Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

2013-11-08 Thread Mark Abraham
On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade johanne...@gmail.comwrote:

 Really?


Of course. With openmp gets to use all your cores for PME+bondeds+stuff
while the GPU does PP. Any version without openmp gets to use one core per
domain, which is bad.


 An what about gcc+mpi? should I expect any improvement?


Run how and compared with what? Using an external MPI library within a
single node is a complete waste of time compared with the alternatives
(thread-MPI, OpenMP, or both).

Mark




 On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

  You will do much better with gcc+openmp than icc-openmp!
 
  Mark
 
 
  On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.com
  wrote:
 
   Did it a few days ago. Not so much of a problem here.
  
   But I compiled everything, including fftw, with it. The only error I
 got
   was that I should turn off the separable compilation, and that the user
   must be in the group video.
  
   My settings are (yes, I know it should go better with openmp, but
 openmp
   goes horrobly in our cluster, I don't know why):
  
   setenv CC  /opt/intel/bin/icc
   setenv CXX /opt/intel/bin/icpc
   setenv F77 /opt/intel/bin/ifort
   setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/
   mkdir build
   cd build
   cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF
   -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON
   -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024
 -DBUILD_SHARED_LIBS=OFF
   -DGMX_PREFER_STATIC_LIBS=ON
   -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/
   make
   make install
   cd ..
   rm -rf build
  
  
   On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.com
   wrote:
  
icc and CUDA is pretty painful. I'd suggest getting latest gcc.
   
Mark
   
   
On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote:
   
 Hi,

 I'm having trouble compiling v 4.6.3 with GPU support using CUDA
   5.5.22.

 The configuration runs okay and I have made sure that I have set
  paths
 correctly.

 I'm getting errors:

 $ make
 [  0%] Building NVCC (Device) object

   
  
 
 src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
 icc: command line warning #10006: ignoring unknown option
  '-dumpspecs'
 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In
 function `_start':
 (.text+0x20): undefined reference to `main'
 CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206
(message):
   Error generating


   
  
 
 /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o


 make[2]: ***

   
  
 
 [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
 Error 1
 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
   Error
2
 make: *** [all] Error 2

 Any help would be appreciated.

 Regards,
 Ahmed.

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Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

2013-11-08 Thread Jones de Andrade
Ok, you convinced me. I'll really give it a try. I'm following this throw
the suposition that openMP implementation on intel compilers is not as good
as GNU compilers. I already tested intel openMP in our cluster, and it just
sucked in comparison to the pure MPI compilation.

Let's hope I can make it work together with the IMPI. I don't want to
install openmpi as just a user also (did it a long time ago as root, not in
limited space).

Thanks again!


On Fri, Nov 8, 2013 at 9:21 AM, Mark Abraham mark.j.abra...@gmail.comwrote:

 On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade johanne...@gmail.com
 wrote:

  Really?


 Of course. With openmp gets to use all your cores for PME+bondeds+stuff
 while the GPU does PP. Any version without openmp gets to use one core per
 domain, which is bad.


  An what about gcc+mpi? should I expect any improvement?
 

 Run how and compared with what? Using an external MPI library within a
 single node is a complete waste of time compared with the alternatives
 (thread-MPI, OpenMP, or both).

 Mark


 
 
  On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham mark.j.abra...@gmail.com
  wrote:
 
   You will do much better with gcc+openmp than icc-openmp!
  
   Mark
  
  
   On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.com
   wrote:
  
Did it a few days ago. Not so much of a problem here.
   
But I compiled everything, including fftw, with it. The only error I
  got
was that I should turn off the separable compilation, and that the
 user
must be in the group video.
   
My settings are (yes, I know it should go better with openmp, but
  openmp
goes horrobly in our cluster, I don't know why):
   
setenv CC  /opt/intel/bin/icc
setenv CXX /opt/intel/bin/icpc
setenv F77 /opt/intel/bin/ifort
setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/
mkdir build
cd build
cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON
-DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024
  -DBUILD_SHARED_LIBS=OFF
-DGMX_PREFER_STATIC_LIBS=ON
-DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/
make
make install
cd ..
rm -rf build
   
   
On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham 
 mark.j.abra...@gmail.com
wrote:
   
 icc and CUDA is pretty painful. I'd suggest getting latest gcc.

 Mark


 On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote:

  Hi,
 
  I'm having trouble compiling v 4.6.3 with GPU support using CUDA
5.5.22.
 
  The configuration runs okay and I have made sure that I have set
   paths
  correctly.
 
  I'm getting errors:
 
  $ make
  [  0%] Building NVCC (Device) object
 

   
  
 
 src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
  icc: command line warning #10006: ignoring unknown option
   '-dumpspecs'
  /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o:
 In
  function `_start':
  (.text+0x20): undefined reference to `main'
  CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206
 (message):
Error generating
 
 

   
  
 
 /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
 
 
  make[2]: ***
 

   
  
 
 [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
  Error 1
  make[1]: ***
 [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
Error
 2
  make: *** [all] Error 2
 
  Any help would be appreciated.
 
  Regards,
  Ahmed.
 
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Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

2013-11-07 Thread Mark Abraham
icc and CUDA is pretty painful. I'd suggest getting latest gcc.

Mark


On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote:

 Hi,

 I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22.

 The configuration runs okay and I have made sure that I have set paths
 correctly.

 I'm getting errors:

 $ make
 [  0%] Building NVCC (Device) object
 src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
 icc: command line warning #10006: ignoring unknown option '-dumpspecs'
 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In
 function `_start':
 (.text+0x20): undefined reference to `main'
 CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message):
   Error generating

 /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o


 make[2]: ***
 [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
 Error 1
 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2
 make: *** [all] Error 2

 Any help would be appreciated.

 Regards,
 Ahmed.

 --
 Scanned by iCritical.

 --
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Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

2013-11-07 Thread Jones de Andrade
Did it a few days ago. Not so much of a problem here.

But I compiled everything, including fftw, with it. The only error I got
was that I should turn off the separable compilation, and that the user
must be in the group video.

My settings are (yes, I know it should go better with openmp, but openmp
goes horrobly in our cluster, I don't know why):

setenv CC  /opt/intel/bin/icc
setenv CXX /opt/intel/bin/icpc
setenv F77 /opt/intel/bin/ifort
setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/
mkdir build
cd build
cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON
-DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF
-DGMX_PREFER_STATIC_LIBS=ON
-DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/
make
make install
cd ..
rm -rf build


On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 icc and CUDA is pretty painful. I'd suggest getting latest gcc.

 Mark


 On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote:

  Hi,
 
  I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22.
 
  The configuration runs okay and I have made sure that I have set paths
  correctly.
 
  I'm getting errors:
 
  $ make
  [  0%] Building NVCC (Device) object
 
 src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
  icc: command line warning #10006: ignoring unknown option '-dumpspecs'
  /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In
  function `_start':
  (.text+0x20): undefined reference to `main'
  CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206
 (message):
Error generating
 
 
 /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
 
 
  make[2]: ***
 
 [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
  Error 1
  make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error
 2
  make: *** [all] Error 2
 
  Any help would be appreciated.
 
  Regards,
  Ahmed.
 
  --
  Scanned by iCritical.
 
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Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

2013-11-07 Thread Mark Abraham
You will do much better with gcc+openmp than icc-openmp!

Mark


On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.comwrote:

 Did it a few days ago. Not so much of a problem here.

 But I compiled everything, including fftw, with it. The only error I got
 was that I should turn off the separable compilation, and that the user
 must be in the group video.

 My settings are (yes, I know it should go better with openmp, but openmp
 goes horrobly in our cluster, I don't know why):

 setenv CC  /opt/intel/bin/icc
 setenv CXX /opt/intel/bin/icpc
 setenv F77 /opt/intel/bin/ifort
 setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/
 mkdir build
 cd build
 cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF
 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON
 -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF
 -DGMX_PREFER_STATIC_LIBS=ON
 -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/
 make
 make install
 cd ..
 rm -rf build


 On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

  icc and CUDA is pretty painful. I'd suggest getting latest gcc.
 
  Mark
 
 
  On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote:
 
   Hi,
  
   I'm having trouble compiling v 4.6.3 with GPU support using CUDA
 5.5.22.
  
   The configuration runs okay and I have made sure that I have set paths
   correctly.
  
   I'm getting errors:
  
   $ make
   [  0%] Building NVCC (Device) object
  
 
 src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
   icc: command line warning #10006: ignoring unknown option '-dumpspecs'
   /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In
   function `_start':
   (.text+0x20): undefined reference to `main'
   CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206
  (message):
 Error generating
  
  
 
 /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
  
  
   make[2]: ***
  
 
 [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
   Error 1
   make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
 Error
  2
   make: *** [all] Error 2
  
   Any help would be appreciated.
  
   Regards,
   Ahmed.
  
   --
   Scanned by iCritical.
  
   --
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Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

2013-11-07 Thread Jones de Andrade
Really? An what about gcc+mpi? should I expect any improvement?


On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 You will do much better with gcc+openmp than icc-openmp!

 Mark


 On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.com
 wrote:

  Did it a few days ago. Not so much of a problem here.
 
  But I compiled everything, including fftw, with it. The only error I got
  was that I should turn off the separable compilation, and that the user
  must be in the group video.
 
  My settings are (yes, I know it should go better with openmp, but openmp
  goes horrobly in our cluster, I don't know why):
 
  setenv CC  /opt/intel/bin/icc
  setenv CXX /opt/intel/bin/icpc
  setenv F77 /opt/intel/bin/ifort
  setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/
  mkdir build
  cd build
  cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF
  -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON
  -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF
  -DGMX_PREFER_STATIC_LIBS=ON
  -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/
  make
  make install
  cd ..
  rm -rf build
 
 
  On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.com
  wrote:
 
   icc and CUDA is pretty painful. I'd suggest getting latest gcc.
  
   Mark
  
  
   On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote:
  
Hi,
   
I'm having trouble compiling v 4.6.3 with GPU support using CUDA
  5.5.22.
   
The configuration runs okay and I have made sure that I have set
 paths
correctly.
   
I'm getting errors:
   
$ make
[  0%] Building NVCC (Device) object
   
  
 
 src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
icc: command line warning #10006: ignoring unknown option
 '-dumpspecs'
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In
function `_start':
(.text+0x20): undefined reference to `main'
CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206
   (message):
  Error generating
   
   
  
 
 /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
   
   
make[2]: ***
   
  
 
 [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
Error 1
make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
  Error
   2
make: *** [all] Error 2
   
Any help would be appreciated.
   
Regards,
Ahmed.
   
--
Scanned by iCritical.
   
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