Hi, I don't see any problems there, but I note that there are run-time settings for the driver/runtime to block until no other process is using the GPU, which may be a contributing factor here.
As Justin noted, if your EM jobs would use a build of GROMACS that is not configured to have access to the GPUs, then there can be no problem. I recommend you do that if you want to continue sharing this node between GPU and non-GPU jobs. There has long been the principle that users must take active steps to keep GROMACS processes away from each other when sharing CPU resources, and this is a similar situation. In the abstract, it would be reasonable to organize mdrun so that we determine that we might want to use a GPU if we have one before we run the GPU detection, however that high-level code is in considerable flux in development branches, and we are highly unlikely to prioritise such a fix in a stable release branch to suit this use case. I didn't think that some of the reorganization since 2016 release would have this effect, but apparently it can. Sorry! Mark On Mon, May 7, 2018 at 6:33 AM Alex <nedoma...@gmail.com> wrote: > Mark, > > I am forwarding the response I received from the colleague who prepared > the box for my GMX install -- this is from the latest installation of > 2018.1. See text below and please let me know what you think. We have no > problem rebuilding things, but would like to understand what is wrong > before we pause all the work. > > Thank you, > > Alex > > "OS Ubuntu 16.04LTS > > After checking gcc and kernel-headers were installed I ran the following > > #sudo lspci |grep -i nvidia > > #curl > > http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/cuda-repo-ubuntu1604_9.1.85-1_amd64.deb > > cuda-repo-ubuntu1604_9.1.85-1_amd64.deb > > #sudo dpkg -i cuda-repo-ubuntu1604_9.1.85-1_amd64.deb > > #sudo apt-key adv > --fetch-keyshttp:// > developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/7fa2af80.pub > > #sudo dpkg -i cuda-repo-ubuntu1604_9.1.85-1_amd64.deb > > #sudo apt update > > #sudo apt upgrade > > #sudo /sbin/shutdown -r now > > After reboot > > #sudo apt-get install cuda > > #export PATH=/usr/local/cuda-9.1/bin${PATH:+:${PATH}} > > #nvidia-smi > > I also compiled the samples in the cuda tree using the Makefile there > and had no problems." > > -- > 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. > -- 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.