Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

On 30/04/2012 3:38 PM, Anirban Ghosh wrote: On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung mailto:adeyo...@andrew.cmu.edu>> wrote: Hi, Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you know, automatic threading is awesome because it allows me to star

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung wrote: > Hi, > > Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you > know, automatic threading is awesome because it allows me to start parallel > runs without calling mpirun. So on version 4.5.5, I can start a job on > eight

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

oops I meant /usr/local/gromacs/bin in PATH also 4.5.4 has support for threading if compiled that way...Most clusters don't use it because nodes on separate chassis usually don't support shared memory with each other. We get really bad performance when using threading-over-scalemp as compared t

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

possibly. Make sure PATH includes /usr/local/bin and LD_LIBRARY_PATH includes the path where libmd_mpi.so and libgmx_mpi.so are located. try using mdrun -v and > somelogfile after the mpirun line (like mpirun blah -np 8 mdrun -v -deffnm etcetc > mpilog). the contents of mpilog will tell you wha

[gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

Hi, Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you know, automatic threading is awesome because it allows me to start parallel runs without calling mpirun. So on version 4.5.5, I can start a job on eight CPUs using simply the command: mdrun -s topol.tpr -nt 8 However, n