Yambo Community Forum

Dear all,
I am trying to install yambo 3.4 in my cluster (Linux cu01 3.10.0-123.el7.x86_64 #1 SMP), but it aways failed. The clusters has intel (composer_xe_2013.1.117) and pgi (pgi-11.3) compiler. Both of them turned to be not suit to yambo and cause troubles. The configure
is right while the err happens after making,


>>>[Making libxc]<<<
Making all in build
Making all in src
libtool: ignoring unknown tag F77
libtool: compile: pgf90 -O4 -fast -Munroll -Mnoframe -Mdalign -c libxc.f90 -o libxc_la-libxc.o
PGF90-S-0034-Syntax error at or near / (/usr/include/stdc-predef.h: 1)
PGF90-S-0034-Syntax error at or near identifier file (/usr/include/stdc-predef.h: 2)
PGF90-S-0034-Syntax error at or near identifier gnu (/usr/include/stdc-predef.h: 4)
PGF90-S-0034-Syntax error at or near identifier it (/usr/include/stdc-predef.h: 5)
PGF90-S-0034-Syntax error at or near identifier as (/usr/include/stdc-predef.h: 6)
PGF90-S-0034-Syntax error at or near real constant 2.0999999E+0 (/usr/include/stdc-predef.h: 7)
PGF90-S-0034-Syntax error at or near identifier gnu (/usr/include/stdc-predef.h: 9)
PGF90-S-0034-Syntax error at or near identifier without (/usr/include/stdc-predef.h: 10)
PGF90-S-0034-Syntax error at or near identifier or (/usr/include/stdc-predef.h: 11)
PGF90-S-0034-Syntax error at or near identifier general (/usr/include/stdc-predef.h: 12)
PGF90-S-0034-Syntax error at or near identifier should (/usr/include/stdc-predef.h: 14)
PGF90-S-0034-Syntax error at or near identifier along (/usr/include/stdc-predef.h: 15)
PGF90-S-0034-Syntax error at or near < (/usr/include/stdc-predef.h: 16)
PGF90-S-0034-Syntax error at or near / (/usr/include/stdc-predef.h: 21)
PGF90-S-0034-Syntax error at or near identifier it (/usr/include/stdc-predef.h: 22)
PGF90-S-0034-Syntax error at or near identifier t (/usr/include/stdc-predef.h: 23)
PGF90-S-0034-Syntax error at or near < (/usr/include/stdc-predef.h: 24)
PGF90-S-0034-Syntax error at or near identifier macros (/usr/include/stdc-predef.h: 25)
PGF90-S-0034-Syntax error at or near identifier includes (/usr/include/stdc-predef.h: 26)
PGF90-S-0034-Syntax error at or near identifier in (/usr/include/stdc-predef.h: 27)
PGF90-S-0034-Syntax error at or near / (/usr/include/stdc-predef.h: 29)
PGF90-S-0034-Syntax error at or near / (/usr/include/stdc-predef.h: 33)
PGF90-S-0034-Syntax error at or near real constant 6.0000000E+0 (/usr/include/stdc-predef.h: 34)
PGF90-S-0034-Syntax error at or near / (/usr/include/stdc-predef.h: 37)
0 inform, 0 warnings, 24 severes, 0 fatal for xc_f90_types_m
PGF90-F-0000-Internal compiler error. interf:new_symbol, symbol not found 582 (./libxc_master.F90: 49)
PGF90/x86-64 Linux 11.3-0: compilation aborted
make[4]: *** [libxc_la-libxc.lo] Error 1
make[3]: *** [all] Error 2
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [libs] Error 2

Can anybody help me, thanks first.

P. L. Gong
ISSP, HeFei, China

Dear P.L Gong,
it looks me you are mixing different compiler and pre-compilers. What you have it seems a precompiler problem.
After typing a
make clean_all
try to launch the configure specifying your compilers in the command line e.g.
./configure F90=ifort et...
or exporting the compiler variable before the configure e.g.

export MKL_LIB=$MKLROOT/lib/intel64
export CPP='icc -E'
export CC=icc
export CXX=icpc
export F77=ifort
export F90=ifort
export PFC=mpiifort
export CFLAGS=-O3
export FFLAGS=" -O2 -assume buffered_io,byterecl"
export FFLAGS_NOOPT=" -O0 -assume buffered_io,byterecl"
./configure \
--with-p2y=5.0 --with-iotk=/s3_home/varsano/codes/espresso-5.0.2/iotk \
--with-blas="-L/$MKL_LIB -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-lapack="-L/$MKL_LIB -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-fftw=/s3_home/varsano/fftw-3.3.4/lib \
--with-fftw-lib=/s3_home/varsano/fftw-3.3.4/lib/libfftw3.a \
--with-netcdf-lib=/s3_home/varsano/netcdf/lib \
--with-netcdf-include=/s3_home/varsano/netcdf/include \
--with-netcdf-link=-lnetcdf \


Of course remove the flag you are not interested in or change the paths accordingly to your machine.
These options works for Intel version 14.0.2 .

Hope it helps,
Daniele

Dear Daniele Varsano,
Thanks for your reply. I have try your method but the problem hold on. I think whether the process for c compiling with gcc or icc is wrong when
it was compiling libxc_master.f90. Also it may be the problem of /usr/include/stdc-predef.h:2.3, or of the version of gcc. Please help me solve it.
Waiting for you reply.
The err is like,

Error: Invalid character in name at (1)
/usr/include/stdc-predef.h:2.3:
Included at ./libxc_master.F90:1:

This file is part of the GNU C Library.
1
Error: Unclassifiable statement at (1)
/usr/include/stdc-predef.h:4.3:
Included at ./libxc_master.F90:1:

The GNU C Library is free software; you can redistribute it and/or
1
Error: Unclassifiable statement at (1)
/usr/include/stdc-predef.h:4.39:
Included at ./libxc_master.F90:1:


Best wishes
P. L. Gong

Dear P.L Gong,

from your config.log and err.log I can see that you are using icc in combination with gfortran, this does not work in general and causes problem with the precompiler which is your case.
As Daniele suggest, export the F77, F90 and PFC variables so to make sure you are using icc, ifort (mpif90) etc. (or gcc, gfortran, etc)
After the configure yambo outputs a report with all the variable set during the configure, e.g. this is what I obtained by ".configure CC=icc FC=ifort"

# [VER] 3.4.1 r.3187
#
# [SYS] linux@x86_64
# [SRC] /data/myrta/Src/yambo-gpl/stable
# [BIN] /data/myrta/Src/yambo-gpl/stable/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [ ] OpenMP
# [ ] PW (5.0) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [ ] NETCDF/HDF5/Large Files
# [XX ] Built-in BLAS/LAPACK/LOCAL
#
# [ CPP ] icc -E -ansi
# [ C ] icc -g -O2 -D_C_US -D_FORTRAN_US
# [MPICC] mpicc -g -O2 -D_C_US -D_FORTRAN_US
# [ F90 ] ifort -assume bscc -O3 -ip -xHost
# [MPIF ] mpif90 -assume bscc -O3 -ip -xHost
# [ F77 ] ifort -assume bscc -O3 -ip -xHost
# [Cmain] -nofor_main
# [NoOpt] -assume bscc -O0 -xHost
#
# [ MAKE ] make
# [EDITOR] vim

those informations are written in config/report.
Before the new configure and make remember to 'make clean_all'

Best
m

Dear myrta gruning,
I have solved the problem with your method and installed yambo 3.4.1 successfully. Thanks your reply and help.

Best wishes
P. L. Gong