CODEWITHSUNDEEP
octaveconfigureatlas
David Parks
David Parks

Reputation: 32091

Building octave from source - did ATLAS get included properly in Octaves ./configure script?

I'm building Octave from sources in order to include the ATLAS libraries. Did I get them included correctly? I don't know what to expect from the Octave configure script. I find "-llapack" suspiciously generic.

./configure --with-lapack=/usr/local/atlas

  Source directory:            .
  Installation prefix:         /usr/local
  C compiler:                  gcc   -Wall -W -Wshadow -Wformat -Wpointer-arith -Wmissing-prototypes -Wstrict-prototypes -Wwrite-strings -Wcast-align -Wcast-qual -g -O2 -pthread
  C++ compiler:                g++   -Wall -W -Wshadow -Wold-style-cast -Wformat -Wpointer-arith -Wwrite-strings -Wcast-align -Wcast-qual -g -O2 -pthread
  Fortran compiler:            gfortran -O
  Fortran libraries:            -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
  Lex libraries:               
  LIBS:                        -lutil -lm  
  ...
  HDF5 libraries:              -lhdf5
  Java home:                   /usr/lib/jvm/java-7-openjdk-amd64
  Java JVM path:               /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server
  Java CPPFLAGS:               -I/usr/lib/jvm/java-7-openjdk-amd64/include -I/usr/lib/jvm/java-7-openjdk-amd64/include/linux
  Java libraries:              
  LAPACK libraries:            -llapack
  LLVM CPPFLAGS:               
  LLVM LDFLAGS:                
  LLVM libraries:              
  Magick++ CPPFLAGS:           -I/usr/include/GraphicsMagick  
  Magick++ LDFLAGS:             
  Magick++ libraries:          -lGraphicsMagick++ -lGraphicsMagick  
  ...

allusers@vbubuntu:~/Downloads/octave-3.8.1$ ll -R /usr/local/atlas/

/usr/local/atlas/:
total 16
drwxr-xr-x  4 root root 4096 May 25 23:01 ./
drwxr-xr-x 13 root root 4096 May 25 23:01 ../
drwxr-xr-x  3 root root 4096 May 25 23:01 include/
drwxr-xr-x  2 root root 4096 May 25 23:01 lib/

/usr/local/atlas/include:
total 60
drwxr-xr-x 3 root root  4096 May 25 23:01 ./
drwxr-xr-x 4 root root  4096 May 25 23:01 ../
drwxr-xr-x 2 root root  4096 May 25 23:01 atlas/
-rw-r--r-- 1 root root 33962 May 25 23:06 cblas.h
-rw-r--r-- 1 root root  9708 May 25 23:06 clapack.h

/usr/local/atlas/include/atlas:
total 604
drwxr-xr-x 2 root root  4096 May 25 23:01 ./
drwxr-xr-x 3 root root  4096 May 25 23:01 ../
-rw-r--r-- 1 root root  2089 May 25 23:06 atlas_buildinfo.h
-rw-r--r-- 1 root root    90 May 25 23:06 atlas_cacheedge.h
...
-rw-r--r-- 1 root root  2716 May 25 23:06 zmm.h
-rw-r--r-- 1 root root   552 May 25 23:06 zXover.h

/usr/local/atlas/lib:
total 26548
drwxr-xr-x 2 root root     4096 May 25 23:01 ./
drwxr-xr-x 4 root root     4096 May 25 23:01 ../
-rw-r--r-- 1 root root 14165306 May 25 23:06 libatlas.a
-rw-r--r-- 1 root root   455844 May 25 23:06 libcblas.a
-rw-r--r-- 1 root root   572392 May 25 23:06 libf77blas.a
-rw-r--r-- 1 root root 10942494 May 25 23:06 liblapack.a
-rw-r--r-- 1 root root   456426 May 25 23:06 libptcblas.a
-rw-r--r-- 1 root root   572788 May 25 23:06 libptf77blas.a
allusers@vbubuntu:~/Downloads/octave-3.8.1$

Additional info:

After spamming echo statements in the config file I've noticed the following:

This line:

$as_echo "$as_me:${as_lineno-$LINENO}: checking for $cheev in $LAPACK_LIBS" >&5

has the correct $LAPACK_LIBS variable in it (the one I passed in). It's this line that appears to be the first failure to find something in the lapack libraries I'm telling it about:

if ac_fn_c_try_link "$LINENO"; then :

Just before that line I see the config file define some c code that I believe it's running to identify whether whatever 'cheeve' is, is found in the libraries.

checking for cheev_ in /usr/local/atlas/lib/... no
checking for cheev_... no
checking for cheev_ in -llapack... yes

configuration script

cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h.  */

/* Override any GCC internal prototype to avoid an error.
   Use char because int might match the return type of a GCC
   builtin and then its argument prototype would still apply.  */
#ifdef __cplusplus
extern "C"
#endif
char $cheev ();
#ifdef F77_DUMMY_MAIN

#  ifdef __cplusplus
     extern "C"
#  endif
   int F77_DUMMY_MAIN() { return 1; }

#endif
int
main ()
{
return $cheev ();
  ;
  return 0;
}
_ACEOF

At this point the C code has gone beyond my comprehension level. It seems like it has something to do with whether the F77 compiler (compiler translator??) is being invoked or not.

Upvotes: 1

Views: 2548

Answers (2)

Wim West
Wim West

Reputation: 1

My successful attempt to compile octave (3.8.2) on CENTOS including atlas: (make sure to remove blas-devel and lapack-devel, just in case)

> yum install atlas-sse3.x86_64
> setenv LDFLAGS -L/usr/lib64/atlas-sse3
>./configure --with-lapack=-latlas --with-blas=-latlas --enable-jit
> make -j20
(as root)> make install

After configure you should see:
    BLAS libraries:              -lcblas -lf77blas -latlas
    LAPACK libraries:            -llapack

Upvotes: 0

David Parks
David Parks

Reputation: 32091

Well, I think I worked this out after a marathon debugging session.

Octave doesn't appear to recognize the atlas libraries unless they're in shared format (.so files not the .a files that are generated by default).

When I build ATLAS with the --shared option added, and I reference the .so files generated by ATLAS, the Octave config script accepts them. Note: Make sure you use libtatlas.so, not libsatlas.so, assuming you want the multithreaded libraries.

Reference material:

ATLAS ./configure arguments:

../configure --shared -b 64 -D c -DPentiumCPS=3000 --with-netlib-lapack-tarfile=/home/allusers/Downloads/lapack-3.5.0.tgz

Octave ./configure arguments:

./configure --with-lapack=/usr/local/atlas/lib/libtatlas.so --with-blas=/usr/local/atlas/lib/libtatlas.so

Expected Octave ./configure output:

...
BLAS libraries:              /usr/local/atlas/lib/libtatlas.so
...
LAPACK libraries:            /usr/local/atlas/lib/libtatlas.so
...

Incorrect Octave ./configure output:

...
BLAS libraries:              -lblas
...
LAPACK libraries:            -llapack
...

My full build process for ATLAS and Octave:

ATLAS setup:
    bunzip2 -c atlas3.10.x.tar.bz2 | tar xfm -
    mv ATLAS atlas3.10.1
    cd atlas3.10.1
    mkdir build_vbubuntu
    cd build_vbubuntu
    sudo apt-get install gfortran f2c libcnf-dev            # ???
    ../configure --shared -b 64 -D c -DPentiumCPS=3000 --with-netlib-lapack-tarfile=/home/allusers/Downloads/lapack-3.5.0.tgz
    make build
    make check      # test serial routines
    make ptcheck    # check parallel routines
    make time
    sudo make install

Octave setup:
    sudo apt-get build-dep octave
    ./configure --with-lapack=/usr/local/atlas/lib/libtatlas.so --with-blas=/usr/local/atlas/lib/libtatlas.so
    sudo make install

Full disclosure: While I've written up this answer because I got octave to admit that the atlas libraries exist (and I don't want to forget to write it later), the end result is still not working, a large scale matrix multiplication doesn't use multiple cores. Hence, if the cause of that issue is related I may be back to edit this answer in the future.

Upvotes: 3

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