Re: [gmx-users] GPU job failed

yes, the normal MD works fine. Even in a CPU based plumed also works. It seems that this function doesn't support PLumed GPU running? On 08/02/2017 01:02 PM, Mark Abraham wrote: Hi, My first guess is that the implementation of PLUMED doesn't support this. Does a normal non-PLUMED simulation run

Re: [gmx-users] GPU job failed

Hi, My first guess is that the implementation of PLUMED doesn't support this. Does a normal non-PLUMED simulation run correctly when called in this manner? Mark On Wed, Aug 2, 2017 at 9:55 AM Albert wrote: > Hello, > > I am trying to run Gromacs with the following command line: > > > mpirun

[gmx-users] GPU job failed

Hello, I am trying to run Gromacs with the following command line: mpirun -np 4 gmx_mpi mdrun -v -g 7.log -s 7.tpr -x 7.xtc -c 7.gro -e 7.edr -plumed plumed.dat -ntomp 2 -gpu_id 0123 but it always failed with the following messages: Running on 1 node with total 24 cores, 48 logical cores,

Re: [gmx-users] GPU job failed

I recompiled Gromacs-5.0.1, finally it works now Probably I made some mistakes in previous compiling thanks a lot guys regards Albert On 09/09/2014 09:16 AM, Carsten Kutzner wrote: Hi, from the double output it looks like two identical mdruns, each with 1 PP process and 10 OpenMP thr

Re: [gmx-users] GPU job failed

thank you for reply. I compiled it with command: env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90 CMAKE_PREFIX_PATH=/home/albert/install/intel-2013/mkl/include/fftw:/home/albert/install/intel-mpi/bin64 cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/home/

Re: [gmx-users] GPU job failed

thank you for reply. I compiled it with command: env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90 CMAKE_PREFIX_PATH=/home/albert/install/intel-2013/mkl/include/fftw:/home/albert/install/intel-mpi/bin64 cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/home/

Re: [gmx-users] GPU job failed

Hi, from the double output it looks like two identical mdruns, each with 1 PP process and 10 OpenMP threads, are started. Maybe there is something wrong with your MPI setup (did you by mistake compile with thread-MPI instead of MPI?) Carsten On 09 Sep 2014, at 09:06, Albert wrote: > Here ar

Re: [gmx-users] GPU job failed

Here are more informations from log file: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 0 Number of hardware threads detected (20) does not match the number reported by OpenMP (10). Consider setting the launch configuration manually! Number of hardw

Re: [gmx-users] GPU job failed

thanks a lot for reply both Yunlong and Szilard. I don't set up PBS system and nodes in the workstation. In the GPU workstation, it contains 1 CPU with 20 cores, and two GPUs. So it is similar to 1 nodes with 2 GPUs. But I don't know why 4.6.5 works, but 5.0.1 doesn't ... Thx again f

Re: [gmx-users] GPU job failed

Same idea with Szilard. How many nodes are you using? On one nodes, how many MPI ranks do you have? The error is complaining about you assigned two GPUs to only one MPI process on one node. If you spread your two MPI ranks on two nodes, that means you only have one at each. Then you can't assig

Re: [gmx-users] GPU job failed

Hi, It looks like you're starting two ranks and passing two GPU IDs so it should work. The only think I can think of is that you are either getting the two MPI ranks placed on different nodes or that for some reason "mpirun -np 2" is only starting one rank (MPI installation broken?). Does the sam

[gmx-users] GPU job failed

Hello: I am trying to use the following command in Gromacs-5.0.1: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 10 but it always failed with messages: 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no,