(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
;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
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
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
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
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
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
T_ROOT_DIR=$CUDAPATH] \
-DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
-DGMX_X11=OFF ../$APP \
-DGMX_THREADS=OFF
Any hints here?
I thank you in advance,
'Eric.
--
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---
Éric Germanea
I figured out by using static libraries.
On 07/10/2013 06:52 AM, Éric Germaneau wrote:
Dear all,
I call cmake the following way and get the error bellow:
CC=mpicc CXX=mpicxx
CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin
\
/lustre/utility/bin/cmake
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
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