Lindqvist -- a blog about Linux and Science. Mostly.: 409.A.GAMESS US with GPU support on debian wheezy. This works (probably).

Update 27/6/2013:
Please note that Kirill Berezovsky has published a series of posts on GAMESS US, including how to compile it for both CPU and GPU use. See
http://biochemicalmatters.blogspot.com.au/2013/06/gamess-us-frequently-asked-questions_26.html
http://biochemicalmatters.blogspot.ru/2013/06/gamess-us-frequently-asked-questions_1687.html
http://biochemicalmatters.blogspot.ru/2013/06/gamess-us-frequently-asked-questions_1447.html
http://biochemicalmatters.blogspot.com.au/2013/06/gamess-us-frequently-asked-questions.html

Update 21 May 2013: See the comments below this post. This approach most likely works -- what has been confusing me is the lack of reports of GPU timings in the output, but this doesn't necessarily mean that the GPU isn't being used. The poster below this post, using nvidia-smi, observed GPU usage, although the speed-up was not major.

Update 10/05/2013: fixed libcchem compile.

Everything compiles fine and computations run fine and fast. To date there's only one other detailed step-by-step example of successful compilation of GAMESS with GPU support out there. At least based on google.

For various reasons I'm beginning to suspect that ATLAS isn't working out for me -- I've had issues getting things to converge with ATLAS, but which work fine with ACML (see post B).

I was in part following http://combichem.blogspot.com.au/2011/02/compiling-gamess-with-cuda-gpu-support.html and ./libcchem/aaa.readme.1st

This took a while to hammer out, so the write-up is a bit messy.

Set up

sudo apt-get install libboost-all-dev build-essential g++ gfortran automake nvidia-cuda-toolkit python-cheetah openmpi-bin libopenmpi-dev zlib1g-dev checkinstall
mkdir ~/tmp

Get gamess (see e.g. http://verahill.blogspot.com.au/2012/09/compiling-and-testing-gamess-us-on.html).

Put gamess-current.tar.gz in ~/tmp

cd ~/tmp
tar xvf gamess-current.tar.gz
sudo mv gamess /opt/gamess_cuda
sudo chown $USER:$USER /opt/gamess_cuda -R


Preparing Boost

Edit /usr/include/boost/mpl/aux_/integral_wrapper.hpp

47 // other compilers (e.g. MSVC) are not particulary happy about it
 48 #if BOOST_WORKAROUND(__EDG_VERSION__, <= 238) || defined(__CUDACC__)
 49     typedef struct AUX_WRAPPER_NAME type;

Edit /usr/include/boost/mpl/size_t_fwd.hpp


20 
 21 BOOST_MPL_AUX_ADL_BARRIER_NAMESPACE_OPEN
 22 #if defined(__CUDACC__)
 23    typedef std::size_t std_size_t;
 24    template< std_size_t N > struct size_t;
 25 #else
 26    template< std::size_t N > struct size_t;
 27 #endif
 28 
 29 BOOST_MPL_AUX_ADL_BARRIER_NAMESPACE_CLOSE

Edit /usr/include/boost/mpl/size_t.hpp


 19 #if defined(__CUDACC__)
 20   #define AUX_WRAPPER_VALUE_TYPE std_size_t
 21   #define AUX_WRAPPER_NAME size_t    
 22   #define AUX_WRAPPER_PARAMS(N) std_size_t N
 23 #else 
 24   #define AUX_WRAPPER_VALUE_TYPE std::size_t
 25   #define AUX_WRAPPER_NAME size_t
 26   #define AUX_WRAPPER_PARAMS(N) std::size_t N
 27 #endif
 28

HDF5
You'll have to compile that yourself for now since H5Cpp.h missing in the debian packages.(i.e. cxx support)

mkdir ~/tmp
cd ~/tmp
wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.10-patch1.tar.gz
tar xvf hdf5-1.8.10-patch1.tar.gz
cd hdf5-1.8.10-patch1/
export CC=/usr/bin/gcc-4.6 && export CXX=/usr/bin/g++-4.6
./configure --prefix=/opt/gamess_cuda/hdf5 --with-pthread --enable-cxx --enable-threadsafe --enable-unsupported
make
mkdir /opt/gamess_cuda/hdf5/lib -p
mkdir /opt/gamess_cuda/hdf5/include -p
sudo checkinstall

This package will be built according to these values: 

0 -  Maintainer: [ root@neon ]
1 -  Summary: [ hdf5-cxx]
2 -  Name:    [ hdf5-1.8.10 ]
3 -  Version: [ 1.8.10-1 ]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ amd64 ]
8 -  Source location: [ hdf5-1.8.10-patch1 ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ hdf5-1.8.10 ]
12 - Conflicts: [  ]
13 - Replaces: [  ]


Make sure to edit the Version field since Patch-1 leads to an error (must start with digit).


Openmpi 1.6

Can't remember why I ended up compiling it myself instead of using the stock debian version. From here.

sudo apt-get install build-essential gfortran
wget http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.tar.bz2
tar xvf openmpi-1.6.tar.bz2
cd openmpi-1.6/

sudo mkdir /opt/openmpi/
sudo chown ${USER} /opt/openmpi/
./configure --prefix=/opt/openmpi/1.6/ --with-sge

make
make install



compiling libcchem

cd /opt/gamess_cuda/libcchem

edit /opt/gamess_cuda/libcchem/rysq/src/externals/boost/cuda/device_ptr.hpp

  4 #include <cstdlib>
  5 #include <iterator>
  6 #include <stddef.h>
  7 
  8 namespace boost {

Edit /opt/gamess_cuda/libcchem/src/externals/boost/cuda/device_ptr.hpp

  4 #include <cstdlib>
  5 #include <iterator>
  6 #include <stddef.h>
  7 
  8 namespace boost {
  9 namespace cuda {

./configure --with-gamess --with-hdf5=/opt/gamess_cuda/hdf5 CPPFLAGS="-I/opt/gamess_cuda/hdf5/include" --with-cuda=/usr --disable-openmp --prefix=/opt/gamess_cuda/libcchem --with-gpu=fermi --with-integer8 --with-cublas
make
make install

Configure Gamess US

Mainly follow this: http://verahill.blogspot.com.au/2012/09/compiling-and-testing-gamess-us-on.html

cd /opt/gamess_cuda
./config


please enter your target machine name: linux64

GAMESS directory? [/opt/gamess_cuda] /opt/gamess_cuda

Setting up GAMESS compile and link for GMS_TARGET=linux64
GAMESS software is located at GMS_PATH=/opt/gamess_cuda
 
Please provide the name of the build locaation.
This may be the same location as the GAMESS directory.
 
GAMESS build directory? [/home/me/tmp/gamess] 

Please provide a version number for the GAMESS executable.
This will be used as the middle part of the binary's name,
for example: gamess.00.x

Version? [00] 12r2

Please enter your choice of FORTRAN: gfortran

gfortran is very robust, so this is a wise choice.

Please type 'gfortran -dumpversion' or else 'gfortran -v' to
detect the version number of your gfortran.
This reply should be a string with at least two decimal points,
such as 4.1.2 or 4.6.1, or maybe even 4.4.2-12.
The reply may be labeled as a 'gcc' version,
but it is really your gfortran version.
Please enter only the first decimal place, such as 4.1 or 4.6:  
4.6


Enter your choice of 'mkl' or 'atlas' or 'acml' or 'none': atlas

Please enter the Atlas subdirectory on your system: /opt/ATLAS/lib

Math library 'atlas' will be taken from /opt/ATLAS
 

If you have an expensive but fast network like Infiniband (IB), and
if you have an MPI library correctly installed,
     choose 'mpi'.
 
communication library ('sockets' or 'mpi')? mpi

Enter MPI library (impi, mvapich2, mpt, sockets): openmpi



Please enter your openmpi's location: /opt/openmpi/1.6

Build Gamess US

cd /opt/gamess_cuda/ddi/
./compddi
cd ../

Edit comp


872 #          see ~/gamess/libcchem/aaa.readme.1st for more information
 873 set GPUCODE=true
 874 if ($GPUCODE == true) then

and


1663 #           -fno-whole-file suppresses argument's data type checking
1664       set OPT='-O0'
1665       if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"

./compall

Edit lked


69 #
  70 set GPUCODE=true
  71 #
  72 #   5. optional MPQC interface

and


958             case openmpi:
 959                set MPILIBS="-L$GMS_MPI_PATH/lib"
 960                set MPILIBS="$MPILIBS -lmpi -lpthread"
 961                breaksw

and


1214 if ($GPUCODE == true) then
1215    echo "   Using 'libcchem' add-in C++ codes for Nvidia/CUDA GPUs."
1216    set GPU_LIBS="-L/opt/gamess_cuda/libcchem/lib -lcchem_gamess -lcchem -lrysq"
1217    set GPU_LIBS="$GPU_LIBS -lcudart -lcublas"
1218    ### GPU_LIBS="$GPU_LIBS -lcudart -lcublas"
1219    set GPU_LIBS="$GPU_LIBS /usr/lib/libboost_thread.a"
1220    set GPU_LIBS="$GPU_LIBS /opt/gamess_cuda/hdf5/lib/libhdf5.a"
1221    set GPU_LIBS="$GPU_LIBS /opt/gamess_cuda/hdf5/lib/libhdf5_cpp.a"
1222    set GPU_LIBS="$GPU_LIBS /opt/gamess_cuda/hdf5/lib/libhdf5_hl.a"
1223    set GPU_LIBS="$GPU_LIBS /opt/gamess_cuda/hdf5/lib/libhdf5.a"
1224    set GPU_LIBS="$GPU_LIBS /opt/ATLAS/lib/libcblas.a"
1225    set GPU_LIBS="$GPU_LIBS -lz"
1226    set GPU_LIBS="$GPU_LIBS -lstdc++"
1227    ### GPU_LIBS="$GPU_LIBS -lgomp"
1228    set GPU_LIBS="$GPU_LIBS -lpthread"
1229    echo "   libcchem GPU code's libraries are"
1230    echo "$GPU_LIBS"
1231 else

./lked gamess gpu.12

Create gpurun


#!/bin/csh
set TARGET=mpi
set SCR=$HOME/scratch
set USERSCR=/scratch
set GMSPATH=/opt/gamess_cuda
set JOB=$1
set VERNO=$2
set NCPUS=$3

   @ NUMGPU=1
   if ($NUMGPU > 0) then
      @ NUMCPU = $NCPUS - 1
      echo libcchem kernels will use $NUMCPU cores and $NUMGPU GPUs per node...
      set echo
      setenv CCHEM_PROFILE 1
      setenv NUM_THREADS $NCPUS
      #--if ($NUMGPU == 0) setenv GPU_DEVICES -1
      #--if ($NUMGPU == 2) setenv GPU_DEVICES 0,1
      #--if ($NUMGPU == 4) setenv GPU_DEVICES 0,1,2,3
      #setenv LD_LIBRARY_PATH /share/apps/cuda/lib64:$LD_LIBRARY_PATH
      ###### LD_LIBRARY_PATH /usr/local/cuda/lib64:$LD_LIBRARY_PATH
      unset echo
   else
      setenv GPU_DEVICES -1
   endif


if ( $JOB:r.inp == $JOB ) set JOB=$JOB:r
echo "Copying input file $JOB.inp to your run's scratch directory..."
cp $JOB.inp $SCR/$JOB.F05

setenv TRAJECT $USERSCR/$JOB.trj
setenv RESTART $USERSCR/$JOB.rst
setenv INPUT $SCR/$JOB.F05
setenv PUNCH $USERSCR/$JOB.dat
if ( -e $TRAJECT ) rm $TRAJECT
if ( -e  $PUNCH ) rm $PUNCH
if ( -e  $RESTART ) rm $RESTART
source $GMSPATH/gms-files.csh

setenv LD_LIBRARY_PATH /opt/openmpi/lib:$LD_LIBRARY_PATH
set path= ( /opt/openmpi/bin $path )
mpiexec -n $NCPUS $GMSPATH/gamess.gpu.$VERNO.x|tee $JOB.out
cp $PUNCH .

echo 'export PATH=$PATH:/opt/gamess_cuda' >> ~/.bashrc
source ~/.bashrc
chmod +x gpurun
cd test/standard/
 gpurun exam44 12 2

The only evidence of GPU usage in the output is e.g. in exam44.out:

388           -----------------------
389           MP2 CONTROL INFORMATION
390           -----------------------
391           NACORE =        6  NBCORE =        6
392           LMOMP2 =        F  AOINTS = DUP
393           METHOD =        2  NWORD  =               0
394           MP2PRP =        F  OSPT   = NONE
395           CUTOFF = 1.00E-09  CPHFBS = BASISAO
396           CODE   = GPU
397 
398           NUMBER OF CORE -A-  ORBITALS =     6
399           NUMBER OF CORE -B-  ORBITALS =     6

but in the summary only CPU utilisation is mentioned.

I modified rungms:

me@neon:/opt/gamess_cuda/tests/standard$ diff /opt/gamess_cuda/gpurungms /opt/gamess/rungms 
59,62c59,62
< set TARGET=mpi
< set SCR=$HOME/scratch
< set USERSCR=/scratch
< set GMSPATH=/opt/gamess_cuda
---
> set TARGET=sockets
> set SCR=/scr/$USER
> set USERSCR=~$USER/scr
> set GMSPATH=/u1/mike/gamess
67d66
< set NNODES=1
513c512
< set PPN=$3
---
>    set PPN=$4
601c600
<          @ PPN2 = $PPN
---
>          @ PPN2 = $PPN + $PPN
742c741
<    @ NUMGPU=1
---
>    @ NUMGPU=0
752c751
< #      setenv LD_LIBRARY_PATH /share/apps/cuda/lib64:$LD_LIBRARY_PATH
---
>       setenv LD_LIBRARY_PATH /share/apps/cuda/lib64:$LD_LIBRARY_PATH
793c792,793
<       /opt/openmpi/1.6/bin/mpiexec -n $NPROCS $GMSPATH/gamess.$VERNO.x < /dev/null
---
>       mpiexec.hydra -f $PROCFILE -n $NPROCS \
>             /home/mike/gamess/gamess.$VERNO.x < /dev/null

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09 May 2013

409.A.GAMESS US with GPU support on debian wheezy. This works (probably).

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