from:"Éric Germaneau"

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

2013-07-22 Thread Éric Germaneau


Dear Szilárd,

I'm making some tests using 2 ranks/node, what I was trying to do.
It seems working now, thank you.

 Éric.

On 07/19/2013 08:56 PM, Szilárd Páll wrote:

Depending on the level of parallelization (number of nodes and number
of particles/core) you may want to try:

- 2 ranks/node: 8 cores + 1 GPU, no separate PME (default):
   mpirun -np 2*Nnodes mdrun_mpi [-gpu_id 01 -npme 0]

- 4 ranks per node: 4 cores + 1 GPU (shared between two ranks), no separate PME
   mpirun -np 4*Nnodes mdrun_mpi -gpu_id 0011 [-npme 0]

- 4 ranks per node, 2 PP/2PME: 4 cores + 1 GPU (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 german...@sjtu.edu.cn 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 multiple nodes LSF jobs using
the maximum of resources.
After reading the documentation
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores
on Acceleration and parallelization I got confused and inquire some help.
I'm just wondering whether someone with some experiences on 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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn
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/ --- 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 
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Re: [gmx-users] Multi-level parallelization: MPI + OpenMP

2013-07-19 Thread Éric Germaneau

I actually submitted  using two MPI process per node but log files do 
not get updated, it's like the calculation gets stuck.


Here is how I proceed:

   mpirun -np $NM -machinefile nodegpu mdrun_mpi  -nb gpu -v -deffnm
   test184000atoms_verlet.tpr  mdrun_mpi.log

with the content of /nodegpu/:

   gpu04
   gpu04
   gpu11
   gpu11

and with

   NM=`cat nodegpu | wc -l`

/bjobs/ gives

   3983hpceric RUN   gpu mu0516*gpu11gromacsJul 19
   12:12
   16*gpu04

/mdrun_mpi.log/ contains the description of the options and 
/test184000atoms_verlet.tpr.log/ stops after PLEASE READ AND CITE THE 
FOLLOWING REFERENCE.


The top of /test184000atoms_verlet.tpr.log/ is:

   Log file opened on Fri Jul 19 13:47:36 2013
   Host: gpu11  pid: 124677  nodeid: 0  nnodes:  4
   Gromacs version:VERSION 4.6.3
   Precision:  single
   Memory model:   64 bit
   MPI library:MPI
   OpenMP support: enabled
   GPU support:enabled
   invsqrt routine:gmx_software_invsqrt(x)
   CPU acceleration:   AVX_256
   FFT library:fftw-3.3.3-sse2-avx
   Large file support: enabled
   RDTSCP usage:   enabled
   Built on:   Mon Jul 15 13:44:42 CST 2013
   Built by:   name@node [CMAKE]
   Build OS/arch:  Linux 2.6.32-279.el6.x86_64 x86_64
   Build CPU vendor:   GenuineIntel
   Build CPU brand:Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
   Build CPU family:   6   Model: 45   Stepping: 7
   Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx
   msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2
   sse3 sse4.1 sse4.2 ssse3 tdt x2apic
   C compiler: /lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicc
   GNU gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)
   C compiler flags:   -mavx-Wextra -Wno-missing-field-initializers
   -Wno-sign-compare -Wall -Wno-unused -Wunused-value  
   -fomit-frame-pointer -funroll-all-loops  -O3 -DNDEBUG

   C++ compiler:
   /lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicxx GNU g++
   (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)
   C++ compiler flags: -mavx   -Wextra -Wno-missing-field-initializers
   -Wno-sign-compare -Wall -Wno-unused -Wunused-value  
   -fomit-frame-pointer -funroll-all-loops  -O3 -DNDEBUG

   CUDA compiler:  /lustre/utility/cuda-5.0/bin/nvcc nvcc: NVIDIA
   (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA
   Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation
   tools, release 5.0, V0.2.1221
   CUDA compiler
   
flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_30,code=compute_30;-use_fast_math;-Xcompiler;-fPIC
   ;
   
-mavx;-Wextra;-Wno-missing-field-initializers;-Wno-sign-compare;-Wall;-Wno-unused;-Wunused-value;-fomit-frame-pointer;-funroll-all-loops;-O3;-DNDEBUG
   CUDA driver:5.0
   CUDA runtime:   5.0

Does any have any idea about what'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 multiple nodes LSF jobs 
using the maximum of resources.
After reading the documentation 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores 
on Acceleration and parallelization I got confused and inquire some 
help.

I'm just wondering whether someone with some experiences on 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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn 
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986


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

2013-07-18 Thread Éric Germaneau


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 multiple nodes LSF jobs 
using the maximum of resources.
After reading the documentation 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores 
on Acceleration and parallelization I got confused and inquire some help.

I'm just wondering whether someone with some experiences on 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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn 
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986


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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 \
-DCMAKE_CXX_COMPILER=/xxx/xxx/intel/impi/4.1.1.036/intel64/bin/mpicxx \
-DCMAKE_C_COMPILER=/xxx/xxx/intel/impi/4.1.1.036/intel64/bin/mpicc \
   -DFFTW_INCLUDE_DIR=$FFTW3DIR/include \
   -DFFTW_LIBRARY=$FFTW3DIR/lib/ \
   -DGMX_MPI=ON \
   -DGMX_GPU=OFF [-DCUDA_TOOLKIT_ROOT_DIR=$CUDAPATH] \
   -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
   -DGMX_X11=OFF ../$APP

   -- Looking for fftwf_plan_r2r_1d in
   /lustre/software/fftw3/fftw-3.3.3_impi/FLOAT/lib/libfftw3f.so - not
   found
   CMake Error at cmake/FindFFTW.cmake:97 (message):
  Could not find fftwf_plan_r2r_1d in
/lustre/software/fftw3/fftw-3.3.3_impi/FLOAT/lib/libfftw3f.so,
   take a look
  at the error message in
/lustre/home/hpceric/soft/science/opensource/gromacs/build-4.6.3/CMakeFiles/CMakeError.log
  to find out what went wrong.  If you are using a static lib (.a)
   make sure
  you have specified all dependencies of fftw3f in FFTWF_LIBRARY by
   hand
  (e.g. -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
   Call Stack (most recent call first):
  CMakeLists.txt:948 (find_package)

Can you please shed some light on this?
Thanks in advance,

'Eric.



--
/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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn 
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986


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[gmx-users] 4.6.3 and MKL

2013-07-10 Thread Éric Germaneau


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 MKL was requested, but was not successful.  The
   include path
  to mkl.h in MKL_INCLUDE_DIR, and the link libraries in
   
MKL_LIBRARIES=/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_thread.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_core.so;/lustre/utility/intel/mkl/lib/intel64/libfftw2xf_double_intel.a;/lustre/utility/intel/mkl/lib/intel64/libmkl_avx2.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_scalapack_lp64.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_lp64.so
  need to match what the MKL documentation says you need for your
   system.
  Use full paths to library files, in the right order, and separated by
  semicolons.

Here is how I use CMAKE:

   CC=mpicc CXX=mpicxx
   CMAKE_PREFIX_PATH=$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin \
  /lustre/utility/bin/cmake \
   -DGMX_FFT_LIBRARY=mkl \
   
-DMKL_LIBRARIES=${MKL}/lib/intel64/libmkl_intel_thread.so;${MKL}/lib/intel64/libmkl_core.so;${MKL}/lib/intel64/libfftw2xf_double_intel.a;${MKL}/lib/intel64/libmkl_avx2.so;${MKL}/lib/intel64/libmkl_scalapack_lp64.so;${MKL}/lib/intel64/libmkl_intel_lp64.so
   \
   -DMKL_INCLUDE_DIR=${MKL}/include \
   -DGMX_MPI=ON \
   -DGMX_GPU=OFF [-DCUDA_TOOLKIT_ROOT_DIR=$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 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/30/931/986


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Re: [gmx-users] 4.6.3 and MKL

2013-07-10 Thread Éric Germaneau


Yes, as one can see in my first post.
One thing is I don't know what libraries I need and in which order.
Thanks,

   Eric.

On 07/11/2013 06:58 AM, Mark Abraham wrote:

Are you following the advice here?
http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL

On Thu, Jul 11, 2013 at 12:24 AM, Éric Germaneau german...@zoho.com 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 MKL was requested, but was not successful.  The
include path
   to mkl.h in MKL_INCLUDE_DIR, and the link libraries in

MKL_LIBRARIES=/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_thread.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_core.so;/lustre/utility/intel/mkl/lib/intel64/libfftw2xf_double_intel.a;/lustre/utility/intel/mkl/lib/intel64/libmkl_avx2.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_scalapack_lp64.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_lp64.so
   need to match what the MKL documentation says you need for your
system.
   Use full paths to library files, in the right order, and separated by
   semicolons.

Here is how I use CMAKE:

CC=mpicc CXX=mpicxx
CMAKE_PREFIX_PATH=$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin \
   /lustre/utility/bin/cmake \
-DGMX_FFT_LIBRARY=mkl \

-DMKL_LIBRARIES=${MKL}/lib/intel64/libmkl_intel_thread.so;${MKL}/lib/intel64/libmkl_core.so;${MKL}/lib/intel64/libfftw2xf_double_intel.a;${MKL}/lib/intel64/libmkl_avx2.so;${MKL}/lib/intel64/libmkl_scalapack_lp64.so;${MKL}/lib/intel64/libmkl_intel_lp64.so
\
-DMKL_INCLUDE_DIR=${MKL}/include \
-DGMX_MPI=ON \
-DGMX_GPU=OFF [-DCUDA_TOOLKIT_ROOT_DIR=$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 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/30/931/986

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--
/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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn 
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986


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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 german...@zoho.com 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 flag
for using MKL, which GROMACS will use if given the chance. But I guess
I wasted my time implementing and documenting it :-)

One thing is I don't know what libraries I need and in which order.

... and neither does anybody else who can't see the documentation for
your system. That's why if you have icc before version 11, the GROMACS
instructions suggest you look at them! That is the price of using mkl
before icc-11.

Mark

Thanks,

Eric.

On 07/11/2013 06:58 AM, Mark Abraham wrote:

Are you following the advice here?
http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL

On Thu, Jul 11, 2013 at 12:24 AM, Éric Germaneau german...@zoho.com
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 MKL was requested, but was not successful. The
include path
to mkl.h in MKL_INCLUDE_DIR, and the link libraries in

MKL_LIBRARIES=/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_thread.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_core.so;/lustre/utility/intel/mkl/lib/intel64/libfftw2xf_double_intel.a;/lustre/utility/intel/mkl/lib/intel64/libmkl_avx2.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_scalapack_lp64.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_lp64.so
need to match what the MKL documentation says you need for your
system.
Use full paths to library files, in the right order, and separated
by
semicolons.

Here is how I use CMAKE:

CC=mpicc CXX=mpicxx
CMAKE_PREFIX_PATH=$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin \
/lustre/utility/bin/cmake \
-DGMX_FFT_LIBRARY=mkl \

-DMKL_LIBRARIES=${MKL}/lib/intel64/libmkl_intel_thread.so;${MKL}/lib/intel64/libmkl_core.so;${MKL}/lib/intel64/libfftw2xf_double_intel.a;${MKL}/lib/intel64/libmkl_avx2.so;${MKL}/lib/intel64/libmkl_scalapack_lp64.so;${MKL}/lib/intel64/libmkl_intel_lp64.so
\
-DMKL_INCLUDE_DIR=${MKL}/include \
-DGMX_MPI=ON \
-DGMX_GPU=OFF [-DCUDA_TOOLKIT_ROOT_DIR=$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 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/30/931/986

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

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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
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/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

--
/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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

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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 german...@zoho.com wrote:

Yes, as one can see in my first post.

One thing is I don't know what libraries I need and in which order.

Mark

Thanks,

Eric.

On 07/11/2013 06:58 AM, Mark Abraham wrote:

Are you following the advice here?
http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL

On Thu, Jul 11, 2013 at 12:24 AM, Éric Germaneau german...@zoho.com
wrote:

Dear all,

Anyone have successfully built the 4.6.3 release using MKL?
I keep getting the following error message:

Here is how I use CMAKE:

CC=mpicc CXX=mpicxx
CMAKE_PREFIX_PATH=$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin \
/lustre/utility/bin/cmake \
-DGMX_FFT_LIBRARY=mkl \

Any hints here?
I thank you in advance,

'Eric.

--
/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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

--
/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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

--
/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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

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Re: [gmx-users] 4.6.3 and MKL

2013-07-10 Thread Éric Germaneau

I have the same feeling too but I'm not in charge of it unfortunately.
Thank you, I appreciate.

On 07/11/2013 07:15 AM, Mark Abraham wrote:

No problems :-) (For the record, the fact that you had to brute-force
static libraries in another thread does not fill me with confidence
that your compiler is installed correctly. But that is for you to
judge! :-)

On Thu, Jul 11, 2013 at 1:11 AM, Éric Germaneau german...@zoho.com 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 german...@zoho.com
wrote:

Yes, as one can see in my first post.

One thing is I don't know what libraries I need and in which order.

Mark

Thanks,

Eric.

On 07/11/2013 06:58 AM, Mark Abraham wrote:

Are you following the advice here?

http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL

On Thu, Jul 11, 2013 at 12:24 AM, Éric Germaneau german...@zoho.com
wrote:

Dear all,

Anyone have successfully built the 4.6.3 release using MKL?
I keep getting the following error message:

Here is how I use CMAKE:

CC=mpicc CXX=mpicxx
CMAKE_PREFIX_PATH=$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin
\
/lustre/utility/bin/cmake \
-DGMX_FFT_LIBRARY=mkl \

Any hints here?
I thank you in advance,

'Eric.

--
/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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

--
/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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

--
/Be the change you wish to see in the world
/ --- Mahatma

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

2013-07-09 Thread Éric Germaneau


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 \
   -DCMAKE_CXX_COMPILER=/xxx/xxx/intel/impi/4.1.1.036/intel64/bin/mpicxx \
   -DCMAKE_C_COMPILER=/xxx/xxx/intel/impi/4.1.1.036/intel64/bin/mpicc \
   -DFFTW_INCLUDE_DIR=$FFTW3DIR/include \
   -DFFTW_LIBRARY=$FFTW3DIR/lib/ \
   -DGMX_MPI=ON \
   -DGMX_GPU=OFF [-DCUDA_TOOLKIT_ROOT_DIR=$CUDAPATH] \
   -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
   -DGMX_X11=OFF ../$APP

   -- Looking for fftwf_plan_r2r_1d in
   /lustre/software/fftw3/fftw-3.3.3_impi/FLOAT/lib/libfftw3f.so - not
   found
   CMake Error at cmake/FindFFTW.cmake:97 (message):
  Could not find fftwf_plan_r2r_1d in
  /lustre/software/fftw3/fftw-3.3.3_impi/FLOAT/lib/libfftw3f.so,
   take a look
  at the error message in
   
/lustre/home/hpceric/soft/science/opensource/gromacs/build-4.6.3/CMakeFiles/CMakeError.log
  to find out what went wrong.  If you are using a static lib (.a)
   make sure
  you have specified all dependencies of fftw3f in FFTWF_LIBRARY by
   hand
  (e.g.  -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
   Call Stack (most recent call first):
  CMakeLists.txt:948 (find_package)

Can you please shed some light on this?
Thanks in advance,

'Eric.

--
/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 Road
Shanghai 200240
China

View Éric Germaneau's profile on LinkedIn 
http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986


/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

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

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

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

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

[gmx-users] 4.6.3 and MKL

Re: [gmx-users] 4.6.3 and MKL

Re: [gmx-users] 4.6.3 and MKL

Re: [gmx-users] 4.6.3 and MKL

Re: [gmx-users] 4.6.3 and MKL

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

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