Re: [gmx-users] Multi-level parallelization: MPI + OpenMP

2013-07-22 Thread Éric Germaneau
(not shared), separate PME mpirun -np 4*Nnodes mdrun_mpi [-gpu_id 01] -npme 2*Nnodes - at high parallelization you may want to try (especially with homogeneous systems) 8 ranks per node Cheers, -- Szilárd On Fri, Jul 19, 2013 at 4:35 AM, Éric Germaneau wrote: Dear all, I'm note a gromacs u

Re: [gmx-users] Multi-level parallelization: MPI + OpenMP

2013-07-18 Thread Éric Germaneau
;s going wrong here? Thanks, Éric. On 07/19/2013 09:35 AM, Éric Germaneau wrote: Dear all, I'm note a gromacs user, I've installed gromacs 4.6.3 on our cluster and making some test. Each node of our machine has 16 cores and 2 GPU. I'm trying to figure how to submit efficient mul

[gmx-users] Multi-level parallelization: MPI + OpenMP

2013-07-18 Thread Éric Germaneau
this matter. I thank you in advance, Éric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm> Shanghai Jiao Tong University Network & Information Center room 205 Minhang Campus 800 Dongchuan Roa

Re: [gmx-users] 4.6.3 and MKL

2013-07-10 Thread Éric Germaneau
your compiler is installed correctly. But that is for you to judge! :-) On Thu, Jul 11, 2013 at 1:11 AM, Éric Germaneau wrote: I see. Thank you. On 07/11/2013 07:08 AM, Mark Abraham wrote: On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau wrote: Yes, as one can see in my first post. No, because we

Re: [gmx-users] 4.6.3 and MKL

2013-07-10 Thread Éric Germaneau
I see. Thank you. On 07/11/2013 07:08 AM, Mark Abraham wrote: On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau wrote: Yes, as one can see in my first post. No, because we can't guess whether your icc is 11 or not. If so, you have a bunch of stuff that is not required. icc 11 has a magic

Re: [gmx-users] 4.6.3 and MKL

2013-07-10 Thread Éric Germaneau
I see. Thank you. On 07/11/2013 07:08 AM, Mark Abraham wrote: On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau wrote: Yes, as one can see in my first post. No, because we can't guess whether your icc is 11 or not. If so, you have a bunch of stuff that is not required. icc 11 has a magic

Re: [gmx-users] 4.6.3 and MKL

2013-07-10 Thread Éric Germaneau
L On Thu, Jul 11, 2013 at 12:24 AM, Éric Germaneau wrote: Dear all, Anyone have successfully built the 4.6.3 release using MKL? I keep getting the following error message: -- Looking for DftiCreateDescriptor - not found CMake Error at CMakeLists.txt:1018 (message): Linking with MK

[gmx-users] 4.6.3 and MKL

2013-07-10 Thread Éric Germaneau
T_ROOT_DIR=$CUDAPATH] \ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \ -DGMX_X11=OFF ../$APP \ -DGMX_THREADS=OFF Any hints here? I thank you in advance, 'Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Éric Germanea

Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6

2013-07-10 Thread Éric Germaneau
I figured out by using static libraries. On 07/10/2013 06:52 AM, Éric Germaneau wrote: Dear all, I call cmake the following way and get the error bellow: CC=mpicc CXX=mpicxx CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin \ /lustre/utility/bin/cmake

[gmx-users] Re: gInstallation Problems with Gromacs4.6

2013-07-09 Thread Éric Germaneau
Mahatma Gandhi --- Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm> Shanghai Jiao Tong University Network & Information Center room 205 Minhang Campus 800 Dongchuan Road Shanghai 200240 China View Éric Germaneau's profile on LinkedIn <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/3