[Q-e-developers] multiple definitions of fftw_version
Lorenzo Paulatto
lorenzo.paulatto at impmc.upmc.fr
Tue Jan 12 12:15:21 CET 2016
On Tuesday, January 12, 2016 10:44:12 AM Filippo SPIGA wrote:
> Ciao Lorenzo,
>
> thanks for reporting this. Did you run the configure and then immediately
> run make directly or did you manually hack the make.sys after configure and
> before run make?
I run configure first, then overwrote it with an older one which I further
edited a bit, I think I also tried to just run configure and compile. I did
however copy the code over rsync with a certain list of --exclude which is
supposed to not overwrite the compiled files and configuration, so that may
also be a cause.
I'm trying now to take a pristine qe 5.3.0., untar configure and make.
This machine is a bit complicated, as I would prefer to use SGI MPT + intel
compiler, but for the sake of argument I'm now using intel MPI, which makes
the make.sys as produced by configure ALMOST work without any hacking (I have
to change openmpi to intelmpi in for blacs)
As long as I stick with the default (I only set MPIF90=mpiifort) everything is
ok, but it link to some system fftw3
ldd bin/pw.x
...
libfftw3.so.3 => /usr/lib64/libfftw3.so.3 (0x00007ffff71ef000)
If I edit make.sys to use intel fftw3 interface I get the same problem as
before. I.e. I only changed:
FFT_LIBS = -lfftw3
to
FFT_LIBS = /opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/lib/
intel64/libfftw3xf_intel.a
Same result if I run ./configure FFT_LIBS=/opt/dev... instead of changing the
makefile by hand
I'm attaching this make sys as well
HTH
>
> --
> Mr. Filippo SPIGA, M.Sc.
> Quantum ESPRESSO Foundation
> http://www.quantum-espresso.org ~ skype: filippo.spiga
>
> *****
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> On Jan 12, 2016, at 10:04 AM, Lorenzo Paulatto
<lorenzo.paulatto at impmc.upmc.fr> wrote:
> > Hello,
> > and thank you for the new 5.3.0 release.
> >
> > I have a problem compiling it with ifort 15.0.0 and linking against the
> > intel fftw3 interface:
> >
> > ifort -o pw.x \
> >
> > pwscf.o libpw.a ../../Modules/libqemod.a
> > ../../FFTXlib/libqefft.a
> >
> > ../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a ../../iotk/src/
> > libiotk.a -Wl,--start-group
> > /opt/dev/intel/2015.0.022/composer_xe_2015.0.090/
> > mkl/lib/intel64/libmkl_scalapack_lp64.a /opt/dev/intel/2015.0.022/
> > composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_lp64.a
> > /opt/dev/intel/
> > 2015.0.022/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_core.a /opt/dev/
> > intel/2015.0.022/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_sequential
> > .a / opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/lib/intel64/
> > libmkl_blacs_sgimpt_lp64.a -Wl,--end-group -lpthread -lm /opt/dev/intel/
> > 2015.0.022/composer_xe_2015/mkl/interfaces/fftw3xf/libfftw3xf_intel.a
> > -L/ opt/sgi/mpt/mpt-2.11/lib -lmpi -lpthread /usr/lib64/libcpuset.so.1
> > /usr/lib64/ libbitmask.so.1
> > /opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/lib/intel64/
> > libmkl_intel_lp64.a(fftw_version.o):(.rodata+0x0): multiple definition of
> > `fftw_version'
> > ../../FFTXlib/libqefft.a(fft_stick.o):(.data+0x430): first defined here
> > ld: Warning: size of symbol `fftw_version' changed from 8 in
> > ../../FFTXlib/
> > libqefft.a(fft_stick.o) to 25 in /opt/dev/intel/2015.0.022/
> > composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_lp64.a(fftw_version.o)
> > make[2]: *** [pw.x] Error 1
> > make[2]: Leaving directory `/lustrework/paulatto/espresso/PW/src'
> > make[1]: *** [pw] Error 1
> > make[1]: Leaving directory `/lustrework/paulatto/espresso/PW'
> > make: *** [pw] Error 1
> >
> >
> > It is not especially clear to me what the source of the problem is, but I
> > guess that the fftw.h which comes with FFTXlib does not match the one in
> > /opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/include/fftw/fftw.h
> >
> > Copying it over does not solve the problem as I get:
> > In file included from fft_stick.c(21):
> > fftw.c(163): error: identifier "notw_codelet" is undefined
> >
> > extern notw_codelet fftw_no_twiddle_1;
> >
> > ^
> >
> > t
> > Neither can I remove fftw.h and add a -I/opt/dev/intel/... because of how
> > the makefile is made:
> > make: *** No rule to make target `fftw.h', needed by `fft_stick.o'. Stop.
> >
> >
> > I noticed that fftw_version is only defined in fftw.c, which, if I
> > understand correctl, should not be compiled as I am using -D__FFTW3, but
> > it is included from fft_stick.c
> >
> >
> > I finally solved the problem by commenting out the definition of
> > ffw_version from FFTXlib/fftw.c, but I'm not sure the solution is ideal
> > and I also have doublt about which fftw is actually being used (the
> > optimized intel one or the one included?)
> >
> >
> >
> > Another solution is to use -D__DFTI instead, which has some other
> > advantages, but Carlo expressed some concern about its thread safety and
> > I'm left with the doubt about what is actually being used in the code.
> >
> >
> > Could the experts have a go at this?
> >
> > I'm attaching the relevant make.sys, renamed
>
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--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/
23-24/4é16 Boîte courrier 115,
4 place Jussieu 75252 Paris Cédex 05
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# make.sys. Generated from make.sys.in by configure.
# compilation rules
.SUFFIXES :
.SUFFIXES : .o .c .f .f90
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# $(MPIF90) $(F90FLAGS) -c $<
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# $(CPP) $(CPPFLAGS) $< -o $*.F90
# $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
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.f90.o:
$(MPIF90) $(F90FLAGS) -c $<
# .f.o and .c.o: do not modify
.f.o:
$(F77) $(FFLAGS) -c $<
.c.o:
$(CC) $(CFLAGS) -c $<
# topdir for linking espresso libs with plugins
TOPDIR = /home/paulatto/work/espresso
# DFLAGS = precompilation options (possible arguments to -D and -U)
# used by the C compiler and preprocessor
# FDFLAGS = as DFLAGS, for the f90 compiler
# See include/defs.h.README for a list of options and their meaning
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# MANUAL_DFLAGS = additional precompilation option(s), if desired
# You may use this instead of tweaking DFLAGS and FDFLAGS
# BEWARE: will not work for IBM xlf! Manually edit FDFLAGS
MANUAL_DFLAGS =
#DFLAGS = -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK $(MANUAL_DFLAGS)
DFLAGS = -D__INTEL -D__DFTI -D__MPI -D__PARA -D__SCALAPACK $(MANUAL_DFLAGS)
FDFLAGS = $(DFLAGS) $(MANUAL_DFLAGS)
# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
IFLAGS = -I../include -I/opt/sgi/mpt/mpt-2.11/include -I/opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/include
#-I/opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/include/fftw/
# MOD_FLAGS = flag used by f90 compiler to locate modules
# Each Makefile defines the list of needed modules in MODFLAGS
MOD_FLAG = -I
# Compilers: fortran-90, fortran-77, C
# If a parallel compilation is desired, MPIF90 should be a fortran-90
# compiler that produces executables for parallel execution using MPI
# (such as for instance mpif90, mpf90, mpxlf90,...);
# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
# If you have a parallel machine but no suitable candidate for MPIF90,
# try to specify the directory containing "mpif.h" in IFLAGS
# and to specify the location of MPI libraries in MPI_LIBS
MPIF90 = ifort
#F90 = ifort
CC = icc
F77 = ifort
# C preprocessor and preprocessing flags - for explicit preprocessing,
# if needed (see the compilation rules above)
# preprocessing flags must include DFLAGS and IFLAGS
CPP = cpp
CPPFLAGS = -P -C -traditional $(DFLAGS) $(IFLAGS)
# compiler flags: C, F90, F77
# C flags must include DFLAGS and IFLAGS
# F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax
CFLAGS = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS = -Ofast -no-ipo -xHost -assume byterecl -g -traceback
# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack
FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback
# compiler flag needed by some compilers when the main is not fortran
# Currently used for Yambo
FFLAGS_NOMAIN = -nofor_main
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LD = ifort
LDFLAGS =
LD_LIBS =
# External Libraries (if any) : blas, lapack, fft, MPI
# If you have nothing better, use the local copy :
# BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a
# BLAS_LIBS_SWITCH = internal
BLAS_LIBS =
BLAS_LIBS_SWITCH = external
# If you have nothing better, use the local copy :
# LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/lapack.a
# LAPACK_LIBS_SWITCH = internal
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order
LAPACK_LIBS =
LAPACK_LIBS_SWITCH = external
ELPA_LIBS_SWITCH = disabled
SCALAPACK_LIBS = -Wl,--start-group /opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_scalapack_lp64.a /opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_lp64.a /opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_core.a /opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_sequential.a /opt/dev/intel/2015.0.022/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_blacs_sgimpt_lp64.a -Wl,--end-group -lpthread -lm
# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)
FFT_LIBS =
# /opt/dev/intel/2015.0.022/composer_xe_2015/mkl/interfaces/fftw3xf/libfftw3xf_intel.a
# For parallel execution, the correct path to MPI libraries must
# be specified in MPI_LIBS (except for IBM if you use mpxlf)
MPI_LIBS =
# IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS
MASS_LIBS =
# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv
AR = ar
ARFLAGS = ruv
# ranlib command. If ranlib is not needed (it isn't in most cases) use
# RANLIB = echo
RANLIB = ranlib
# all internal and external libraries - do not modify
FLIB_TARGETS = all
LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a
LIBS = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(LD_LIBS) -L/opt/sgi/mpt/mpt-2.11/lib -lmpi -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1
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PREFIX = $(INSTALLDIR)
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