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'.
The hit 'c' again. If there were no issues, hit 'g' which writes the configuration and exits.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
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:
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
If you don't have cmake:
cp INSTALL/make.inc.gfortran make.inc
Edit make.inc
15 FORTRAN = gfortranEdit Makefile
16 OPTS = -O2 -fPIC -m64
17 DRVOPTS = $(OPTS)
18 NOOPT = -O0 -fPIC -m64
19 LOADER = gfortran
20 LOADOPTS =
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 -----
