[QE-users] Installation error With iFort QE v6.4.1 on macOS
Will DeBenedetti
wjd74 at cornell.edu
Sun Aug 11 00:55:34 CEST 2019
My apologies, as usual, this was in issue with defining the correct paths
to libraries in the include file (make.inc). For anyone interested, I am
copying the make.inc file below for what worked on macOS 10.13.6 and 10.14
using the most recent Intel Fortran compilers and mpich. Several libraries
from the most recent Intel compiler suite were missing and required manual
installation after the parallel studio download
(compilers_and_libraries_2019.4.233, update 4), which, with the correct
statements in the make.inc resulted in a successful parallel compilation on
a MacBook Pro.
./configure did not find any of the installed libraries despite defining
explicit paths to MKL libs, so manual input did the trick.
--Begin make.inc--
# compilation rules
.SUFFIXES :
.SUFFIXES : .o .c .f .f90
# most fortran compilers can directly preprocess c-like directives: use
# $(MPIF90) $(F90FLAGS) -c $<
# if explicit preprocessing by the C preprocessor is needed, use:
# $(CPP) $(CPPFLAGS) $< -o $*.F90
# $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
# remember the tabulator in the first column !!!
.f90.o:
$(MPIF90) $(F90FLAGS) -c $<
# .f.o and .c.o: do not modify
.f.o:
$(F77) $(FFLAGS) -c $<
.c.o:
$(CC) $(CFLAGS) -c $<
# Top QE directory, useful for locating libraries, linking QE with plugins
# The following syntax should always point to TOPDIR:
TOPDIR = $(dir $(abspath $(filter %make.inc,$(MAKEFILE_LIST))))
# if it doesn't work, uncomment the following line (edit if needed):
# TOPDIR = /Users/wjid/qe
# DFLAGS = precompilation options (possible arguments to -D and -U)
# used by the C compiler and preprocessor
# To use libxc (v>=3.0.1), add -D__LIBXC to DFLAGS
# See include/defs.h.README for a list of options and their meaning
# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas
# MANUAL_DFLAGS = additional precompilation option(s), if desired
# BEWARE: it does not work for IBM xlf! Manually edit
FDFLAGS
MANUAL_DFLAGS =
DFLAGS = -D__FFTW -D__MPI -D__SCALAPACK
FDFLAGS = $(DFLAGS) $(MANUAL_DFLAGS)
# IFLAGS = how to locate directories with *.h or *.f90 file to be included
# typically -I$(TOPDIR)/include -I/some/other/directory/
# the latter contains .e.g. files needed by FFT libraries
# for libxc add -I/path/to/libxc/include/
IFLAGS = -I$(TOPDIR)/include -I$(TOPDIR)/FoX/finclude
-I$(TOPDIR)/S3DE/iotk/include/
# MOD_FLAG = flag used by f90 compiler to locate modules
MOD_FLAG = -I
# BASEMOD_FLAGS points to directories containing basic modules,
# while BASEMODS points to the corresponding module libraries
# Each Makefile can add directories to MODFLAGS and libraries to QEMODS
BASEMOD_FLAGS= $(MOD_FLAG)$(TOPDIR)/iotk/src \
$(MOD_FLAG)$(TOPDIR)/Modules \
$(MOD_FLAG)$(TOPDIR)/FFTXlib \
$(MOD_FLAG)$(TOPDIR)/LAXlib \
$(MOD_FLAG)$(TOPDIR)/UtilXlib \
$(MOD_FLAG)$(TOPDIR)/FoX/finclude
# 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 = mpif90
F90 = ifort
CC = gcc
F77 = ifort
# GPU architecture (Kepler: 35, Pascal: 60, Volta: 70 )
GPU_ARCH=
# CUDA runtime (Pascal: 8.0, Volta: 9.0)
CUDA_RUNTIME=
# CUDA F90 Flags
CUDA_F90FLAGS=
# 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 -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) $(CUDA_F90FLAGS)
$(IFLAGS) $(MODFLAGS)
FFLAGS = -O2 -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 program is not
fortran
# Currently used for Yambo
FFLAGS_NOMAIN = -nofor_main
# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty
# for libxc, set LD_LIBS=-L/path/to/libxc/lib/ -lxcf90 -lxc
LD = mpif90
LDFLAGS =
LD_LIBS =
# External Libraries (if any) : blas, lapack, fft, MPI
# If you have nothing better, use the local copy via "--with-netlib" :
# BLAS_LIBS = /your/path/to/espresso/LAPACK/blas.a
# BLAS_LIBS_SWITCH = internal
BLAS_LIBS =
/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_blas95_ilp64.a
/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_lapack95_ilp64.a
-L/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/
-lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -lpthread -lm -ldl
BLAS_LIBS_SWITCH = external
# If you have nothing better, use the local copy via "--with-netlib" :
# LAPACK_LIBS = /your/path/to/espresso/LAPACK/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 =
/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_blas95_ilp64.a
/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_lapack95_ilp64.a
-L/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/
-lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -lpthread -lm -ldl
LAPACK_LIBS_SWITCH = external
SCALAPACK_LIBS =
/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_blas95_ilp64.a
/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_lapack95_ilp64.a
-L/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/
-lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core
-lmkl_blacs_mpich_ilp64 -lpthread -lm -ldl
# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)
FFT_LIBS =
-L/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libfftw3xf_gnu.a
# HDF5
HDF5_LIB =
FOX_LIB = -L$(TOPDIR)/FoX/lib -lFoX_dom -lFoX_sax -lFoX_wxml -lFoX_common\
-lFoX_utils -lFoX_fsys
FOX_FLAGS =
# 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 =
# CUDA libraries
CUDA_LIBS=
CUDA_EXTLIBS =
# 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 -c
# all internal and external libraries - do not modify
FLIB_TARGETS = all
LIBOBJS = $(TOPDIR)/clib/clib.a $(TOPDIR)/iotk/src/libiotk.a
LIBXC_LIBS =
QELIBS = $(CUDA_LIBS) $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FOX_LIB)
$(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(HDF5_LIB) $(LIBXC_LIBS)
$(LD_LIBS)
# wget or curl - useful to download from network
WGET = curl -o
# Install directory - "make install" copies *.x executables there
PREFIX = /usr/local
--End make.inc--
On Fri, Aug 9, 2019 at 2:45 PM Will DeBenedetti <wjd74 at cornell.edu> wrote:
> All,
>
> I am attempting to compile Quantum Espresso v6.4.1 against MPICH and the
> iFort Intel Fortan compiler suite and am running into an odd error that I
> have not seen before, I am pasting a truncated undefined symbol error
> below. I am also listing my machine info and compiler info.
>
> *System Info:*
> Macbook Pro 11,2
> OS:Macintosh OS X
> OSVERSION:10.14.5
> Darwin dhcp-ccc-6847.redrover.cornell.edu 18.6.0 Darwin Kernel Version
> 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64
> x86_64
> Intel(R) Core(TM) i7-4750HQ CPU @ 2.00GHz
>
> *Intel Compiler*
> Intel compilers_and_libraries_2019.4.233
>
> The output from the command $make PW is below:
>
>
> Compiler:compilers_and_libraries_2019.4.233
> Undefined symbols for architecture x86_64:
> "_dfti_commit_descriptor_external", referenced from:
> _fft_scalar_dfti_mp_cft_1z_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cft_2xy_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cfft3d_ in libqefft.a(fft_scalar.DFTI.o)
> "_dfti_compute_backward_z", referenced from:
> _fft_scalar_dfti_mp_cft_2xy_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cfft3d_ in libqefft.a(fft_scalar.DFTI.o)
> "_dfti_compute_backward_zz", referenced from:
> _fft_scalar_dfti_mp_cft_1z_ in libqefft.a(fft_scalar.DFTI.o)
> "_dfti_compute_forward_z", referenced from:
> _fft_scalar_dfti_mp_cft_2xy_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cfft3d_ in libqefft.a(fft_scalar.DFTI.o)
> "_dfti_compute_forward_zz", referenced from:
> _fft_scalar_dfti_mp_cft_1z_ in libqefft.a(fft_scalar.DFTI.o)
> "_dfti_create_descriptor_1d", referenced from:
> _fft_scalar_dfti_mp_cft_1z_ in libqefft.a(fft_scalar.DFTI.o)
> "_dfti_create_descriptor_highd", referenced from:
> _fft_scalar_dfti_mp_cft_2xy_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cfft3d_ in libqefft.a(fft_scalar.DFTI.o)
> "_dfti_free_descriptor_external", referenced from:
> _fft_scalar_dfti_mp_cft_1z_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cft_2xy_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cfft3d_ in libqefft.a(fft_scalar.DFTI.o)
> "_dfti_set_value_dblval", referenced from:
> _fft_scalar_dfti_mp_cft_1z_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cft_2xy_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cfft3d_ in libqefft.a(fft_scalar.DFTI.o)
> "_dfti_set_value_intval", referenced from:
> _fft_scalar_dfti_mp_cft_1z_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cft_2xy_ in libqefft.a(fft_scalar.DFTI.o)
> _fft_scalar_dfti_mp_cfft3d_ in libqefft.a(fft_scalar.DFTI.o)
> ld: symbol(s) not found for architecture x86_64
> make[2]: *** [pw.x] Error 1
> make[1]: *** [pw] Error 1
> make: *** [pw] Error 1
>
> I will note that I receive a very similar message when attempting to
> compile VASP against the same compiler suite, although this message is
> returned from the file: fftw3xf.lst
>
> All of my Paths are set to the correct libraries *etc*
>
> Many thanks,
>
> Will DeBenedetti
> Cornell University
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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