Re: [gmx-users] gromacs 2020, bug? high total energy

Hi, It was not gromacs 2020, but my fault and mixing up various tools (grompp, mdrun) from 2019 and 2020 versions. I am sorry. Bests, Tamas On 4/14/20 4:44 PM, Tamas Hegedus wrote: Hi, There might be some bug(?) in gromacs 2020. I can not decide. I just installed 2020.1 today using

[gmx-users] gromacs 2020, bug? high total energy

-equilibrated initial configuration, incorrect interactions or parameters in the topology. I tried two different systems (two different soluble proteins, ff charmm-36m). However, if I start the simulations with 2019.4, there is no problem at all. Have a nice day, Tamas -- Tamas Hegedus, PhD Senior

[gmx-users] multidir, Segmentation fault

)[0x7f94ab7e209b] [myhost:39226] [17] /opt/gromacs-2018.6/bin/mdrun_mpi(+0xd4b7a)[0x55efb965fb7a] [myhost:39226] *** End of error message *** -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233

Re: [gmx-users] slurm, gres:gpu, only 1 GPU out of 4 is detected

I had the misconception that I have to set gpuid by CUDA_VISIBLE_DEVICES set by slurm. However, slurm exposes the gpu for gromacs by a different mechanism. On 11/13/19 4:55 PM, Tamas Hegedus wrote: Hi, I run gmx 2019 using GPU There are 4 GPUs in my GPU hosts. I have slurm and configured gres

[gmx-users] slurm, gres:gpu, only 1 GPU out of 4 is detected

. $CUDA_DEVICE_ORDER is set to PCI_BUS_ID I can not decide if this is a slurm config error or something with gromacs, as $CUDA_VISIBLE_DEVICES is set correctly by slurm and I expect gromacs to detect all 4GPUs. Thanks for your help and suggestions, Tamas -- Tamas Hegedus, PhD Senior Research Fellow

[gmx-users] pinoffset w LINCS error

that memory, file naming, and setting parameters (pinoffset, gpuid) are OK and some magical problem exists. Do you have any suggestion? Thanks, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233

Re: [gmx-users] gmx 2019 performance issues

Thanks for the inputs! * I will go with the cheaper CPU * I am looking forward to the gpu-only gromacs; impatiently On 01/15/2019 01:55 PM, Mark Abraham wrote: Hi, On Tue, Jan 15, 2019 at 1:30 PM Tamas Hegedus wrote: Hi, I do not really see an increased performance with gmx 2019 using

[gmx-users] gmx 2019 performance issues

16/32 cores works similarly as 16/16 cores. E.g. 2990 has slower memory access compared to 2950; I do not expect this to influence gmx runs too much. However, if it decreases by 10-15 percentage then most likely it does not worth to invest into the 32 core processor. Thanks for your feedback

Re: [gmx-users] gmx 2019 running problems

Hi, Thanks for the feed-backs. Yes, I could build gmx 2019 on a hosts running with nvidia driver 4.10 Tamas On 01/14/2019 09:06 PM, Tamas Hegedus wrote: Hi, I tried to install and use gmx 2019 on a single node computer with 4 GPUs. I think that the build was ok, but the running

[gmx-users] gmx 2019 running problems

---+ Thanks for your suggestions, Tamas -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University | fax: (36) 1-266 6656 Tuzolto utca 37-47 | mailto:ta...@

Re: [gmx-users] different nvidia-smi/gmx GPU_IDs

Tamas Hegedus, wrote: Hi, I have a node with 4 nvidia GPUs. From nvidia-smi output: 0 Quadro P6000 1 GeForce RTX 208 2 GeForce GTX 108 3 GeForce RTX 208 However, the order of GPUs is differently detected by gmx 2018.3 Number of GPUs detected: 4 #0: NVIDIA GeForce

[gmx-users] different nvidia-smi/gmx GPU_IDs

RTX 2080 Ti #2: NVIDIA Quadro P6000 #3: NVIDIA GeForce GTX 1080 Ti Why is this? This makes difficult to plan/check the running of two gmx jobs on the same node. Thanks for your suggestion. Tamas -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group

Re: [gmx-users] ramachandran plot

to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Tamas Hegedus, PhD Senior Research

Re: [gmx-users] AMD 32 core TR

but rather was caused by the my models or my compilation methods. Hope this addresses your questions and helps any other users contemplating using a Ryzen TR. Paul On Jan 3, 2019, at 2:09 PM, Tamas Hegedus wrote: Please provide more information. If you use gmx 2018 then I think that gmx

Re: [gmx-users] AMD 32 core TR

questions and helps any other users contemplating using a Ryzen TR. Paul On Jan 3, 2019, at 2:09 PM, Tamas Hegedus wrote: Please provide more information. If you use gmx 2018 then I think that gmx limits the gcc version to 6 and not cuda 10. You did not specify what type of and how many

Re: [gmx-users] AMD 32 core TR

possible -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University | fax: (36) 1-266 6656 Tuzolto utca 37-47 | mailto:ta...@hegelab.org Budapest, 1094

Re: [gmx-users] AMD vs Intel, nvidia 20xx

at 10:50:42AM +0200, Tamas Hegedus wrote: Hi, I am planning to buy 1 or 2 GPU workstations/servers for stand alone gromacs and gromacs+plumed (w plumed I can efficiently use only 1 GPU). I would like to get some suggestions for the best performance/price ratio. More specifically, some info

[gmx-users] AMD vs Intel, nvidia 20xx

become the limiting factor. Thanks for all the opinion and suggestion, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47| mailto:ta...@hegelab.org Budapest, 1094

Re: [gmx-users] gmx 5.1.4, cuda9, Unsupported gpu architecture 'compute_20'

Tamas Hegedus wrote: Hi, I have to rerun a simulation done in gmx 5.1.4 to save also the water and ions. First, I took the equilibrated gro and the modified mdp to generate the input tpr for the production run using gmx 2018.1. The results are significantly different (I think that this is ok

[gmx-users] gmx 5.1.4, cuda9, Unsupported gpu architecture 'compute_20'

/libgromacs_generated_copyrite_gpu.cu.o.cmake.pre-gen -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University | fax: (36) 1-266 6656 Tuzolto utca 37-47 | mailto:ta...@hegelab.org Budapest

[gmx-users] lipid / -OH oscillation period

step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Thanks for your help and suggestion, Tamas -- Tamas Hegedus, PhD Senior Research Fellow MTA-SE Molecular Biophysics Research Group Hungarian Academy of Sciences | phone: (36) 1-459 1500/60233 Semmelweis University

[gmx-users] steered md - pushing

Hi, I have a protein with four domains. I know the conformation of the full protein in one state. In the other state I know only the conformation of two of the domains. I would like to move the two domains, whose positions are known in both conformations, and observe movements in the other two