how to compile lapack so that it can be used correctly during installation of octave? - gcc

Question

I'm trying to install the latest octave 3.8.1 from source in a cluster running redhat+IBM LSF. I don't have write access to anywhere else except my own home dir, that's why I have to install octave from source. The blas and lapack provided by the cluster does not work so I have to build them by myself. I have now finished compiling both blas and lapack and passed the ./configure, but when I run make, an error is reported as follows:
These are steps I used to build my own BLAS and LAPACK. The source of BLAS is in ~/src/BLAS while the source of LAPACK is in ~/src/lapack-3.5.0 and the source of octave 3.8.1 is in ~/src/octave-3.8.1.
With only two module, 1) pcre/8.33 2) acml/5.3.1/gfortran64, loaded, I compiled BLAS shared library using
gfortran -shared -O2 *.f -o libblas.so -fPIC
and static library using
gfortran -O2 -c *.f -fPIC
ar cr libblas.a *.o
Then I copy the shared library libblas.so to ~/src/octave-3.8.1. The contents of make.inc file in lapack's dir is:
####################################################################
# LAPACK make include file. #
# LAPACK, Version 3.5.0 #
# November 2013 #
####################################################################
#
SHELL = /bin/sh
#
# Modify the FORTRAN and OPTS definitions to refer to the
# compiler and desired compiler options for your machine. NOOPT
# refers to the compiler options desired when NO OPTIMIZATION is
# selected. Define LOADER and LOADOPTS to refer to the loader and
# desired load options for your machine.
#
FORTRAN = gfortran
OPTS = -shared -O2 -fPIC
DRVOPTS = $(OPTS)
NOOPT = -O0 -frecursive
LOADER = gfortran
LOADOPTS =
#
# Timer for the SECOND and DSECND routines
#
# Default : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME
#TIMER = EXT_ETIME
# For RS6K : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME_
# TIMER = EXT_ETIME_
# For gfortran compiler: SECOND and DSECND will use a call to the INTERNAL FUNCTION ETIME
TIMER = INT_ETIME
# If your Fortran compiler does not provide etime (like Nag Fortran Compiler, etc...)
# SECOND and DSECND will use a call to the INTERNAL FUNCTION CPU_TIME
# TIMER = INT_CPU_TIME
# If neither of this works...you can use the NONE value... In that case, SECOND and DSECND will always return 0
# TIMER = NONE
#
# Configuration LAPACKE: Native C interface to LAPACK
# To generate LAPACKE library: type 'make lapackelib'
# Configuration file: turned off (default)
# Complex types: C99 (default)
# Name pattern: mixed case (default)
# (64-bit) Data model: LP64 (default)
#
# CC is the C compiler, normally invoked with options CFLAGS.
#
CC = gcc
CFLAGS = -O3
#
# The archiver and the flag(s) to use when building archive (library)
# If you system has no ranlib, set RANLIB = echo.
#
ARCH = ar
ARCHFLAGS= cr
RANLIB = ranlib
#
# Location of the extended-precision BLAS (XBLAS) Fortran library
# used for building and testing extended-precision routines. The
# relevant routines will be compiled and XBLAS will be linked only if
# USEXBLAS is defined.
#
# USEXBLAS = Yes
XBLASLIB =
# XBLASLIB = -lxblas
#
# The location of the libraries to which you will link. (The
# machine-specific, optimized BLAS library should be used whenever
# possible.)
#
#BLASLIB = ../../librefblas.a
BLASLIB = ~/src/BLAS/libblas.a
LAPACKLIB = liblapack.a
TMGLIB = libtmglib.a
LAPACKELIB = liblapacke.a
Then I type make to compile LAPACK. After compilation, I copied the output liblapack.a to ~/src/octave-3.8.1.
The ./configure command line is:
./configure --prefix=$HOME/bin/octave --with-blas=./libblas.so --with-lapack=$HOME/src/octave-3.8.1/liblapack.a --disable-readline --enable-64
I can pass the ./configure. Then I type make to try to build octave 3.8.1 and I got the above error.
From the make.inc file it can be seen that I have followed the suggestion of the compiler "recompile with -fPIC" and modified the make.inc accordingly. I also add -shared switch in the OPTS variable. In addition, I have tried using old LAPACK version but not working. I really have no idea why the error still comes out. So I wonder if you could please tell me how to compile the LAPACK library so that it can be correctly used during installation of octave 3.8.1. The following two points may be worth considering. (1) should I compile lapack as a static library or a shared library? (2) should -fPIC switch be applied to lapack compilation or octave's make? If the latter, how to apply -fPIC to make? You don't have to get restricted to the above two points since there may be other reasons for the error. Any advice to solve this problem is welcomed. If you need any other information please tell me. Thank you.

Answer 1

Just compiled the lapack shared lib on my boss's beast... Here's a link which almost did it right.
I made some changes:
(1) Adding -fPIC to
OPTS & NOOPT in make.inc
(2) Change the names in make.inc to .so
BLASLIB = ../../libblas.so
LAPACKLIB = ../liblapack.so
(3) In ./SRC, change the Makefile from
../$(LAPACKLIB): $(ALLOBJ)
$(ARCH) $(ARCHFLAGS) $# $(ALLOBJ)
$(RANLIB) $#
to
../$(LAPACKLIB): $(ALLOBJ)
$(LOADER) $(LOADOPTS) -shared -Wl,-soname,liblapack.so -o $# $(ALLOBJ) ../libblas.so
Cuz lapack is calling blas, if you miss the very last part, your liblapack.so will fail! You need to LINK liblapack.so against libblas.so ( libatlas.so is also OK). You can use "ldd liblapack.so" to check its dependency. If you see libblas.so in there, pretty much you did it right.
(4) In ./BLAS/SRC, change the Makefile from
$(BLASLIB): $(ALLOBJ)
$(ARCH) $(ARCHFLAGS) $# $(ALLOBJ)
$(RANLIB) $#
to
$(BLASLIB): $(ALLOBJ)
$(LOADER) $(LOADOPTS) -z muldefs -shared -Wl,-soname,libblas.so -o $# $(ALLOBJ)
(5) I don't need libtmg.so so that I didn't change it...
Run
make blaslib
Then
make lapacklib
You will have both of them compiled. I check the liblapack.so with building a numpy on it and Python ctypes.cdll loading. All work for me to solve eigenvalues and eigenvectors... So it should be fine...
(6) YOU MAY NEED TO SET UP LD_LIBRARY_PATH to where you keep your library files.
google it... If not set by admin, then
export LD_LIBRARY_PATH=path-to-lib
If already set, then
export LD_LIBRARY_PATH=path-to-lib:$LD_LIBRARY_PATH
to overwrite your default libs.
So that you won't have ld linking errors. Good luck!!
In lapack-3.7.0, there are redundant lines in the SRC/Makefile. Simply deleting them will solve your error.

Answer 2

I would suggest using OpenBLAS.
> git clone https://github.com/xianyi/OpenBLAS.git
> make
> make make --PREFIX=INSTALL_DIR install
move the librabries from OpenBLAS to /usr/lib64
> cp /path/to/OpenBLAS/lib/* /usr/lib64/
then go to the octave installation path and run
> "your specific flags" ./configure "your specific arguments" --with-blas="-lopenblas"