235. CPMD with Netlib's lapack, blas and your own fftw3 on ROCKS 5.4.3/CentOS 5.6

Update 8 Feb 2013:
I somehow had forgot to include some of the instructions for the BLAS part. Fixed now.

Post:
This is done pretty much like how it's done on Debian (-march=native didn't work in the BLAS compilation though, nor was -fno-whole-file accepted when compiling cpmd)

1. Compile cmake according to this post:
http://verahill.blogspot.com.au/2012/05/compiling-openbabel-231-and-cmake-on.html

2. Compile BLAS
sudo mkdir /share/apps/tools/netlib/blas/lib -p
sudo chown $USER /share/apps/tools/netlib -R

mkdir ~/tmp
cd ~/tmp
wget http://www.netlib.org/blas/blas.tgz
tar xvf blas.tgz
cd BLAS/

Edit make.inc

OPTS     = -O3 -shared -m64 -fPIC

make all

gfortran -shared -Wl,-soname,libnetblas.so -o libblas.so.1.0.1 *.o -lc
ln -s libblas.so.1.0.1 libnetblas.so
cp lib*blas* /share/apps/tools/netlib/blas/lib

3. Compile LAPACK
sudo mkdir /share/apps/tools/netlib/lapack -p
sudo chown $USER /share/apps/tools/netlib -R

wget http://www.netlib.org/lapack/lapack-3.4.1.tgz

tar xvf lapack-3.4.1.tgz
cd lapack-3.4.1/
mkdir build
cd build
ccmake ../

Hit 'c' and edit the values:

 BUILD_COMPLEX                    ON
 BUILD_COMPLEX16                  ON
 BUILD_DOUBLE                     ON
 BUILD_SHARED_LIBS                ON
 BUILD_SINGLE                     ON
 BUILD_STATIC_LIBS                ON
 BUILD_TESTING                    ON
 CMAKE_BUILD_TYPE                    
 CMAKE_INSTALL_PREFIX             /share/apps/tools/netlib/lapack
 LAPACKE                          OFF
 LAPACKE_WITH_TMG                 OFF
 USE_OPTIMIZED_BLAS               ON
 USE_XBLAS                        OFF

Hit 'c' again, then hit 'g'.

Edit CMakeCache.txt and add the following lines at the beginning:

########################
# EXTERNAL cache entries
########################
BLAS_FOUND:STRING=TRUE
BLAS_GENERIC_FOUND:BOOL=TRUE
BLAS_GENERIC_blas_LIBRARY:FILEPATH=/share/apps/tools/netlib/blas/lib/libnetblas.so
BLAS_LIBRARIES:PATH=/share/apps/tools/netlib/blas/lib/libnetblas.so

Do
ccmake ../
again, hit 'c', then 'g'.

Now,
make
make install

4. Compile FFTW3

sudo mkdir /share/apps/tools/fftw3
sudo chown $USER /share/apps/tools/fftw3
cd ~/tmp
wget http://www.fftw.org/fftw-3.3.1.tar.gz
tar -xvf fftw-3.3.1.tar.gz
cd fftw-3.3.1
make distclean
./configure --enable-float --enable-mpi --enable-threads --with-pic --prefix=/share/apps/tools/fftw3/single
make
make install
make distclean
./configure --disable-float --enable-mpi --enable-threads --with-pic --prefix=/share/apps/tools/fftw3/double
make 
make install

5. Compile CPMD
I downloaded the cpmd file to a client computer, then uploaded it to the ROCKS front node:
sftp me@rocks:/home/me/tmp

Connected to rocks.
Changing to: /home/me/tmp
sftp> put cpmd-v3_15_3.tar.gz
Uploading cpmd-v3_15_3.tar.gz to /home/me/tmp/cpmd-v3_15_3.tar.gz
cpmd-v3_15_3.tar.gz                100% 2937KB 587.4KB/s   00:05
sftp> exit

I then logged in via ssh as normal.

cd ~/tmp
tar xvf cpmd-v3_15_3.tar.gz
cd CPMD/CONFIGURE

Create a new file LINUX-x86_64-ROCKS

     IRAT=2
     CFLAGS='-c -O2 -Wall'
     CPP='/lib/cpp -P -C -traditional'
     CPPFLAGS='-D__Linux -D__PGI -D__GNU -DFFT_FFTW3 -DPARALLEL -DPOINTER8'
     FFLAGS='-c -O2 -fcray-pointer -fsecond-underscore'
LFLAGS='-L/share/apps/tools/fftw3/double/lib -lfftw3-lfftw3_mpi -lfftw3_threads -I/usr/include -L/share/apps/tools/netlib/blas/lib -lnetblas -L/share/apps/tools/netlib/lapack/lib -llapack -L/opt/openmpi/lib -lpthread -lmpi'
     FFLAGS_GROMOS='  $(FFLAGS)' 
      FC='mpif77 -fbounds-check'
      CC='mpicc'
      LD='mpif77 -fbounds-check'

NOTE: I don't think the -I belongs in the LFLAGS statement, but I'm presuming that I put it there for a reason back when I did it the first time.

Go to ~/tmp/CPMD, and edit wfnio.F (basically replace 3 with 2 and remove 'L'):

 15       CHARACTER(len=*) TAG
 63         IF(TAG(1:2).EQ.'NI') THEN
201       IF(TAG(1:2).NE.'NI') THEN
271         IF(TAG(1:2).EQ.'NI') THEN

Finally, edit Makefile and change

  23 LD = f95 -O

to

  23 LD = mpif77 -fbounds-check

Time to compile

./mkconfig.sh LINUX-x86_64-ROCKS > Makefile
make
sudo mkdir /share/apps/cpmd
sudo chown $USER /share/apps/cpmd
cp cpmd.x /share/apps/cpmd

echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/tools/netlib/blas/lib:/share/apps/tools/netlib/lapack/lib:/share/apps/tools/fftw3/double/lib' >>~/.bashrc
echo 'export PATH=$PATH:/share/apps/cpmd' >> ~/.bashrc
echo "export PP_LIBRARY_PATH=/share/apps/cpmd/PP_LIBRARY" >>~/.bashrc

You're now done compiling. To test, you need to get some pseudopotential files -- look at e.g. the end of http://verahill.blogspot.com.au/2012/07/not-solved-compiling-cpmd-on-debian.html for instructions.

234. CPMD with netlib lapack, blas and your own fftw on debian testing

This is a minor update to my previous post on CPMD. Back in the days I had issue linking to my Openblas libs (got a binary which would not run properly) but I've since had success with the netlib lapack and blas libs.

1. Compile the netlib lapack and blas libraries according to this post: http://verahill.blogspot.com.au/2012/09/compiling-netlibs-lapack-and-blas-on.html

2. Compile the fftw libraries according to this post (ignore the sections on Openblas and Gromacs):
http://verahill.blogspot.com.au/2012/05/gromacs-with-external-fftw3-and-blas-on.html

3. Compile CPMD. We'll be following this post in large parts.
Register with cpmd.org. Once you're approved download the cpmd source to ~/tmp.

sudo apt-get install libopenmpi-dev openmpi-bin

cd ~/tmp
tar -xvf cpmd-v3_15_3.tar.gz
cd CPMD/CONFIGURE

Create the file LINUX-x86_64-DEBIAN:

   
     IRAT=2
     CFLAGS='-c -O2 -Wall'
     CPP='/lib/cpp -P -C -traditional'
     CPPFLAGS='-D__Linux -D__PGI -D__GNU -DFFT_FFTW3 -DPARALLEL -DPOINTER8'
     FFLAGS='-c -O2 -fcray-pointer -fno-whole-file -fsecond-underscore'
     LFLAGS='-l:/opt/fftw/fftw-3.3.2/double/lib/libfftw3.a -l:/opt/fftw/fftw-3.3.2/double/lib/libfftw3_mpi.a -l:/opt/fftw/fftw-3.3.2/double/lib/libfftw3_threads.a -I/usr/include -l:/opt/netlib/blas/lib/libnetblas.so -l:/opt/netlib/lapack/lib/liblapack.so -lpthread -lmpi'
     FFLAGS_GROMOS='  $(FFLAGS)' 
      FC='mpif77 -fbounds-check'
      CC='mpicc'
      LD='mpif77 -fbounds-check'

Next edit ~/tmp/CPMD/wfnio.F and change the following lines:

 15       CHARACTER(len=*) TAG
 63         IF(TAG(1:2).EQ.'NI') THEN
201       IF(TAG(1:2).NE.'NI') THEN
271         IF(TAG(1:2).EQ.'NI') THEN

Now, in ~/tmp/CPMD, run

./mkconfig.sh LINUX-x86_64-DEBIAN > Makefile
make
sudo mkdir /opt/cpmd
sudo chown $USER /opt/cpmd
cp cpmd.x /opt/cpmd

And follow everything below 'Done! Almost.' in this post: http://verahill.blogspot.com.au/2012/07/not-solved-compiling-cpmd-on-debian.html

233. Compiling netlib's lapack and blas on Debian Testing (Wheezy)

In addition to specific BLAS/LAPACK libs such as ACML, MKL, and ATLAS netlib provides (what I understand to be) reference versions of BLAS and LAPACK. Presumably these are slower than optimised versions of blas/lapack, but it doesn't hurt being familiar with them.

Here's how to compile those versions.

---

BLAS

sudo mkdir /opt/netlib
sudo chown $USER /opt/netlib
mkdir /opt/netlib/blas/lib -p
wget http://www.netlib.org/blas/blas.tgz
tar xvf blas.tgz
cd BLAS/

Edit make.inc
OPTS = -O3 -shared -m64 -march=native -fPIC

make all
gfortran -shared -Wl,-soname,libnetblas.so -o libblas.so.1.0.1 *.o -lc
ln -s libblas.so.1.0.1 libnetblas.so
cp lib*blas* /opt/netlib/blas/lib

To see whether everything linked ok:
 ldd libnetblas.so 

        linux-vdso.so.1 =>  (0x00007ffff1bc6000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b42ec030000)
        libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00002b42ec3b8000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002b42ec6ce000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002b42ec950000)
        libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002b42ecb67000)
        /lib64/ld-linux-x86-64.so.2 (0x00002b42ebaf3000)

---

LAPACK
(inspired by this and this)
mkdir -p /opt/netlib/lapack
sudo apt-get install cmake-curses-gui
cd ~/tmp
wget http://www.netlib.org/lapack/lapack-3.4.1.tgz
tar xvf lapack-3.4.1.tgz
cd lapack-3.4.1/
mkdir build
cd build
ccmake ../

Hit 'c' to generate a configuration. Navigate with arrow keys and hit enter to change values. Change to the values in red:

 
 BUILD_COMPLEX                   *ON
 BUILD_COMPLEX16                 *ON
 BUILD_DOUBLE                    *ON
 BUILD_SHARED_LIBS               *ON
 BUILD_SINGLE                    *ON
 BUILD_STATIC_LIBS               *ON
 BUILD_TESTING                   *ON
 CMAKE_BUILD_TYPE                *     
 CMAKE_INSTALL_PREFIX            */opt/netlib/lapack
 LAPACKE                         *OFF
 LAPACKE_WITH_TMG                *OFF
 USE_OPTIMIZED_BLAS              *ON
 USE_XBLAS                       *OFF

Then hit 'c' which might give you (change the values in red) -- I got some errors about ACML/eula here, but don't worry about that.

NOTE: this will only work if you already have blas installed in a standard location. If you don't get the BLAS_FOUND etc. then you should hit 'c' again and then 'g'. Next edit your CMakeCache.txt and paste the variables (without line numbers) you find below this section, then do ccmake ../ again and make sure everything looks ok, and generate using 'g'.

 BLAS_FOUND                       TRUE
 BLAS_GENERIC_FOUND               ON
 BLAS_GENERIC_blas_LIBRARY        /opt/netlib/blas/lib/libnetblas.so
 BLAS_LIBRARIES                   /opt/netlib/blas/lib/libnetblas.so
 BLAS_LINKER_FLAGS
 BUILD_COMPLEX                   *ON
 BUILD_COMPLEX16                 *ON
 BUILD_DOUBLE                    *ON
 BUILD_SHARED_LIBS               *OFF
 BUILD_SINGLE                    *ON
 BUILD_STATIC_LIBS               *ON
 BUILD_TESTING                   *ON
 CMAKE_BUILD_TYPE                *     
 CMAKE_INSTALL_PREFIX            */usr/local 
 LAPACKE                         *OFF
 LAPACKE_WITH_TMG                *OFF
 USE_OPTIMIZED_BLAS              *ON
 USE_XBLAS                       *OFF

The hit 'c' again. If there were no issues, hit 'g' which writes the configuration and exits.


make

[100%] Building Fortran object TESTING/EIG/CMakeFiles/xeigtstz.dir/__/__/INSTALL/dsecnd_INT_ETIME.f.o
Linking Fortran executable ../../bin/xeigtstz
[100%] Built target xeigtstz

make install

Install the project...
-- Install configuration: ""
-- Installing: /opt/netlib/lapack/lib/pkgconfig/lapack.pc
-- Installing: /opt/netlib/lapack/lib/cmake/lapack-3.4.1/lapack-config.cmake
-- Installing: /opt/netlib/lapack/lib/cmake/lapack-3.4.1/lapack-config-version.cmake
-- Installing: /opt/netlib/lapack/lib/cmake/lapack-3.4.1/lapack-targets.cmake
-- Installing: /opt/netlib/lapack/lib/cmake/lapack-3.4.1/lapack-targets-noconfig.cmake
-- Installing: /opt/netlib/lapack/lib/liblapack.so
-- Removed runtime path from "/opt/netlib/lapack/lib/liblapack.so"
-- Installing: /opt/netlib/lapack/lib/libtmglib.so
-- Removed runtime path from "/opt/netlib/lapack/lib/libtmglib.so"

tree /opt/netlib/ -d
/opt/netlib/
|-- blas
|   `-- lib
`-- lapack
    `-- lib
        |-- cmake
        |   `-- lapack-3.4.1
        `-- pkgconfig

7 directories

---

CMakeCache.txt variables:

 16 
 17 BLAS_FOUND:STRING=TRUE
 18 
 19 //Whether not the GENERIC library was found and is usable
 20 BLAS_GENERIC_FOUND:BOOL=TRUE
 21 
 22 //Path to a library.
 23 BLAS_GENERIC_blas_LIBRARY:FILEPATH=/opt/netlib/blas/lib/libnetblas.so
 24 
 25 BLAS_LIBRARIES:PATH=/opt/netlib/blas/lib/libnetblas.so
 26 

---

Testing the libraries:
I built gromacs against the new libs to make sure they 'worked'

sudo mkdir /opt/gromacs
sudo chown ${USER} /opt/gromacs
cd ~/tmp
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz
tar xvf gromacs-4.5.5.tar.gz
cd gromacs-4.5.5/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/netlib/blas/lib:/opt/netlib/lapack/lib
export LDFLAGS="-l:/opt/netlib/blas/lib/libnetblas.so -l:/opt/netlib/lapack/lib/liblapack.so"
./configure --disable-mpi --enable-float --with-external-blas --with-external-lapack --program-suffix=_netlib --prefix=/opt/gromacs/gromacs-4.5.5
make

make install

Check that it linked ok:

ldd /opt/gromacs/gromacs-4.5.5/bin/grompp_netlib
        linux-vdso.so.1 =>  (0x00007fffb83f2000)
        libgmxpreprocess.so.6 => /opt/gromacs/gromacs-4.5.5/lib/libgmxpreprocess.so.6 (0x00002b6411cfa000)
        libmd.so.6 => /opt/gromacs/gromacs-4.5.5/lib/libmd.so.6 (0x00002b6411fcd000)
        libfftw3f.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3f.so.3 (0x00002b64123ad000)
        libxml2.so.2 => /usr/lib/x86_64-linux-gnu/libxml2.so.2 (0x00002b64127b0000)
        libgmx.so.6 => /opt/gromacs/gromacs-4.5.5/lib/libgmx.so.6 (0x00002b6412b10000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002b6412fe5000)
        libnetblas.so => /opt/netlib/blas/lib/libnetblas.so (0x00002b64131e9000)
        liblapack.so => /opt/netlib/lapack/lib/liblapack.so (0x00002b64134cc000)
        libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00002b6413ece000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002b64140e6000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00002b6414369000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b6414585000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00002b641490c000)
        liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00002b6414b24000)
        /lib64/ld-linux-x86-64.so.2 (0x00002b6411ad8000)
        libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00002b6414d47000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002b641505d000)
        libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002b6415274000)

Here are some input files (it's not a 'real' md run -- I just needed something small and quick to run):
step1.top:

#include "/opt/gromacs/gromacs-4.5.5/share/gromacs/top/ffoplsaa.itp"
#include "/opt/gromacs/gromacs-4.5.5/share/gromacs/top/oplsaa.ff/tip4p.itp"

[system]
test 

[molecules]

step1.mdp:

integrator = md
define      = -DFLEXIBLE
emtol      = 1000.0
emstep     = 0.001
nsteps     = 5000
nstlist    = 1
ns_type    = grid 
rlist      = 0.9
coulombtype= PME  
rcoulomb   = 0.9  
rvdw       = 1.0  
pbc        =  xyz

genbox_netlib -o step1.gro -cs /opt/gromacs/gromacs-4.5.5/share/gromacs/top/tip4p.gro -box 4x4x4 -p step1.top

grompp_netlib -f step1.mdp -po step2.mdp -p step1.top -pp step2.top -c step1.gro -o step2.tpr

mdrun_netlib -v -s step2.tpr -o step3.trr -x step3.xtc -cpo step3.cpt -c step3.gro -e step3.edr -g step3.log

On my old AMD II X3 I got about 7.7 GFLOPS with Openblas and 7.8 GFLOPS with the above libs. Note that the run is shorter than a minute so it's pretty useless for benchmarking. However, there's no obvious MAJOR penalty.

---

---

If you don't have cmake:
cp INSTALL/make.inc.gfortran make.inc

Edit make.inc

 15 FORTRAN  = gfortran
 16 OPTS     = -O2 -fPIC -m64
 17 DRVOPTS  = $(OPTS)
 18 NOOPT    = -O0 -fPIC -m64
 19 LOADER   = gfortran
 20 LOADOPTS =

Edit Makefile

 11 #lib: lapacklib tmglib
 12 lib: blaslib variants lapacklib tmglib

Run make

make

-->  Tests passed: 13176


   -->   LAPACK TESTING SUMMARY  <--
  Processing LAPACK Testing output found in the TESTING direcory
SUMMARY              nb test run  numerical error    other error  
================    =========== ================= ================  
REAL              1077227  0 (0.000%) 0 (0.000%) 
DOUBLE PRECISION 1078039  0 (0.000%) 0 (0.000%) 
COMPLEX           522814  0 (0.000%) 0 (0.000%) 
COMPLEX16          552410  0 (0.000%) 0 (0.000%) 

--> ALL PRECISIONS 3230490  0 (0.000%) 0 (0.000%) 

---

---

Older version:
In the oldest version of this post I did the blas compilation by hand:

gfortran -O2 -fPIC -m64 -march=native -funroll-all-loops -c *.f

To build a static library:
ar rvs libblas.a *.o

To build a shared/dynamic library:
gfortran -shared -Wl,-soname,libnetblas.so -o libblas.so.1.0.1 *.o -lc 

ldd libblas.so.1.0.1

        linux-vdso.so.1 =>  (0x00007fff301af000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002aeeac390000)
        libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00002aeeac718000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002aeeaca2e000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002aeeaccb0000)
        libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002aeeacec7000)
        /lib64/ld-linux-x86-64.so.2 (0x00002aeeabedd000)

Either way:
cp libblas* /opt/netlib/blas/lib

To test:
wget http://www.netlib.org/blas/sblat1
mv sblat1 sblat1.f

And EITHER
gfortran sblat1.f -l:libblas.a

OR
ln -s libblas.so.1.0.1 libnetblas.so
gfortran sblat1.f -l:libnetblas.so

THEN
./a.out

 
Real BLAS Test Program Results
Test of subprogram number  1             SDOT 
                                    ----- PASS -----

 Test of subprogram number  2            SAXPY 
                                    ----- PASS -----

 Test of subprogram number  3            SROTG 
                                    ----- PASS -----

 Test of subprogram number  4             SROT 
                                    ----- PASS -----

 Test of subprogram number  5            SCOPY 
                                    ----- PASS -----

 Test of subprogram number  6            SSWAP 
                                    ----- PASS -----

 Test of subprogram number  7            SNRM2 
                                    ----- PASS -----

 Test of subprogram number  8            SASUM 
                                    ----- PASS -----

 Test of subprogram number  9            SSCAL 
                                    ----- PASS -----

 Test of subprogram number 10            ISAMAX
                                    ----- PASS -----