[gmx-users] Error installing during CXX Executable stage

Hello, On Ubuntu 16.04, I have tried cmake with the following command: *cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-8.0 -DGMX_GPU=ON -DGMX_MPI=ON * This process completes (with some warnings), and when you try to make, it gets to the following stage and fails:

Re: [gmx-users] GPU Not Being Utilized during mdrun

Just wanted to ping this and see if anyone had any ideas :) On Fri, Jul 15, 2016 at 10:30 AM, Vito Spadavecchio <spadavecc...@gmail.com> wrote: > My apologies! I meant to include the logfile as well. You can view it > here: > > https://www.dropbox.com/s/8ddm226gpgs5kpr/md_0_2.l

Re: [gmx-users] GPU Not Being Utilized during mdrun

My apologies! I meant to include the logfile as well. You can view it here: https://www.dropbox.com/s/8ddm226gpgs5kpr/md_0_2.log?dl=0 Thanks! On Fri, Jul 15, 2016 at 2:45 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/14/16 10:35 PM, Vito Spadavecchio wrote: > &g

Re: [gmx-users] GPU Not Being Utilized during mdrun

g output > does not confirm much, e.g. it does not show the performance table and > the final performance. > > Could you please run again and look at (and share if approapriate): > - the entire log, not just parts, in particular we want to see the > header, perf table > - the output of

Re: [gmx-users] GPU Not Being Utilized during mdrun

ers-boun...@maillist.sys.kth.se> on behalf of Vito > Spadavecchio <spadavecc...@gmail.com> > Sent: Thursday, July 14, 2016 2:28 PM > To: gmx-us...@gromacs.org > Subject: [gmx-users] GPU Not Being Utilized during mdrun > > Hello > > After building GROMACS with G

[gmx-users] GPU Not Being Utilized during mdrun

Hello After building GROMACS with GPU support and running some simple MD, I am only getting ~20ns/day (which is what I would expect to get out of my i7-6700k cpu only. My machine currently has a 1080 GTX in it, which should even on moderately large systems, be getting ~100ns/day) I've tried

[gmx-users] Mn/Mn2+ Parameters included in Amberff

Hello It looks like parameters for Mn/Mn2+ were (somewhat) recently developed for Amber forcefield (http://pubs.acs.org/doi/abs/10.1021/ct400055v); I'd like to use these parameters for a simulation I'd like to run on MntR (PDB: 1ON2 ), but