[gmx-users] make manual fails

thanks Szilard for the reply! below is the output of the cmake and make command, i doesn't find sphinx, but then i doesn't seem to look for it either ...anyway, on this second attempt I get a different error, no idea why, only diff: the first time i first made gromacsand only then the manual, th

[gmx-users] make manual fails

hi,so I say:prompt> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_C_COMPILER=gcc-7 -DCMAKE_CXX_COMPILER=g++-7 -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=/home/michael/local/gromacs-2019-3-bin -DGMX_BUILD_MANUAL=onprompt> make -j 4prompt> make install prompt> make manualmanual cannot be built because Sphinx

[gmx-users] delay at start

Hi, thanks Szilard for the reply, below I include what i get to stdout/stderr and the mdp (log file is too long) obviously the timings are not accurate due to buffering but to me it looks as if Gromacs spent reproducibly about 2 minutes running on ONE thread, and only then switches to use 4. This

[gmx-users] trap invalid opcode

Hi running a gmx job on a newly set-up debian-buster, with intel i7-3820 CPU, and one Nvidia 1060 GTX-6Gb architecture, the job dies without further notice, nothing in log file, nor in stdout/stderr ...however in /var/syslogi find exactly at the time when gromacs stops this message: Jan 26 23

[gmx-users] delay at start

hi, i notice that gromacs, when i start an MD simulation usuallyspends up to a few minutes using only one (out of several possible) threads.after a while it seems to have figured something out and then starts to runusing more threads. This is particularly conspicuous if also GPU is used.It is no

[gmx-users] Unexpected cudaStreamQuery failure: unspecified launch failure

Hi, gromacs started dying on me lately with rather obscure error messages as in the caption of this mail. Errors seem to be related to the nvidia driver (see below for more output,and further below for the mdp file) ... i perform a large number of short (2ns) sims and this happens perhapsone ou

[gmx-users] gmx kill computer?

, the 1060 in combination with gmx can give particularlylarge spikes or changes in energy consumption so that even a 700W PSU cannot cope? cheers,michael >On 23.10.2018 15:12, Michael Brunsteiner wrote: >> the computers are NOT overclocked, cooling works, cpu temperatures are well >&

[gmx-users] gmx kill computer?

Hi, this might be considered off-topic, but i believe there is some evidence to the contrary ... what i see is this: I have a couple of (fairly new) workstations (specs below) and on at least two of them, on at least three differentoccasions, i recently saw the following behaviour:computer is h

Re: [gmx-users] compiling 2018.3 ... problems with hwloc

figured it out ... hwloc version 2.0.2 was too new ... oncei used hwloc-1.11.11 instead things worked ... mic -- 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/Supp

[gmx-users] compiling 2018.3 ... problems with hwloc

Hi, In the past I compiled gmx 2016.4 on our old cluster and this worked as expected. Now I just compiled 2018.3 only to find that the resulting binary was unexpectedly slow ... On each node I have a multi-core architecture with 12 logical threads, but htop shows that gmx uses only one thread.

[gmx-users] stride

 hi about my hardware gmx has to say:   Hardware topology: Basic     Sockets, cores, and logical processors:   Socket  0: [   0   6] [   1   7] [   2   8] [   3   9] [   4  10] [   5  11] if i want to run two gmx jobs simultaneously on this one node,i usually do something like: promt> gmx md

[gmx-users] 2018: large performance variations

Hi,I ran a few MD runs with identical input files (the SAME tpr file. mdp included below) on the same computer with gmx 2018 and observed rather large performance variations (~50%) as in: grep Performance */mcz1.log7/mcz1.log:Performance:   98.510    0.244 7d/mcz1.log:Performance:  140

[gmx-users] gmx, threads, pinoffset and stride

doing some test runs to optimize the mdrun settings for my hardwarei noticed a couple of things i fail to understand (everything below is gmx-2018on an intel CPU 6 cores, 2 threads each, and GTX 1060) 1) when i start a run as in, e.g.:  prompt> gmx mdrun -v -nt 12 -ntmpi 1 -ntomp 12  -deffnm mc

Re: [gmx-users] 2018 performance question

= 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref-p  = 1 1 1 0 0 0 ; annealing  = single annealing-npoints  = 2 annealing-time = 0 10 annealing-temp = 511 491 From: Szilárd Páll To: Michael Brunsteiner Sent: Thursday, February 22, 2018 4:15 PM Subject: Re: [gmx-users] 2

[gmx-users] 2018 performance question

hi just installed gmx-2018 on a x86_64 PC with a Geforce GTX 780 and the cudasoftware directly from the nvidia webpage (didn't work using the debian nvidia packages) output of lscpu is included below. i find that: 1) 2018 is slightly faster (~5%) than 2016.2) both 2016 and 2018 use the GPU, but

Re: [gmx-users] compiling 2018 with GPU doesn't work on my debian stretch

Szilárd wrote:> Option A) Get a gcc 5.x (e.g. compile from source) > Option B) Install CUDA 9.1 (and required driver) which is compatible > with gcc 6.3 > (http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html) didn't try A (there might be a good reason why stretch does not have gcc

[gmx-users] further compilation issues on stretch

as compilation of gmx-2018 idn't work for me i went back to 2016.4 after some google-ing i found that the following commands work, and gmx compiles without any complaints... > cmake .. -DGMX_GPU=on  -DNVML_FOUND=1 > -DNVML_LIBRARY=/usr/lib/x86_64-linux-gnu/libnvidia-ml.so.1 > -DNVML_INCLUDE_DIR=

[gmx-users] compiling 2018 with GPU doesn't work on my debian stretch

Hi, I have problems compiling gromacs-2018 (January 10 release) on debian stretch (vanilla) my specs: Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.65-3+deb9u1 (2017-12-23) x86_64 GNU/Linux gcc-6.3.0,Cuda compilation tools, release 8.0, V8.0.44 graphics: Geforce GTX 780. I do: > cmake .. -DGMX_GPU=on w

[gmx-users] problem compiling gmx-2016.4 with CUDA on debian stable/stretch

hi, I just tried to install gmx (2015.4) on my desktop with vanilla debian (stable/stretch with the debian nvidia/cuda driver packages installed) as recommended in INSTALL ... prompt> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=/home/user/local/gromacs-2016-4-bin finishes

[gmx-users] MD for inorganic compound

> Anjali Patel wrote:> What is the procedure of using gromacs specially for > inorganic compound??> I am beginner for gromacs simulation package, I used it > for organic > compounds. But unable to understand how to deal with inorganic compounds > and what about the force field and solvent we can

[gmx-users] performance issue with many short MD runs

Thanks Peter and Mark! I'll try running on single cores ... however, comparing the timings I believe the bottleneck might be the time spent in I/O(reading/writing to disk) and here running several jobs on a single node with multiple coresmight make things even worse. also funny: In the log files

[gmx-users] performance issue with many short MD runs

Hi,I have to run a lot (many thousands) of very short MD reruns with gmx.Using gmx-2016.3 it works without problems, however, what i see is thatthe overall performance (in terms of REAL execution time as measured with the unix time command)which I get on a relatively new computer is poorer than

[gmx-users] net charge correction

.00 0.00 ATOM 8 CMP1 8 23.000 30.000 103.000 0.00 0.00 -- ===== Michael Brunsteiner, PhD Senior Researcher, Area II Research Center Pharmaceutical Engineering GmbH A-8010 Graz, Inffeldgasse 13 phone: +43 316 873 30908 mobile: +43 66

[gmx-users] problem compiling template

ch file or directory #include ^ compilation terminated. any ideas how to resolve this? thanks, Michael -- ============= Michael Brunsteiner, PhD Senior Researcher, Area II Research Center Pharmaceutical Engineering Gm

[gmx-users] normal mode analysis and system size ...

hi , I've been trying to perform a nromal mode analysis using (after a thorough energy minimization of my system) prompt> mdrun_d -v -s nm.tpr  -o nm.trr -mtx nm.mtx[...] Maximum force: 8.56366e+00 The force is probably not small enough to ensure that you are at a minimum. Be aware that negative

Re: [gmx-users] append does not work for me

On 4/21/15 10:41 AM, Michael Brunsteiner wrote: >> >> Hi, >> I just tried to continue a simulation, after having extended the total time >> using >> >> gmx convert-tpr -s original-xxx.tpr -o xxx.tpr -until 40 >> mdrun -nt 4 -deffnm xxx -cpi xxx.c

[gmx-users] append does not work for me

Hi, I just tried to continue a simulation, after having extended the total time using gmx convert-tpr -s original-xxx.tpr -o xxx.tpr -until 40 mdrun -nt 4 -deffnm xxx -cpi xxx.cpt xxx.cpt, xxx.log, and xxx.trr are present  in the working directory and are the original output files, i.e.,

Re: [gmx-users] GPU waits for CPU, any remedies?

you could be normal? > > From: Szilárd Páll >To: Michael Brunsteiner >Cc: Discussion list for GROMACS users ; >"gromacs.org_gmx-users@maillist.sys.kth.se" > >Sent: Wednesday, September 17, 2014 4:18 PM >Subject: Re:

Re: [gmx-users] GPU waits for CPU, any remedies?

ilárd Páll wrote: Subject: Re: [gmx-users] GPU waits for CPU, any remedies? To: "Michael Brunsteiner" Cc: "Discussion list for GROMACS users" , "gromacs.org_gmx-users@maillist.sys.kth.se" Date: Tuesday, September 16, 2014, 6:52 PM Well, it looks like you are i)

[gmx-users] GPU waits for CPU, any remedies?

hi, testing a new computer we just got i found that for the system i use performance is sub-optimal as the GPU appears to be about 50% faster than the CPU (see below for details) the dynamic load balancing that is performed automatically at the beginning of each simulation does not seem to impro

[gmx-users] performance question

Dear all, i just got new hardware, and ran a couple of tests, comparing performance of the new machine to results from another five years old computer. I found the outcome (see below) somewhat disappointing, and write to see if other people got similar results, or if perhaps i overlooked somethin

Re: [gmx-users] hardware setup for gmx

be normal? > > From: Szilárd Páll >To: Michael Brunsteiner >Sent: Thursday, July 17, 2014 2:00 AM >Subject: Re: [gmx-users] hardware setup for gmx > > >Dear Michael, > >I'd appreciate if you kept the further discussion on the gmx-users list. > >On

[gmx-users] gmx-5.0 does not seem to honour plus/minus signs in topology files

Hi, I made myself a force field for an organic polymer using a terminology/syntax similar to amino acids, so that i can make topoly files directly from pdb files using pdb2gmx. This worked nicely up to gmx-4.6.5, but when trying 5.0 pdb2gmx complains about not finding particular atoms in a pdb f

[gmx-users] gmx-5.0 features

Hi, I am sorry in case I overlooked the answers in the release-notes, but I didn't find there answers to: 1) does gmx-5.0 support free energy calculations + GPU ? 2) does gmx-5.0 support double precision + GPU ? cheers michael === Why be happy when you could be

[gmx-users] hardware setup for gmx

Hi, can anybody recommend a hardware setup to perform MD runs (with PME) that has a good price-performance ratio? ... in particular I'd be interested in learning which combinations of CPU and GPU can be expected to provide a good FLOPS-per-dollar ratio with the more recent gmx versions (4.6

Re: [gmx-users] Excess Heat of mixing

Hi Amninder, DeltaU_mix = - * N_A - * N_B ... average total intermolecular energy of the blend ... the average interaction energy of a single molecule of type A in a pure sample of A ... the average interaction energy of a single molecule of type B in a pure sample of B N_A ... the numb

[gmx-users] hydrogen bond auto correlation

Dear all, I am interested in H-bond life-times and tried to use g_hbond with the - ac option (gmx 4.6.5) - but i am not sure how to interpret the outout ... 1) in the output written to stdout there is a table: Type    Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2 Forward etc...