of physical cores, unless you use some kind of hyperthreading or simultaneous multiprocessing in which case -nt is twice the number of physical cores. mdrun reads the number of threads from your system via sysconf(). Carsten Any advice will be welcome. Thanks in advance. Best Regards, Arnau Cordomí -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] g_tune_pme big standard deviation in perf.out output
Dear Yanbin, On Dec 30, 2010, at 9:20 PM, WU Yanbin wrote: I'm simulating a SPC/E water box with the size of 4nm by 4nm by 4nm. The command g_tune_pme was used to find the optimal PME node numbers, Coulomb cutoff radius and grid spacing size. The following command is used: g_tune_pme -np 24 -steps 5000 -resetstep 500 ... rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The simulation is done with no error. Below is the output: --- Line tpr PME nodes Gcycles Av. Std.dev. ns/dayPME/fDD grid 0 0 12 2813.762 187.1159.6040.3614 3 1 1 0 11 2969.826 251.2109.1120.510 13 1 1 2 0 10 2373.469 154.005 11.3850.4452 7 1 3 09 2129.519 58.132 12.6650.6015 3 1 4 08 2411.653 265.233 11.2480.5704 4 1 5 07 2062.770 514.023 13.4900.616 17 1 1 6 06 1539.237 89.189 17.5470.7486 3 1 7 00 1633.318 113.037 16.548 - 6 4 1 8 0 -1( 4) 1330.146 32.362 20.2761.0504 5 1 --- The optimal -npme is 4. It seems to me that the Std. dev is too huge. This is the standard deviation resulting from multiple runs with the same settings. If you do not specify -r for the number of repeats explicitly to g_tune_pme, it will do two tests for each setting. For the optimum of 4 PME nodes the standard deviation is 2.4 percent of the mean, thus not large at all. Can anyone tell me the meaning of Gcycles Av. and Std. dev and their relations to the accuracy of ns/day? Both the number of CPU cycles as the ns/day values are determined from the md.log output file of the respective runs. g_tune_pme does the averaging for you, but you can also look at the individual results, these log files are still there after the tuning run. The standard deviation is printed only for the Gcycles - maybe it is a good idea to also print the standard deviation for the ns/day values. If the standard dev is X percent of the mean for the cycles, then it is also X percent of the mean ns/day. Another question: I tried g_tune_pme -np 24 -steps 1000 -resetstep 100 ... (the default value of g_tune_pme) rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The optimal -npme is 6, different from -npme=4 as obtained with big -nsteps. Should I increase -nsteps even more to get better estimate, or what else parameters should I try? In principle the results will become more exact, the longer the test runs are. For your system it seems that the load between the processes is not yet optimally balanced after the default 100 steps so that -resetstep 500 gives you a more accurate value. I think the -steps 5000 value is large enough, but another test with a higher resetstep value would answer your question. Since you already know that 7-12 PME nodes will not perform well, I would try g_tune_pme -np 24 -steps 5000 -resetstep 5000 -min 0.16 -max 0.25 ... Regards, Carsten Do let me know if the questions are not made clear. Thank you. Best, Yanbin -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] stopping mdrun without error massage
Dear Karim, a (small) load imbalance is perfectly normal for a parallel simulation and no need to switch over to particle decomposition (both domain and particle decomposition should however work). Are you shure you get no error message? People will need some more information here to be able to help. It is usually a good idea to include which MPI lib you are using and the exact command line how you invoked mdrun. You could anyway try to run on a single processor only and see whether this scenario also stops or whether you get a proper error message or core file. Carsten On Dec 22, 2010, at 12:34 PM, Mahnam wrote: In God We Trust Hello Dear GMX users I want to do MD on one peptide in water with gromacs 4.5.3. I minimized and equilibrated my system in NPT and NVT for 50 ps , but when I do final mdrun it has load imbalance and when I try -pd option it stops after 265 ps without any error massage !, can everybody help me. Here is my mdp file . constraints = hbonds integrator = md dt = 0.002 nsteps = 5000 nstcomm = 10 comm_mode = Linear comm_grps = protein nstxout = 250 nstvout = 1000 nstfout = 0 nstcalcenergy = 10 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb= 1.2 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes energygrps = protein SOL ; Berendsen temperature coupling is on in three groups Tcoupl = v-rescale tau_t = 0.1 1 tc-grps = protein bulk ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-Rahman tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] how to add a electric field to the water box when do a simulation
On Dec 20, 2010, at 12:09 PM, 松啸天 wrote: dear: I would like to use the electric field inside a box defined by gromacs. So I added E_x 1 10 0in the .mdp file, is it the right approach? Yes, this will add an electric field of strength 10 V/nm acting in x-direction. Carsten i hope people who knows will help me to add the electric field when i do a simulation.that's all.thank you! yours sincerely -- 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 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] pullx.xvg / pullf.xvg
On Dec 16, 2010, at 2:23 PM, Poojari, Chetan wrote: Hi, Following were the commands which i used in the umbrella sampling simulations: grompp -f md_umbrella.mdp -c conf500.gro -p topol.top -n index.ndx -o umbrella500.tpr mdrun -v -deffnm umbrella500 Output:umbrella500.xvg, umbrella500.xtc, umbrella500.trr, umbrella500.log, umbrella500.gro, umbrella500.edr, umbrella500.cpt pullf.xvg and pullx.xvg files were not produced. With -deffnm you specified a default filename for all output files. Try to use mdrun -pf pullf.xvg -px pullx.xvg -s input.tpr Adding -h to mdrun will show you how your output files will be called. Carsten Please can I know should i mention -px pullx.xvg and -pf pullf.xvg in the mdrun? Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: 15 December 2010 17:00 To: gmx-users@gromacs.org Subject: [gmx-users] pullx.xvg / pullf.xvg please copy and paste your commands your output. It is unlikely that any of us are going to do that tutorial in order to understand your question. -- original message -- Hi, I am following the umbrella sampling tutorial written by Justin Lemkul. I was successfully able to run the umbrella sampling simulations, but for each configuration it outputted a single xvg file. For the data analysis i should have pullf.xvg / pullx.xvg filesbut these files are not outputted after the simulation run. I haven't made any changes to the .mdp files mentioned in the tutorial. Please can i know what might have gone wrong that it has not produced pullf.xvg and pullx.xvg files. Kind regards, chetan. -- 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 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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 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] g-WHAM
Hi Mohsen, for a start, it is always a good idea to read the help text of a command you are interested in, or to check the most recent version of the manual. Using Gromacs 4.5 g_wham -h will guide you to a JCTC paper about g_wham, which is a nice starting point. Check out this paper as well as the references therein! Also Google is your friend here: http://pubs.acs.org/doi/abs/10.1021/ct100494z http://onlinelibrary.wiley.com/doi/10.1002/jcc.540130812/pdf Carsten On Dec 14, 2010, at 9:20 AM, mohsen ramezanpour wrote: Dear All What is the algorithm of g-WHAM? in the other words ,what is the weighted histogeram analysis method? Thanks in advance for your reply Mohsen -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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 building Gromacs 4.5.3 using the Intel compiler
Hi, you might also need to use the mpiicc compiler wrapper instead of the mpicc to enforce using icc instead of gcc. Carsten On Dec 13, 2010, at 2:20 PM, Mark Abraham wrote: On 12/13/10, Miah Wadud Dr (ITCS) w.m...@uea.ac.uk wrote: Hello, I am trying to build Gromacs 4.5.3 using the Intel compiler, but I am encountering the following problems when I type make: It seems like there's some mismatch between how FFTW was compiled and how you're linking to it. Try a fresh FFTW compilation with this compiler, etc. Mark /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -L/gpfs/grace/fftw-3.2.2/lib -o grompp grompp.o libgmxpreprocess_mpi_d.la ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -lnsl -lm mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -o grompp grompp.o -L/gpfs/grace/fftw-3.2.2/lib ./.libs/libgmxpreprocess_mpi_d.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a ../mdlib/.libs/libmd_mpi_d.a /gpfs/grace/fftw-3.2.2/lib/libfftw3.a /gpfs/ueasystem/grace/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a -lnsl -lm /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(mapflags.o): In function `timelimit_to_flags': /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/ueasystem/grace/fftw-3.2.2/api/./mapflags.c:70: undefined reference to `__fmth_i_dlog' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(timer.o): In function `elapsed': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./cycle.h:244: undefined reference to `__mth_i_dfloatuk' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(generic.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./generic.c:73: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_r2hc': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(lt8-generic.o): In function `apply_hc2r': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./generic.c:128: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(vrank3-transpose.o): In function `transpose_toms513': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./vrank3-transpose.c:536: undefined reference to `__c_mzero1' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(trig.o): In function `real_cexp': /gpfs/ueasystem/grace/fftw-3.2.2/kernel/./trig.c:65: undefined reference to `__fmth_i_dsincos' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `apply': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:79: undefined reference to `__c_mzero8' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dht-rader.o): In function `mkomega': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:184: undefined reference to `__c_mzero8' /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./dht-rader.c:187: undefined reference to `__c_mcopy8_bwd' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(ct-hc2c-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./ct-hc2c-direct.c:130: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(dftw-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./dftw-direct.c:103: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/dft/./direct.c:74: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(direct-r2c.o): In function `iterate': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./direct-r2c.c:129: undefined reference to `__builtin_alloca' /gpfs/grace/fftw-3.2.2/lib/libfftw3.a(hc2hc-direct.o): In function `apply_buf': /gpfs/ueasystem/grace/fftw-3.2.2/rdft/./hc2hc-direct.c:96: undefined reference to `__builtin_alloca' make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/gpfs/ueasystem/grace/gromacs-4.5.3/src' make: *** [all-recursive] Error 1 [r...@head00 gromacs-4.5.3]# Any help will be greatly appreciated. The configure command prints the following: [r...@head00 gromacs-4.5.3]# ./configure --enable-double --enable-mpi --program-suffix=_mpi_d --prefix=/gpfs/grace/gromacs-4.5.3 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar
[gmx-users] Re: trouble parallelizing a simulation over a cluster
On Dec 8, 2010, at 1:03 PM, Hassan Shallal wrote: Thanks a lot Justin for the very helpful answers concerning the pressure equilibration. Using Berendsen Barostat over 200 ps has lead to the correct average pressure... I have another issue to discuss with you and with the Gromacs mailing list members; I have been trying to run a simulation on a computer cluster for the first time using a sub file script. What happened is that the .sub file attempted to run the simulation 24 times instead of parallelizing it over the 24 processors Here are the contents of run_1.sub file I tried to use to parallelize the simulation using qsub run_1.sub #PBS -S /bin/bash #PBS -N run_1 #PBS -l nodes=3:ppn=8 module load openmpi/gnu mpirun -np 24 /home/hassan/bin/bin/mdrun_mpi -deffnm run_1 -v run_1_update.txt exit $? What happens it that it outputs 24 run_1.log files, starting from #run_1.log1# all the way to #run_1.log23#...Has anyone faced this problem before? and If yes, any hints or solutions? This typically happens when using a serial mdrun. You should check with ldd whether mdrun_mpi is linked to the correct mpi library. Carsten I do appreciate any help in that domain Hassan From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Mon 12/6/2010 6:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pressure fluctuations Hassan Shallal wrote: Dear Gromacs users, I have some concerns about the both the pressure fluctuations and averages I obtained during the equilibration phase. I have already read through several similar posts as well as the following link http://www.gromacs.org/Documentation/Terminology/Pressure. I understand the pressure is a macroscopic rather than instantaneous property and the average is what really matters. I also found out through similar posts that negative average pressure indicates the system tendency to contract. In the above link, it mentioned that pressure fluctuations should decrease significantly with increasing the system's size. In my cases, I have a fairly big systems (case_1 with *17393* water molecules and case_2 with *11946 *water molecules). However, the pressure still has huge fluctuations (around 500 bars) from the reference value (1 bar). Here are the average pressure and density values resulting from the equilibration phases of two cases, please notice the negative average pressure values in both cases... Case_1_pressure: Energy Average Err.Est. RMSD Tot-Drift --- Pressure *-2.48342* 0.92369.709 -4.89668 (bar) Case_1_density: Energy Average Err.Est. RMSD Tot-Drift --- Density 1022.89 0.38 3.82532.36724 (kg/m^3) Case_2_pressure: Energy Average Err.Est. RMSD Tot-Drift --- Pressure *-8.25259*2.6423.681 -12.1722 (bar) Case_2_density: Energy Average Err.Est. RMSD Tot-Drift --- Density 1034.11 0.372.499641.35551 (kg/m^3) So I have some questions to address my concerns: 1- each of the above systems has a protein molecule, NaCl to give 0.15 M system and solvent (water) molecules... Could that tendency to contract be an artifact of buffering the system with sodium and chloride ions? I suppose anything is possible, but given that these are fairly standard conditions for most simulations, I tend to doubt it. My own (similar) systems do not show this problem. 2- how to deal with the tendency of my system to contract? Should I change the number of water molecules in the system? or Is it possible to improve the average pressure of the above systems by increasing the time of equilibration from 100 ps to may be 500 ps or even 1 ns? 3- Is there a widely used range of average pressure (for ref_p = 1 bar) that indicates acceptable equilibration of the system prior to the production? To answer #2 and #3 simultaneously - equilibration is considered finished when your system stabilizes at the appropriate conditions (usually temperature and pressure). Your results indicate that your equilibrium is insufficient. 4- I can't understand how the system has a tendency to contract whereas the average density of the solvent is already slightly higher than it should be (1000 kg/m^3). The contraction causes the density to rise. Pressure and density are not independent; density is a result of pressure. I would like
Re: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
On Dec 2, 2010, at 6:16 AM, WU Yanbin wrote: Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group. I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK. For this situation, is there a way of suppressing this error? Or what else can I do? If the system is small enough, you can run it on a single core and the problem cannot occur. You could also try to use particle decomposition (-pd) instead of domain decomposition. Or use less domains, i.e. less cores in total or at least less PP nodes if you use PME/PP splitting. This will at least reduce the probability for the problem to occur. Carsten PS: the GROMACS version I'm using is GROMACS4.5. Thank you. Best, Yanbin -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] installation
On Nov 24, 2010, at 4:04 PM, Rossella Noschese wrote: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: GMXRC is for setting the paths to your Gromacs executables. You can do that by typing source GMXRC, but this you have already done in your bashrc, so everything is already set up and fine! You will find all the Gromacs programs at your fingertips, e.g. mdrun -h prints out help for the main MD program. Carsten [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? -- 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 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] unexpexted stop of simulation
Hi, there was also an issue with the locking of the general md.log output file which was resolved for 4.5.2. An update might help. Carsten On Nov 3, 2010, at 3:50 PM, Florian Dommert wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11/03/2010 03:38 PM, Hong, Liang wrote: Dear all, I'm performing a three-day simulation. It runs well for the first day, but stops for the second one. The error message is below. Does anyone know what might be the problem? Thanks Liang Program mdrun, VERSION 4.5.1-dev-20101008-e2cbc-dirty Source code file: /home/z8g/download/gromacs.head/src/gmxlib/checkpoint.c, line: 1748 Fatal error: Failed to lock: md100ns.log. Already running simulation? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sitting on a rooftop watching molecules collide (A Camp) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 32 gcq#348: Sitting on a rooftop watching molecules collide (A Camp) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- [node139:04470] [[37327,0],0]-[[37327,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) -- mpiexec has exited due to process rank 0 with PID 4471 on node node139 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpiexec (as reported here). Perhaps the queueing system of your cluster does not allow running a job longer than 24h. Or the default is 24h and you have to supply the corresponding information to the submission script. /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzRdrEACgkQLpNNBb9GiPm1sgCg3LkRUWgiZvOOH/GIjp5ifbZI bJcAn1aamCMWlWTokD1+eDCLG1WhT/rd =4Vs3 -END PGP SIGNATURE- -- 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 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] Fwd: -pbc nojump
Hi, with the nojump option, your water molecules will slowly diffuse out of the home box and appear far away from your protein if you display the MD system with VMD or pymol. You can split your trajectory in two parts (using index groups) and use different options on them individually: a) on the water part (and also on the ions, if they are present), use trjconv -pbc mol b) on the rest, use trjconv -pbc nojump Then overlay both results in the visualization program. Carsten On Oct 27, 2010, at 9:40 AM, David van der Spoel wrote: I did simulation of protein-dna complex in water solvent. After simulation, two strands of dna was separated when I displayed my a.xtc with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc nojump) and problem fixed. But now I have another problem. Before using –pbc nojump, there were water molecules in interface of between protein and dna but, After using of –pbc nojump, 1) there was no water molecule in interface of between protein and dna. 2) The distance between water molecules and protein or dna was increased. I want to survey interfacial water molecules and dynamics of water medited hydrogen bonds. I had sent my question to gromacs mailing list, before, but my problem was not solved. -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Fwd: -pbc nojump
On Oct 27, 2010, at 10:05 AM, leila karami wrote: Hi Carsten Thanks for your answer. You got my case very well. I understand your mean as follows: 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group =protein-dna) Is that true? Yes, I would try it that way. You said, (Then overlay both results in the visualization program). How? In pymol for example, just load both PDBs. Carsten -- 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] g_dipole ? =salt-molecule = Does Gromacs consider counter ions?
On Oct 22, 2010, at 4:14 PM, Chih-Ying Lin wrote: Hi Sorry, I ask the same question again because i am not a decent person in this field. If possible, someone can give me a quick answer while i am trying to get understanding the source codes. My basic understanding is that Gromacs has other approach of calculating dipole moment instead of the following equation. dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. Gromacs does not have another approach. It exactly calculates the above equation. Take a look at the function mol_dip( ) in gmx_dipoles.c. There, the dipole moment is calculated for a single molecule. A molecule is a group of atoms connected by chemical bonds. g_dipoles will only consider the molecules of the group you are prompted to provide. If you for example choose 'solvent' then you will get the sum of all the individual dipole moments of the water molecules in your system. Carsten When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not consider counter ions to calculate the dipole moment ??? Sorry for disturbing people in the Gromacs mailing list. Thank you Lin On 2010-10-22 00.49, Chih-Ying Lin wrote: Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not consider counter ions to calculate the dipole moment ??? Thank you Lin you should try to understand what is going on yourself rather than sending many email to the mailing list. Please read the source code of the program. -- -- 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 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] Gromacs 4.5.1 on 48 core magny-cours AMDs
Hi, does anyone have experience with AMD's 12-core Magny-Cours processors? With 48 cores on a node it is essential that the processes are properly pinned to the cores for optimum performance. Numactl can do this, but at the moment I do not get good performance with 4.5.1 and threads, which still seem to be migrating around. Carsten -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Gromacs 4.5.1 on 48 core magny-cours AMDs
Hi Sander, On Oct 21, 2010, at 12:27 PM, Sander Pronk wrote: Hi Carsten, As Berk noted, we haven't had problems on 24-core machines, but quite frankly I haven't looked at thread migration. I did not have any problems on 32-core machines as well, only on 48-core ones. Currently, the wait states actively yield to the scheduler, which is an opportunity for the scheduler to re-assign threads to different cores. I could set harder thread affinity but that could compromise system responsiveness (when running mdrun on a desktop machine without active yielding, the system slows down noticeably). One thing you could try is to turn on the THREAD_MPI_WAIT_FOR_NO_ONE option in cmake. That turns off the yielding which might change the migration behavior. I will try that, thanks! BTW What do you mean with bad performance, and how do you notice thread migration issues? A while ago I benchmarked a ~80,000 atom test system (membrane+channel+water, 2 fs time step, cutoffs @ 1 nm) on a 48-core 1.9 GHz AMD node. My first try gave a lousy 7.5 ns/day using Gromacs 4.0.7 and IntelMPI. According to AMD, parallel applications should be run under control of numactl to be compliant to the new memory hierarchy. Also, they suggest using OpenMPI rather than other MPI libs. With OpenMPI and numactl - which pins the processes to the cores - the performance was nearly doubled to 14.3 ns/day. Using Gromacs 4.5 I got 14.0 ns/day with OpenMPI+numactl and 15.2 ns/day with threads (here no pinning was necessary for the threaded version!) Now on another machine with identical hardware (but another Linux) I get 4.5.1 timings that vary a lot (see g_tune_pme snippet below) even between identical runs. One run actually approaches the expected 15 ns/day, while the others with also 20 PME-only nodes) do not. I cannot be shure that thread migration is the problem here, but correct pinning might be necessary here. Carsten g_tune_pme output snippet for mdrun with threads: - Benchmark steps : 1000 dlb equilibration steps : 100 Repeats for each test : 4 No. scaling rcoulomb nkx nky nkz spacing rvdw tpr file 0 -input- 1.00 90 88 80 0.119865 1.00 ./Aquaporin_gmx4_bench00.tpr Individual timings for input file 0 (./Aquaporin_gmx4_bench00.tpr): PME nodes Gcycles ns/dayPME/fRemark 24 1804.4428.7361.703OK. 24 1805.6558.7301.689OK. 24 1260.351 12.5050.647OK. 24 1954.3148.0641.488OK. 20 1753.3868.9921.960OK. 20 1981.0327.9582.190OK. 20 1344.375 11.7211.180OK. 20 1103.340 14.2870.896OK. 16 1876.1348.4041.713OK. 16 1844.1118.5511.525OK. 16 1757.4148.9721.845OK. 16 1785.0508.8331.208OK. 0 1851.6458.520 - OK. 0 1871.9558.427 - OK. 0 1978.3577.974 - OK. 0 1848.5158.534 - OK. -1( 18) 1926.2028.1821.453OK. -1( 18) 1195.456 13.1840.826OK. -1( 18) 1816.7658.6771.853OK. -1( 18) 1218.834 12.9310.884OK. Sander On 21 Oct 2010, at 12:03 , Carsten Kutzner wrote: Hi, does anyone have experience with AMD's 12-core Magny-Cours processors? With 48 cores on a node it is essential that the processes are properly pinned to the cores for optimum performance. Numactl can do this, but at the moment I do not get good performance with 4.5.1 and threads, which still seem to be migrating around. Carsten -- 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] Gromacs 4.5.1 on 48 core magny-cours AMDs
On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote: Thanks for the information; the OpenMPI recommendation is probably because OpenMPI goes to great lengths trying to avoid process migration. The numactl doesn't prevent migration as far as I can tell: it controls where memory gets allocated if it's NUMA. My understanding is that processes get pinned to cores with the help of the --physcpubind switch to numactl, but please correct me if I am wrong. Carsten-- 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 on install Gromacs 4
On Oct 20, 2010, at 5:17 AM, Son Tung Ngo wrote: Dear experts, I have just install gromacs 4.5.1 on my cluster (using CentOS that was install openmpi1.5, Platform MPI, fftw3, g77, gcc , g++) but I have problem with size of int : [r...@icstcluster gromacs-4.5.1]# ./configure --prefix=/shared/apps/gromacs --enable-mpi --enable-double snip checking for _aligned_malloc... no checking size of int... 0 checking size of long int... 0 checking size of long long int... 0 checking size of off_t... configure: error: in `/shared/apps/source/gromacs-4.5.1': configure: error: cannot compute sizeof (off_t) Any idea about this? Hi Son, search the config.log file for your error message cannot compute sizeof (off_t). There you can find some more explanation. Could be a missing library. Carsten-- 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] MPI and dual-core laptop
Hi, if you only want to use the two processors of you laptop you can simple leave away the --enable-mpi flag. Then it will work in parallel using threads. Use mdrun -nt 2 -s ... to specify two threads. If you anyhow want to compile with MPI, take a look at the config.log file (search for 'Cannot compile and link MPI code') to check the actual cause of your problem, probably some library was not found. Carsten On Sep 27, 2010, at 8:42 PM, simon sham wrote: Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Re: efficient use of pme with gromacs
Hi Léo, please keep Gromacs-related issues on the Gromacs-users mailing list. This will give others with similar problems the possibility to profit from already answered questions by searching this list. Also, please choose a descriptive subject (I have done that for you). Thank you! The message you see DD step 543999 vol min/aver 0.331 load imb.: force 76.6% pme mesh/force 0.909 is just meant for your information, meaning that the PME mesh processors finish their calculation earlier than the short-range Coulomb force processors. To balance that optimally, please use the g_tune_pme tool that is provided since version 4.5. If you need this tool for 4.0, look here: http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ The DD info message is however no reason for mdrun to stop. So there must be another problem here. Can you find an error message in any of the output files? Best, Carsten On Sep 21, 2010, at 8:01 PM, Léo Degrève wrote: Prof. Kutzner, I found papers and other materials that you have published on the efficient use of pme with the gromacs software. I have a problem that maybe you can help me, if you wish, to solve since I didn’t found what to do. Using gromacs on 96 processors the program stops systematically after warnings like: DD step 543999 vol min/aver 0.331 load imb.: force 76.6% pme mesh/force 0.909 Defining –npme according to grompp, the result is the same. Is there a solution? Thank you for your attention. Léo Degrève Grupo de Simulação Molecular Departamento de Química - FFCLRP Universidade de São Paulo Av. Bandeirantes, 3900 14040-901 Ribeirão Preto - SP Brazil Fax: +55 (16) 36024838 Fone: +55 (16) 3602-3688/ 3602-4372 e-mail: l...@obelix.ffclrp.usp.br l...@ffclrp.usp.br http://obelix.ffclrp.usp.br Sent via the WebMail system at srv1.ffclrp.usp.br -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] git gromacs
Hi Alan, 'bleeding edge' gromacs development is as always in the 'master' branch. The latest bugfixes for the 4.5.x versions you are going to find in the 'release-4-5-patches' branch. Carsten On Sep 7, 2010, at 12:09 PM, Alan wrote: Hi there, Now that gromacs 4.5.1 is released I was wondering which branch should I checkout if I want to test the bleeding edge gromacs development. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- 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 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 with installing mdrun-gpu in Gromacs-4.5
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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] help with git
On Aug 24, 2010, at 12:57 PM, Alan wrote: Hi there, I want to change from release-4-5-patches to master I am trying: git reset master git checkout master git pull error: Your local changes to 'include/resall.h' would be overwritten by merge. Aborting. Please, commit your changes or stash them before you can merge. git stash Saved working directory and index state WIP on master: 5e3473a Merge branch 'release-4-5-patches' HEAD is now at 5e3473a Merge branch 'release-4-5-patches' But I don't want branch 'release-4-5-patches'! Indeed, I am finding git very annoying to use. All I wanted in svn lingo is to change to a branch and if there's conflict, ignore all changes in my side and revert any modification to what's in the repository. git reset --hard will remove all your modifications to that branch that are not checked in yet. You might want to save include/resall.h elsewhere if you still need your modifications. Then git checkout master will check out the master branch. You might need to git pull after you checked out the master so that you are up-to-date with the gromacs repository. Carsten Is it possible with git? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] decomposition
Hi Jacopo, from somewhere the information about the 7 nodes must have come. What are the exact commands you used? What MPI are you using? Carsten On Jul 26, 2010, at 12:35 PM, Jacopo Sgrignani wrote: Dear all i'm trying to run a MD simulation using domain decomposition but after two days i'm only able to get this error: There is no domain decomposition for 7 nodes that is compatible with the given box and a minimum cell size of 2.37175 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition I don't select a number of nodes but i use the default options, but the simulation does not run. So could you give me advices to run with domain decomp, or where can I find exaples about this? Thanks a lot Jacopo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installing gromacs from git
(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 -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- 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 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 -- Quaerendo Invenietis-Seek and you shall discover. -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] P4_error for extending coarse grained MD simulations
with MARTINI CG simulation? Could you give me some suggestions? Many thanks! Justin -- 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 -- 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 -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] P4_error for extending coarse grained MD simulations
On Jul 9, 2010, at 11:29 AM, 张春雷 wrote: Hi Carsten, The error message I post is got on a single core with MPI. p0_6991: p4_error: interrupt SIGSEGV: 11 So it states p0_. I dont think the error is due to the MPI progrom. Am I right? Yes, but there must be some more diagnostic information from mdrun about what has gone wrong. Please check stderr / stdout output files as well as md.log. Carsten Justin Zhang 在 2010年7月9日 下午4:00，Carsten Kutzner ckut...@gwdg.de写道： Hi Justin, what kind of error message do you get if you run this system on a single core without MPI? Carsten On Jul 8, 2010, at 9:36 PM, 张春雷 wrote: Dear all, I have post this question about a two weeks ago. During these days, I followed suggestions from Mark and weixin, but did not fix it. Here, I repeat it again to seek more help. I attempt to extend MD simulation for a coarse-grained system. CG models are in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07. I tried to use check point file state.cpt to extend my simulation. The mdrun program can read to the check file. But it reported error like this: Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I check the state.cpt file using gmxdump and compare it with other checkpoint files that can be used for extending All-atom simulations. I found that in the CG check point file, some sections are missing: box-v (3x3) and thermostat-integral. I am not sure whether this missing sections cause my run crash. If it is, could any one tell me possible reasons that result in the loss of box-v and thermostat-integral and how to fix the problem? Your suggestions are greatly helpful and appreciated. Justin Zhang 在 2010年6月25日 下午4:45，张春雷 chunleizhang@gmail.com写道： Information shown by gmxcheck: Checking file state.cpt # Atoms 9817 Last frame -1 time 36.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Checking file state_prev.cpt # Atoms 9817 Last frame -1 time 359010.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Checking file md_360ns.trr trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 # Atoms 9817 Reading frame2000 time 30.000 Item#frames Timestep (ps) Step 2401150 Time 2401150 Lambda2401150 Coords2401150 Velocities2401150 Forces 0 Box 2401150 Is anything wrong? 2010/6/25 Mark Abraham mark.abra...@anu.edu.au - Original Message - From: 张春雷 chunleizhang@gmail.com Date: Friday, June 25, 2010 16:46 Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org The last .gro file only provides coordinates of the system. No velocity is recorded. Actually, what I attempt to achieve is a binary identical trajectory. So I think the velocity from the last step is critical. I have tried another approach in which the checkpoint file is neglected. $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g md_720ns.log It works. So the checkpoint file appears to contain some error. But it is generated by a normally finished production simulation. What does gmxcheck say about all the files involved? Mark Have you encountered similar things? Thank you for your suggestions! 在 2010年6月25日 上午9:16，weixin xwx...@gmail.com写道： How about using the last .gro file to continue your simulation? 2010/6/24 张春雷 chunleizhang@gmail.com Dear GMX-users, This is Justin. I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model. I have successfully completed a 360ns simulation, during which the time step is 30 fs. I would like to extend the simulation to 1micro-second. The commands I used are: $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt However, I received the following message: Checkpoint file is from part 1, new output files will be suffixed part0002. Getting Loaded... Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded
Re: [gmx-users] mpi run
Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the output of it? Best, Carsten On Jul 8, 2010, at 9:41 AM, nanogroup wrote: Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
Hi, you can check with ldd mdrun_mpi whether really all needed libraries were found. Is libimf.so in /opt/intel/fc/10.1.008/lib ? The intel compilers also come with files called iccvars.sh or ictvars.sh. If you do source /path/to/iccvars.sh everything should be set as needed. Check the Intel Compiler documentation. Carsten On Jul 8, 2010, at 10:52 AM, zhongjin wrote: Dear users, When I am using GROMACS 4.0.7 on the Compute node ，executing command: mpiexec -n 4 mdrun_mpi -deffnm SWNT66nvt /dev/null and then met a problem :mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory but I have added export LD_LIBRARY_PATH=/opt/intel/fc/10.1.008/lib in the .bash_profile, the libimf.so is in this directory. However,when executing command:mdrun -deffnm SWNT66nvt ，it's OK ! Anybody could help me? Thanks a lot! Zhongjin He -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Fwd: missing atom
Dear Abdul, please keep all Gromacs-related questions on the mailing list. Best, Carsten Begin forwarded message: From: abdul wadood wadoodbiochem...@hotmail.com Date: July 3, 2010 8:40:29 AM GMT+02:00 To: ckut...@gwdg.de Subject: missing atom Dear Carsten I am running simulation using gromacs with amber forcefields on my protein. I have prepared the input file accordingly and have all the required library. But the problem is that when i run pdb2gmx for the top file the following error come: WARNING: atom H is missing in residue LEU 2 in the pdb file You might need to add atom H to the hydrogen database of residue LEU in the file ff???.hdb I tried my best to solve the problem, searching on the gromacs website and manual but cannot succeed. If you kindly help me in this respect your help will be highly appreciated by our group our research. the input file is attached. Many regards Abdul Wadood, Research Scholar, Dr.Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi-75720, Pakistan. Email:wadoodbiochem...@hotmail.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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ED sampling
Hi Vijaya, could it be that you mixed something up when making the .edi file? The tool make_edi reads the total number of atoms from the provided .tpr file and saves this number with the other ED sampling information to the .edi file. The ED sampling module in mdrun then compares the number of atoms from the .edi file with the .tpr file provided to mdrun - to ensure that the .edi file was produced for the same MD system. Carsten On Jun 29, 2010, at 6:57 PM, vijaya subramanian wrote: Hi I need some information about how ED sampling works when a subset of the atoms are used for covariance analysis. Basically I would like to move the system along the first eigenvector obtained from covariance analysis of the C-alpha atoms only. From the paper Toward an Exhaustive Sampling of the Configurational Spaces of two forms of the Peptide Hormone Guanylin it appears only the C-alpha atoms are used to define the essential subspace but when I use the following commands, I get an error message saying: Fatal error: Nr of atoms in edsamp26-180fit.edi (4128) does not match nr of md atoms (294206) The commands are: tpbconv -s full180.tpr -f full180.trr -extend 5 -o edsam26-180f180.tpr -e full180.edr aprun -n 60 $GROMACS_DIR/bin/mdrun -s edsam26-180f180.tpr -nosum -o edsam26-180f180.trr -x edsam26-180f180.xtc -ei edsamp26-180fit.edi -c edsam26-180f180.gro -e edsam26-180f180.edr -g edsam26-180f180.log The ED sampling method I am using is linfix not radacc. Thanks Vijaya The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. Get busy. -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the job is not being distributed
Hi Syed, you have to give more information for other people to be able to understand what you are doing. What is the exact sequence of commands you use to start the mdrun job? How does your OpenMPI hostfile look like, how are your nodes called, what does mdrun print on the first lines. Without that information, nobody can help you because there is no chance to tell what is possibly going wrong. Carsten On Jun 30, 2010, at 8:21 PM, Syed Tarique Moin wrote: Hello, I have successfully compiled gromacs with openmpi but i see the same problem that the jobs is still not distributed to other nodes but showing all the processor in node and it should be distributed. Thanks and regards Syed Tarique Moin -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the job is not being distributed
On Jun 28, 2010, at 2:34 PM, Syed Tarique Moin wrote: hello, I am running a simulation on dual core processor using the following command mpirun -np 8 mdrun_mpi -s top The job is running but it is not distributed on other node, i mean i cant see the process on other nodes as well. I see only on node01 but it has only 4 processors. Can anybody suggest me! Hi, find out how you generally run a simple parallel job with the MPI framework that you are using. If that works, Gromacs should also run in parallel. You are going to have to provide some kind of machine / host / nodefile. Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the job is not being distributed
So which MPI library are you using? Carsten On Jun 28, 2010, at 3:33 PM, Syed Tarique Moin wrote: Hi, In case Amber simulation, i run command of mpirun and the jobs are distributed into different nodes 4 on each machines but in case i am observing that all the 8 processes are on node01 but no indication on node02 unlike in case of amber. Thanks Syed Tarique Moin -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Should I use separate PME nodes
Hi Gaurav, separate PME nodes usually pay off on a larger number of nodes (16). In rare cases, you will see a performance benefit on a small number of nodes as well. Just try it! Or use g_tune_pme ... ;) Carsten On Jun 25, 2010, at 3:32 PM, Gaurav Goel wrote: I ran my simulation in parallel on 4 nodes (with zero separate PME nodes). Below is the information printed in md.log. I see that PME-Mesh calculations took 60% of CPU time. Any recommendations on using 1 or more separate PME nodes to speed up? Computing: M-Number M-Flops % Flops --- Coul(T) + VdW(T) 1761401.496982 119775301.79520.2 Outer nonbonded loop 106414.135764 1064141.358 0.2 Calc Weights 32400.006480 1166400.233 0.2 Spread Q Bspline 2332800.466560 4665600.933 0.8 Gather F Bspline 2332800.46656027993605.599 4.7 3D-FFT 47185929.437184 377487435.49763.6 Solve PME 675840.13516843253768.651 7.3 NS-Pairs 823453.92765617292532.481 2.9 Reset In Box2160.0021606480.006 0.0 CG-CoM 2160.0043206480.013 0.0 Virial 11700.002340 210600.042 0.0 Ext.ens. Update10800.002160 583200.117 0.1 Stop-CM10800.002160 108000.022 0.0 Calc-Ekin 10800.004320 291600.117 0.0 --- Total 593905146.863 100.0 --- R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 4101 3859.416 1488.1 0.6 Comm. coord. 4501 1874.635 722.8 0.3 Neighbor search410178640.72230322.211.2 Force 4501 180659.90269658.525.8 Wait + Comm. F 4501 2578.994 994.4 0.4 PME mesh 4501 422268.834 162817.760.4 Write traj.4 10001 17.5266.8 0.0 Update 4501 2981.794 1149.7 0.4 Comm. energies 4501 2633.176 1015.3 0.4 Rest 43580.341 1380.5 0.5 --- Total 4 699095.342 269556.0 100.0 --- Thanks, Gaurav -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 134
Amin,
maybe your MPI-enabled executable is called mdrun_mpi. Check
the directory where mdrun is and make shure (with ldd for example)
the mdrun* you are using is linked to the MPI library you are using.
Carsten
On Jun 24, 2010, at 6:51 AM, Amin Arabbagheri wrote:
Carsten,
Thanks for your help, I used something like mpirun -np 3 mdrun -s topol.tpr,
it works but its something like repeating a single job 3 times,
simultaneously.
here is the output on the screen :
{
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.2#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.3#
Back Off! I just backed up ener.edr to ./#ener.edr.3#
starting mdrun 'Protein in water'
100 steps, 1000.0 ps.
starting mdrun 'Protein in water'
100 steps, 1000.0 ps.
starting mdrun 'Protein in water'
100 steps, 1000.0 ps.
step 736900, will finish Fri Jun 25 07:45:04 2010
}
the estimated time is as long as one single job!
--- On Mon, 21/6/10, gmx-users-requ...@gromacs.org
gmx-users-requ...@gromacs.org wrote:
From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org
Subject: gmx-users Digest, Vol 74, Issue 134
To: gmx-users@gromacs.org
Date: Monday, 21 June, 2010, 9:03
Send gmx-users mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than Re: Contents of gmx-users digest...
Today's Topics:
1. (no subject) (Amin Arabbagheri)
2. Re: (no subject) (Justin A. Lemkul)
3. Re: (no subject) (Linus ?stberg)
4. Re: (no subject) (Carsten Kutzner)
5. Help with defining new residue (OXY--HEME) (Omololu Akin-Ojo)
6. Re: Help with defining new residue (OXY--HEME) (Justin A. Lemkul)
--
Message: 1
Date: Mon, 21 Jun 2010 05:00:04 -0700 (PDT)
From: Amin Arabbagheri amin_a...@yahoo.com
Subject: [gmx-users] (no subject)
To: gmx-users@gromacs.org
Message-ID: 180446.74209...@web50607.mail.re2.yahoo.com
Content-Type: text/plain; charset=utf-8
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
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Message: 2
Date: Mon, 21 Jun 2010 08:05:15 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4c1f557b.4090...@vt.edu
Content-Type: text/plain; charset=UTF-8; format=flowed
Amin Arabbagheri wrote:
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.
Regarding grompp:
http://www.gromacs.org/Documentation/FAQs
As for mdrun, please provide your actual command line. The mdrun -np flag is
nonfunctional, instead the number of nodes are taken from, i.e. mpirun -np
from
which mdrun is launched.
-Justin
Bests,
Amin
--
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
--
Message: 3
Date: Mon, 21 Jun 2010 14:07:54 +0200
From: Linus ?stberg bio...@talavis.eu
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users gmx-users@gromacs.org
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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
Re: [gmx-users] (no subject)
Amin, the -np flag is not necessary any more for grompp in Gromacs 4.0. For mdrun, just use something like mpirun -np 4 mdrun -s topol.tpr Carsten On Jun 21, 2010, at 2:00 PM, Amin Arabbagheri wrote: 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76
Hi Abdul, please keep Gromacs-related questions on the list. The error is exactly as printed: You have more than 128 backups of md.log in your directory, at this point mdrun does not make more backups of md.log any more. You have to delete the #md.log.*# files. Carsten On Jun 18, 2010, at 7:24 AM, abdul wadood wrote: Dear Carsten When I reduce the number of steps in mdp file the error change which now 0: Fatal error: 0: Won't make more than 128 backups of md.log for you 0: --- 0: 0: I Wonder, Should I Get Up... (J0: p0_27074: p4_error: : -1 . Lennon) 0: 0: Halting program mdrun_mpi 0: 0: gcq#46: I Wonder, Should I Get Up... (J. Lennon) 0: 0: [0] MPI Abort by user Aborting program ! 0: [0] Aborting program! 0: p4_error: latest msg from perror: No such file or directory Abdul Wadood, Research Scholar, Dr.Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi-75720, Pakistan. Email:wadoodbiochem...@hotmail.com From: ckut...@gwdg.de Subject: Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76 Date: Thu, 17 Jun 2010 16:36:51 +0200 To: wadoodbiochem...@hotmail.com On Jun 17, 2010, at 3:57 PM, abdul wadood wrote: Dear Carsten I give the path for the topol.tpr file now the error is change which is Fatal error: 3: Too many LINCS warnings (4254) 3: If you know what you are doing you can adjust the lincs warning threshold in your mdp file 3: or set the environment variable GMX_MAXCONSTRWARN to -1, 3: but normally it is better to fix the problem 3: --- 3: Maybe your system is not well equilibrated, or your time step is too long. Carsten Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. See how. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76
On Jun 17, 2010, at 3:42 PM, abdul wadood wrote: Dear Carsten the command which i give is mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s topol.tpr with this command the same error come which is Can not open file: 3: topol.tpr 3: --- Maybe . (the current directory) is not in your path. Either try mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s ./topol.tpr or give the full path name: mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s /absolute/path/to/topol.tpr Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parallel installation
Hi, you either have to add the directory where mdrun_mpi resides to your path or you have to give mpirun the full path name of mdrun_mpi. You can add the Gromacs executables to your path by the command source /path/to/your/installed/gromacs/bin/GMXRC Or use mpirun -np 12 /path/to/your/installed/gromacs/bin/mdrun_mpi -s topol.tpr ... Carsten On Jun 14, 2010, at 7:20 AM, abdul wadood wrote: Hello, I am new user of gromacs. I have installed the gromacs and enable the mpi but when I run the command mpirun -np 12 mdrun_mpi -s topol.tpr -o test.trr -x test.xtc -c confout.gro -e test.edr -g test.log The error come that Program mdrun_mpi either does not exist, is not executable, or is an erroneous argument to mpirun. I have search the problem on mailing list but I do not found satisfactory answer to solve my problem. If you kindly help me in this respect I will be very thankful to you. Your help will be highly appreciated by our research group. Many regards Abdul Wadood, Research Scholar, Dr.Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi-75720, Pakistan. Email:wadoodbiochem...@hotmail.com Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. Learn more. -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about how to install g_tune_pme
Hi Yi,
the most convenient way in my opinion is to copy the
Makefile.arch from the already installed gromacs-4.0.7
version and copy it into the directory where g_tune_pme.c
is. Rename Makefile.arch to Makefile and inside it
exchange the three occurences of template by g_tune_pme.
Type make and you are going to get a g_tune_pme
executable which you can copy to the installed gromacs-4.0.7
bin directory. If you also copy the provided completion.*
files to the gromacs bin directory, tab completion will also
work for g_tune_pme.
Example:
Let's assume gromacs is installed in /usr/local/gromacs/407/
tar -xvf g_tune_pme.tgz
cd tune
cp
/usr/local/gromacs/407/share/gromacs/template/Makefile.x86_64-unknown-linux-gnu
.
cat Makefile.x86_64-unknown-linux-gnu | sed {s/template/g_tune_pme/g} Makefile
make
cp g_tune_pme /usr/local/gromacs/407/bin
cp completion.* /usr/local/gromacs/407/bin
That should do the trick.
Best,
Carsten
On Jun 10, 2010, at 11:02 PM, Yi Peng wrote:
Hi, Everyone,
We want to install g_tune_pme tool to our Gromacs-4.0.7 on our cluster. We
don't know which Makefile in the template directory we should use, should we
run make in the tune directory, or even configure, or should we compile this
together with gromacs? Should we use mpi library? which one?Thanks a lot.
Yi
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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Re: [gmx-users] DSSP
Hi Shahid, I have fixed the problem in do_dssp. You can either pull the newest release-4-0-patches branch from the git repository or change ./src/tools/do_dssp.c, line 80 from snew(ssbuf,nres+10); to: snew(ssbuf, 2*nres-1); Carsten On May 19, 2010, at 9:48 AM, Carsten Kutzner wrote: Hi, there was a problem in do_dssp when used on proteins with more than 10 chains. Is this the case? I just saw that I only fixed that in the head, but not in 4.0.x. Carsten On May 18, 2010, at 3:49 PM, shahid nayeem wrote: Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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
Re: [gmx-users] DSSP
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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] very low speed in simulation !( need for help)
Hi, On May 18, 2010, at 9:35 AM, delara aghaie wrote: Dear gmx-usres, In our university we have a cluster containing 20 nodes each with 4 processors, which I want to use that for the simulation project. As a test I submitted a run that I have tested it before in the Imperial College (London). Here the structure of the cluster is so that I should specify on which nodes I want the simulation to be done. for this we have a folder (gromacs launcher), in which there are some files. in the file (lamhosts.txt) the node numbers that I can have access to them, have been specified by the head of cluster. And in the file (hosts.txt) I can choose the nodes which I want to simulate my system with them, (I am resricted to use only the nodes that are listes in the lamhosts.txt). whan I want to use the grompp order, it wants me to specify the -np option(number of processors). For example I can have access to 12 processors (or 3 nodes). I write these commands: /usr/local/gromacs/bin/grompp -c ~.gro -f ~.mdp -p ~.top -n ~.ndx -o topol.tpr -np 12 mpiexec /usr/local/gromacs/bin/mdrun -v -s topol.tpr -np 12 I think the -np 12 should go directly after the mpiexec. I receive the error that I should include the server name in the list of nodes . I did it for both the lamhosts.txt and hosts.txt file. If you are using LAM MPI, you have to set up the parallel environment with the command lamboot before you start any parallel job with mpirun or mpiexec. LAM requires that the node you run lamboot on is in the list of hosts. This is what the error message says. You can boot a parallel environment with more nodes than you actually use for your parallel job, and I think there is probably a way to tell lam which of the lambooted nodes it should then use for the run. (i.e. all but the server in your case). The other solution would be to log in to one of the nodes which is in the hosts file and issue the lamboot and the mpirun/mpiexec commands there. For better scalability you might also want to upgrade to Gromacs 4. Carsten Then I should write number of processors 13 instead of 12. In this way the simulation goes very very slowly, as I see that if I run the simulation on one processor the speed is more satisfying !!!. I think this low speed is because of including the server in the processor list, and because the server is always busy with other jobs, the speed falls down. Now: 1) Is the reason for low speed , including the server in the list? 2) is the way that let me not to include the server in the list of lamhosts.txt and hosts.txt? It would be greatly appreciated if you guide me as I am completely confused !!! thanks in advance. D. M -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] make_edi, g_covar -nofit
On May 4, 2010, at 10:56 PM, vijaya subramanian wrote: Hi Carsten A couple of quick questions: I already have gromacs-4.0.7 downloaded from the gromacs website. I found that I couldn't use git checkout --track -b release-4-0-patches origin/release-4-0-patches to get the patches. fatal: Not a git repository Do I have to uninstall gromacs-4.0.7 and re-install gromacs obtained from the git site as below, then install gromacs again? Hi, if the git clone command worked, then the git checkout --track should also work. Maybe you forgot to change into the gromacs directory that was produced by the first command? You have to do the checkout --track in the directory where a .git subdir is present. git clone git://git.gromacs.org/gromacs.git cd gromacs git checkout --track -b release-4-0-patches origin/release-4-0-patches Carsten -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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
