Re: [gmx-users] NTMPI / NTOMP combination: 10 threads not "reasonable" for GROMACS?
Le 20/03/2019 à 22:42, Stéphane Téletchéa a écrit : Dear all, Those CPUs are 10 cores +HT (so not 4 or 6). Is it only a warning ? Dear all, Any answer from core developpers on this, should a file a bug? Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Help on MD performance, GPU has less load than CPU.
Le 12/07/2017 à 18:15, Mark Abraham a écrit : Hi, Sure. But who has data that shows that e.g. a free-energy calculation with the defaults produces lower quality observables than you get with the defaults? Mark Hi, As defaults are defaults ... who knows :-) To get number in front of these assumptions is hard, and probably nobody wants to do this on a large scale ... But I'm too close to holidays to argue on this point by now! Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Help on MD performance, GPU has less load than CPU.
Le 11/07/2017 à 15:24, Mark Abraham a écrit : Guessing wildly, the cost of your simulation is probably at least double what the defaults would give, and for that cost, I'd want to know why. Estimated colleague, Since this is a wild guess, I'd think to add some guesses myself. I remember "some time" back having used a lower tolerance on Ewald for amber simulations (around amber 4/5/6 ...) and it was more common at this time I presume. This may also be linked to the fact that amber has a short cut-off at 8 angstrom for electrostatics ... Someone apparently "ill" at the time already found this stane in 2009: http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/vTjpMdwU/gromacs-preformance-versus-amber Out of my memroy, I remembered using 10-6 for Ewald tolerance in AMBER, and this is mentioned here: http://ambermd.org/Questions/ewald.html ... apparently linked to DNA simulation as found in JACS 117,4193 (1995) In short, this value may come in back and forth for "historical" reasons (and misuse, of course). Others may have additional comments :-) Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs on GPU
Le 16/06/2017 à 20:07, Mohsen Ramezanpour a écrit : Thanks Justin. So, can we say that simulation on CPU and GPU (as far as we use the same version of Gromacs) are compatible? If yes, is that okay to continue a simulation which was done with CPU (say till 100 ns) to 500 ns (using GPU)? Or I should start from t=0 with GPU? It is important for my case as the allocations on supercomputers change from CPU to GPU. So, not sure if I should start all again or it is fine to continue. Cheers Dear Moshen, What I'm doing daily is using my "small" workstation with CPU then continue once equilibration and primary production has worked well. Go for GPU for a boost in performance (big) once the primary steps are ok :-) Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Performance advice for newest Pascal architecture
Dear colleagues, We are willing to invest on nodes for GROMACS-specific calculations, and trying to best the best for our bucks (as everyone). For now our decisions comes close to nodes using the following configuration: 2 * Xeon E5-2630 v4 1 P100 or 2 * P5000 or 2 * K40 Cluster node interconnection: Intel OmniPath Our system will will range from 50k to 200k atoms most of the time, using AMBER-99SB-ILDn, GROMCAS 2016.1 and above. I am aware of various benchmark and recommandations like "Best Bang for your Bucks", but is there any reference (internal may be) for latest Pascal architecture, or any general advice against/for ? Thanks a lot in advance for the feedback, if we are able to benchmark on our systems using the different setups above we'll share as possible by the upstream vendor the results. Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology
Le 27/02/2017 à 13:20, Dayhoff, Guy a écrit : I have made changes to my topol.top file. Now in my command for em.mdp I am getting 19 errors stating "NO DEFAULT BOND TYPE, ANGLE TYPE, ETC.” Dear Guy, Just to be sure, pay attention to the order of molecules in your top file, if your protein is before the ligand in the gro file (and waters, and ions, etc), the includes in your top file should match exactly the same order, for instance: ; Include geneic force field #include "forcefield.itp" ; Include ligand-specific force-field #include "ligand.itp" HTH, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GROMACS 2016 release candidate available!
Le 11/07/2016 16:22, Mark Abraham a écrit : Please do build it and try it out on your important workload - if it's broken when doing essential dynamics with velocity-verlet, on an AMD GPU running OpenCL, with LJ-PME, you might be the only person who can help us learn that! Dear Mark and GROMACS developpers, I have downloaded and built it fine with (and without) CUDA. So far I have tested on my machine and some tests fail, so I'll test again next week, the benchmarks are from http://www.gromacs.org/GPU_acceleration (RNAse, Villin, ADH). Failing tests are non cuda gmx run (it seems the cuda runs are fine) : (gmx mdrun) rnase_dodec_vsites pme_verlet_vsites.mdp (mdrun_cuda) rnase_dodec_vsites pme_verlet_vsites.mdp Performance: 131.7320.182 rnase_dodec_vsites rf_verlet_vsites.mdp rnase_dodec_vsites rf_verlet_vsites.mdp Performance: 154.6710.155 villin_vsites pme_verlet_vsites.mdp villin_vsites pme_verlet_vsites.mdp Performance: 351.318 0.068 villin_vsites rf_verlet_vsites.mdp villin_vsites rf_verlet_vsites.mdp Performance: 405.076 0.059 For the other tests it works ok : adh_cubic pme_verlet_vsites.mdp Performance:8.349 2.875 adh_cubic pme_verlet_vsites.mdp Performance: 10.274 2.336 adh_cubic rf_verlet_vsites.mdp Performance:8.505 2.822 adh_cubic rf_verlet_vsites.mdp Performance: 10.378 2.313 adh_cubic_vsites pme_verlet_vsites.mdp Performance: 18.0471.330 adh_cubic_vsites pme_verlet_vsites.mdp Performance: 23.3491.028 adh_cubic_vsites rf_verlet_vsites.mdp Performance: 22.4281.070 adh_cubic_vsites rf_verlet_vsites.mdp Performance: 21.7431.104 adh_dodec pme_verlet_vsites.mdp Performance:9.643 2.489 adh_dodec pme_verlet_vsites.mdp Performance: 13.856 1.732 adh_dodec rf_verlet_vsites.mdp Performance:9.355 2.565 adh_dodec rf_verlet_vsites.mdp Performance: 12.181 1.970 adh_dodec_vsites pme_verlet_vsites.mdp Performance: 19.9751.201 adh_dodec_vsites pme_verlet_vsites.mdp Performance: 31.1700.770 adh_dodec_vsites rf_verlet_vsites.mdp Performance: 27.1700.883 adh_dodec_vsites rf_verlet_vsites.mdp Performance: 29.7340.807 rnase_cubic pme_verlet_vsites.mdp Performance: 43.722 0.549 rnase_cubic pme_verlet_vsites.mdp Performance: 52.268 0.459 rnase_cubic rf_verlet_vsites.mdp Performance: 41.776 0.574 rnase_cubic rf_verlet_vsites.mdp Performance: 52.487 0.457 rnase_dodec pme_verlet_vsites.mdp Performance: 50.300 0.477 rnase_dodec pme_verlet_vsites.mdp Performance: 70.137 0.342 rnase_dodec rf_verlet_vsites.mdp Performance: 50.141 0.479 rnase_dodec rf_verlet_vsites.mdp Performance: 70.940 0.338 (this is a simple grep for 'Performance' on md.log). The "bench" is launched using a script : #!/bin/bash gmxver=2.016-rc1 rm bench-$gmxver module load gromacs/$gmxver for d in adh_cubic adh_cubic_vsites adh_dodec adh_dodec_vsites rnase_cubic rnase_dodec rnase_dodec_vsites villin_vsites; do for p in pme_verlet_vsites.mdp rf_verlet_vsites.mdp; do cd $d gmx grompp -f $p gmx mdrun -pin on echo "$d $p `grep Performance md.log`" >> ../bench-$gmxver mdrun_cuda -pin on echo "$d $p `grep Performance md.log`" >> ../bench-$gmxver cd .. done done I'll check on other systems and again on these system later on, but if this rings a bell, I thought It would be helpfull. More information on next monday probably. Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU
Le 22/04/2016 14:33, Szilárd Páll a écrit : Additionally, I suggest amending the post to note that the GDK and NVML that's picked up from it is optional and it is only useful with Quadro/Tesla cards. Dear Szilárd, I hope I'll find time to produce a proper bug report, but using the Ubuntu binaries with the ubuntu cuda runtime (so exact same version) 352.xx (same for cuda and nvidia driver), gromacs failed to detect the GPU. Up-to-now I have not traced down where the problems lies. This was I think already stated in the previous entry (section at the end: To sum up* avoid ubuntu packages and install upstream drivers and dependencies*.) But since it seems not clear enough I have corrected some typos and added the disclaimer as requested. I hope Gromacs developper do not feel "angry", this was not my goal, I am a long term GNU/Linux contributor and keen to echaustive bug reports. This article was more a short recipe to get it working and not a complaint. I hope the clarifications on the web site are now better, and this it may help others in getting a proprely working installation ... Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU
Le 22/04/2016 01:50, treinz a écrit : cudaGetDeviceCount returned 35 -> CUDA driver version is insufficient for CUDA runtime version Result = FAIL Unfortunately for any machine installed by now the setup is now as described, and works. There is one machine were this setup was not updated and YES I have the same result as you : ./deviceQuery ./deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 35 -> CUDA driver version is insufficient for CUDA runtime version Result = FAIL On this machine the driver is rather old: dpkg -l |grep nvidia ii nvidia-331 340.96-0ubuntu0.14.04.1 amd64 Transitional package for nvidia-331 ii nvidia-340 340.96-0ubuntu0.14.04.1 amd64 NVIDIA binary driver - version 340.96 ii nvidia-340-uvm 340.96-0ubuntu0.14.04.1 amd64 Transitional package for nvidia-340 ii nvidia-libopencl1-340 340.96-0ubuntu0.14.04.1 amd64 NVIDIA OpenCL Driver and ICD Loader library ii nvidia-opencl-icd-340 340.96-0ubuntu0.14.04.1 amd64 NVIDIA OpenCL ICD ii nvidia-prime 0.6.2 amd64 Tools to enable NVIDIA's Prime ii nvidia-settings 331.20-0ubuntu8 amd64 Tool for configuring the NVIDIA graphics driver But I wrote my "tutorial" since the latest package available in Ubuntu is "nvidia-352 - NVIDIA binary driver - version 352.63", and apparently cuda expects 352.79, the minor revision in the driver is sufficient to have CUDA + GROMACS failing, and apparently this is from CUDA :-) You have the answer: use the exact driver of the CUDA runtime and nothing else ... Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] sugar puckering
Le 21/04/2016 04:24, bharat gupta a écrit : Dear Gmx Users, I am interested in calculating cremer-pople parameters for a trisachharide ligand from its simulation docked with a protein. I found one tool g_puckering for calculating the parameters but it was written for Gromacs version 4.0.x and I am using version 5.0.4. I am not able to compile this tool for my current version of gromacs. So can anybody tell me how can I calculate such parameters in gromacs ?? 1 - contact the authors 2 - adjust the code (I'm interested if you do it ...) 3 - compile it using the version it was meant for, if it parses xtc files it should not matter a lot ... Best, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] creating representative structures
Le 16/03/2016 16:54, Shyno Mathew a écrit : I wrote a tcl script to do cluster analysis, using gromos method. My results are slightly different from the g_cluster results. I see the difference is coming from RMSD values. For example, with g_cluster, “The RMSD ranges from 0.149614 to 0.220387 nm” However with the tcl script, and after converting RMSD from Å to nm, the value ranges from 0.173347 to 0.234409 nm! I am using the same selection in both cases for RMSD calculations. Dear Shyno, As Tserk mentioned earlier you may have different selections, but be very careful when you compare floating point numbers especially in interpreted languages, since most of the time their precision is not very "reliable". See the discussions in http://wiki.tcl.tk/11969 and http://wiki.tcl.tk/879 for instance... Either way you have to test :-) Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France Tél : +33 251 125 636 - Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] creating representative structures
Le 08/02/2016 18:23, Shyno Mathew a écrit : I have few questions regarding creating representative structures. Dear Shyno, For what its worth, I have been playing with gmx cluster settings lately, and found the "Jarvis-Patrick" method (default parameters) to provide me more accurate and "independent" snapshots of the 100 ns-long simulation (150 000 atoms). The bad news is that it took nearly 5 days to compute, but considering the results, this is really what I was searching for. HTH, Stéphane -- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Short how-to for installing GROMACS with CUDA ...
Le 17/12/2015 18:06, Szilárd Páll a écrit : PS: One more thing. If the CUDA SDK samples linked against the CUDA runtime library (libcudart) did really work and gmx/mdrun did not (assuming the same driver/kernel module), the only reasonable explanation I can think of is that the two were using different runtimes. Note that GROMACS sets RPATH, so it does not need nor is it affected by LD_LIBRARY_PATH tinkering while the SDK samples need LD_LIBRARY_PATH to point to the correct libcudart! OK, I'll open a bug report on it, and for the purging of configuration files, of course I did pay a lot of attention to this, again I went straight to the point for newcomers so they have an "executive résumé", but this seems also strange to me, so we'll continue on the bug report :-) This will certainly be in January now, when the machine will not be busy anymore :-) Best, Stéphane -- Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Short how-to for installing GROMACS with CUDA ...
Dear all, I have struggled recently in getting gromacs-aware of cuda capabilities. After searching for a "while" (one afternoon), I removed the ubuntu-provided drivers and packages (which worked in the past) and installed everything "from scratch". It seems this is both coming from NVIDIA requiring the "GPU deployment kit" in addition to the cuda toolkit, and from GROMACS only warning about the missing NVML (but not failing while asking for GPU compilation). In short, I have put the executive commands there: http://www.steletch.org/spip.php?article89 As some messages on the list are about this "problem", I thought it would be helpful to all. Best, Stéphane -- Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How can I split .xtc file to two part?
Le 23/11/2015 15:56, Hassan Aaryapour a écrit : for resolving this problem, can I split .xtc file to two part? how? Dear Hassan, Except if you have a specific interest in water molecules, you should probably reduce your system to the molecule of interest by doing a subselection of it (only the protein for instance), and then visualize it in vmd. You will get rid of the memory limit, since 16GB is already large enough for most systems :-) Best, Stéphane -- Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] 5ns simulation in 2 hours
Le 29/10/2015 04:24, Sana Saeed a écrit : is it possible? yes. -- Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs GPU got hang
Le 29/09/2015 23:40, M Teguh Satria a écrit : Any of you experiencing similar problem ? Is there any way to troubleshoot/debug to see the cause ? Because I didn't get any warning or error message. Hello, This can be a driver issue (or hardware, think of temperature, dust, ...), and happens to me from time to time. The only solution I found was to reset the GPU (see nvidia-smi options), if this is not sufficient you will have to reboot (and use the cold boot: turn off the computer for more than 30s, and then boot again). If this happens too often, you may have a defective card, see your vendor in that case... Best, Stéphane Téletchéa -- Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] files related to commands in C or FORTRAN
Le 12/06/2015 20:44, Justin Lemkul a écrit : If you're looking for the source code, download it from the GROMACS website. Packaged distributions don't include the source. -Justin It's simpler than downloading the file, use the -devel or -dev package from the officiale repositories, for instance: - https://apps.fedoraproject.org/packages/gromacs-devel/ in Fedora - http://packages.ubuntu.com/trusty/amd64/gromacs-dev in Ubuntu But for sure using the upstream tarball and reading the README and INSTALL files (and others) is certainly recommended :-) Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France Tél : +33 251 125 636 - Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Unable to download GROMACS 5.x series
Dear all, It seems the latest gromacs series have disappeared from the official download links (http://www.gromacs.org/Downloads), could it be fixed please? Thanks a lot in advance, Stéphane Téletchéa -- Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?
Le 24/02/2015 13:29, David McGiven a écrit : I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test system using a 2 fs time step I get 24 ns/d on 64 AMD cores 6272 16 ns/d on 32 AMD cores 6380 36 ns/d on 32 AMD cores 6380 with 1x GTX 980 40 ns/d on 32 AMD cores 6380 with 2x GTX 980 27 ns/d on 20 Intel cores 2680v2 52 ns/d on 20 Intel cores 2680v2 with 1x GTX 980 62 ns/d on 20 Intel cores 2680v2 with 2x GTX 980 I think 20 Intel cores means 2 x 10 cores each. But Szilard just mentioned in this same thread : If you can afford them get the 14/16 or 18 core v3 Haswells, those are *really* fast, but a pair can cost as much as a decent car. I know for sure gromacs escalates VERY well on 4 x 16 cores latests AMD (Interlagos, Bulldozer, etc.) machines. But have no experience with Intel Xeon. My experience with latest gromacs and fftw build on my machine is that one should not consider the hyperthreaded cores , but only the real cores. My system has 24 cores (E5-2620 v2 @ 2.10GHz + NVIDIA K4000), but really only 12 real cores. Using pin, running only one test system with optimized conditions I used the benchmarks available at the gromacs web site (ADH, rnase, villin, http://www.gromacs.org/GPU_acceleration), My results were : *** rnase_cubic 45,75 ns/day with -nt 6 and gpu on 47,10 ns/day with -nt 12 and gpu on 27,66 ns/day with -nt 24 and gpu on 35,31 ns/day with -nt 12 and gpu off 21,37 ns/day with -nt 24 and gpu off The results are more or less similar in the other benchmarks, 6 cores + GPU close to 12 cores + GPU, and faster than 24 cores... The difference in the GPU case is the aveage GPU usage, which is more than 85 % during the tests runs when not all processors are in use while it drops to 50 % if all cores are in use (using a rough observation of the GPU usage using nvidia-smi-tool). I have no explanation for the CPU-only benchmarked though, since I have enabled or disabled pinning, ensured that only one job was running at a time, etc. I have not played a lot with -nt, either omp or mpi, since this machine is a single node. Hope this helps in showing that more expensive may not be the way... Best, Stéphane -- Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?
Le 24/02/2015 17:18, Szilárd Páll a écrit : Thanks! Let me note that those observations are particular to your machine. There are multiple factors that cumulatively affect the multi-threaded scaling: - physical vs HT threads - crossing socket boundaries - iteration time/data per thread - GPU and GPU performance In your case all these three factors are somewhat disadvantageous for good scaling. You have two sockets so your runs are crossing CPU socket boundaries. The input is quite small and with GPUs the HyperThreading disadvatages can increase - especially with a slow GPU. Also note: - your Quadro 4000 can likely not keep up with the 12 CPU cores and there is probably some Wait GPU time (see log file) - if you want to test 1 CPU + 1 GPU using HT vs not using it you should run make sure to run with -pinstride 1 -ntomp 12 in the latter case! - -nt is partially deprecated/backward compatibility flag and should only be used if its meaning is use this many tMPI or OpenMP threads and decide which one is better, which is not the case here! Cheers, Sz. Dear Szilard, Thanks for the informations, this was a rapid bench, but I have all the logs if needed. I know this is bounded to my system and setup but if that can help others, I'd be happy in extending my tests with required parameters and adding them to the wiki if needed. Concerning the Wait GPU time, you are right, the numbers go from 8% to 72.4% ... Just let me know if you need more data and logs, I'd be happy to extend this benchmark to some other computers available here with variable setups and hardware (including amd too), to share on real cases what should be an optimal setting for performance/cpu best throughput. Best, Stéphane -- Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Installing GTX 980 on linux - which distro should i use?
Le 22/12/2014 17:47, Carlos Navarro Retamal a écrit : I just bought a workstation with 2 GTX 980 (in order to improve my simulations on gromacs), but i’m not able to install it properly. I first start with Centos 7, but my motherboard has an issue with this version, so i couldn’t pass the boot step. I would recommend Ubuntu but choose the server edition, otherwise you may encounter problems for installing the system. My choice goes for 14.04 since this is an LTS release so you know that your system will be stable for some time. If possible, for critical applications, use the nvidia binaries (driver and cuda), be also sure to *not* mess with nvidia from the repositories and from upstream nvidia, otherwise you'll have to remove some parts by hand (nvidia-common comes to my mind, but also dkms-compiled binaries). I will recommend against Scientific Linux or other CentOS-like distribution since they offer for free the recompiled version of the Red Hat upstream release, but without professional support and a lot of segfaults with their recompiled binaries (a simple 'dmesg' on installed computers would show you that). Good luck for your installation, at first this can be really an headache. Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France Tél : +33 251 125 636 - Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding Gromacs 5.0.3 parallel computation
Le 10/12/2014 07:22, Bikash Ranjan Sahoo a écrit : I tried to do a small simulation in Gromacs 4.5.5 using 30 cores for 200 ps. The computation time was 4.56 minutes . The command used was dplace -c 0-29 mdrun -v -s md.tpr -c md.gro -nt 30 . Next I ran the same system using Gromacs 5.0.3. The command used was dplace -c 0-29 mpirun -np 30 mdrun_mpi -v -s md.tpr -c md.gro. The simulation was extremely slow and took 37 minutes to complete only 200 ps MD. Dear Bikash, You are more or less benchmarking threads versus mpi, right? Note also that dplace for such rounded number (30) is probably not optimal either except if your number of processors is in the multiplicity of 30 (hexacores?). Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding Gromacs 5.0.3 parallel computation
Le 10/12/2014 12:28, Bikash Ranjan Sahoo a écrit : Dear Dr. Stéphane, Thank you for your quick reply. How can I solve this? Can you please guide me in getting the right command to run mdrun as fast as gromacs 4.5.5 -nt command. I am pasting the architecture of my cluster below. Kindly help me understanding how can I modify the mdrun_mpi command to access multi cores in my cluster. Dear Bikash, Why not using the -nt option in gromacs 5.0.3 too? My point was that you should use the same parameters for comparison of performance... What I would do is: mdrun -nt 30 -pin auto Try first using the gromacs tools (-pin auto) than using the dplace command since in your case you ask it to split you job on different cpu according to the diagram you showed. At least you could use the logical architecture for the dplace command: http://techpubs.sgi.com/library/tpl/cgi-bin/getdoc.cgi?coll=linuxdb=bkssrch=fname=/SGI_Developer/LX_AppTune/sgi_html/ch05.html Last, you should also try to first tune the pme decomposition using the tunepme option on a short run to see if the rather rough domain decomposition done by mdrun in a first approach is optimal for your system. You should also try to use cpu multiplicity and power of two for maximal performance, in your case, probably something like -nt 12, -nt 24 or -nt 36, since each cpu seems to be a 12-core ... See their respective manuals and command line helps for more info. Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pressure Question
Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based instantaneous pressure (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good book on molecular simulation). But, as others already pointed out, this P' is well-known to show extremelly large fluctuations, meaning that its average computed from the simulation has usually a very large statistical spread. In other words, although the ensemble average of P' is strictly equal to P, its simulation average is a random variable that often shows large deviations from P (especially for short simulations). To get an idea of what is an acceptable error for the average of P', you may look at its distribution histogram in the NPT simulation. Dear Antonio, Sorry if my message sound aggressive when I talked about totally irrevelevant, I will clarify my thoughts. From a theoretical point of view, you are right, each ensemble is accessible. From a biological point of view, though, the concept of fixing the volume is less reasonable: we live at constant pressure and temperature, and also at tighly controlled pH, and salt concentrations. The volume varies though, as you feel it when the weather is getting hot or cold. My point was exactly what your are telling in a more formal way than me: this P' is well-known to show extremely large fluctuations Well, digging a bit more on my feeling, I also found opposite arguments on the AMBER mailing list, like here: http://archive.ambermd.org/201103/0431.html So I'll got back again on my research and adjust my mind on the actual bleeding edge simulations taking into account all the recent code and force fields progresses. Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pressure Question
Le 04/11/2014 18:00, Johnny Lu a écrit : Hi. If my NVT simulation of a protein in 30k molecules of water has a pressure of 11 bar (error 0.5 bar from g_energy), will the dynamics (not distribution of conformations) change enough that the mechanism inferred from this simulation be significantly more unreliable than the mechanism inferred from a 1 bar simulation? (Will the reviewers cut my paper into ribbons?) Thanks again. Hi, Considering only your NVT parameters for your simulation, I would consider it totally irrelevant to talk about pressure where your constrain the volume. This value or any other one has not really a meaning in this situation, and I seen many variations in the pressure value in this microcanonical ensemble without paying too much attention on it. In an NPT simulation, then you should be able to find back a normal 1 bar simulation I think. Do you have any reason to do first an NPT simulation, and then an NVT one? I would personally let the system equilibrate in NVT, then swith to the more natural NPT, provided actual code and force fields are now good enough in this ensemble. Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
