[QE-users] Error compiling qe5.1 linked to libbeef-v0.1.1, “Nonexistent include directory .. [-Wmissing-include-dirs]”

[Paolo Giannozzi]

Previously you had this error:
           READ(dftout(5:), '(i)', IOSTAT=i) beeftype
Error: Nonnegative width required in format string at (1)

Why don't you try to fix it as a first attempt? this might do the job:
           READ(dftout(5:), *, IOSTAT=i) beeftype

On Fri, Dec 27, 2019 at 9:46 AM Delgado DelgadoJorge <
delgadodelgado.jorge at aist.go.jp> wrote:

> Dear Paolo,
>
>
>
> Thank you very much for the quick reply. After reading your comments and
> considering that some of the contributors of the mailing list succeeded in
> the compilation of qe5.1 using gcc 4.8.5, I tried to test additional
> compilations using this compiler (gcc 4.8.5). Although the make pw lasted
> longer than when using the default gcc 7.4.0, the compilation is
> interrupted and a different error appeared this time:
>
>
>
> ranlib libpw.a
>
> mpif90 -g -pthread -o pw.x \
>
>    pwscf.o  libpw.a ../../Modules/libqemod.a ../../flib/ptools.a
> ../../flib/flib.a ../../clib/clib.a ../../iotk/src/libiotk.a
> /home/jorge/20191226-qe51-compilations/26/espresso.5.1.r11289.pybeef/espresso/lapack-3.2/lapack.a
>
> /home/jorge/20191226-qe51-compilations/26/espresso.5.1.r11289.pybeef/espresso/BLAS/blas.a
> -L/home/jorge/20191226-qe51-compilations/26/libbeef/lib -lbeef
>
> /usr/bin/ld: ../../clib/clib.a(c_mkdir.o): relocation R_X86_64_32 against
> `.rodata.str1.8' can not be used when making a PIE object; recompile with
> -fPIC
>
> /usr/bin/ld: ../../clib/clib.a(copy.o): relocation R_X86_64_32 against
> `.rodata.str1.1' can not be used when making a PIE object; recompile with
> -fPIC
>
> /usr/bin/ld: ../../clib/clib.a(cptimer.o): relocation R_X86_64_32 against
> `.bss' can not be used when making a PIE object; recompile with -fPIC
>
> /usr/bin/ld: ../../clib/clib.a(eval_infix.o): relocation R_X86_64_32S
> against undefined symbol `stack_op' can not be used when making a PIE
> object; recompile with -fPIC
>
> /usr/bin/ld: ../../clib/clib.a(fft_stick.o): relocation R_X86_64_32S
> against `.text' can not be used when making a PIE object; recompile with
> -fPIC
>
> /usr/bin/ld: ../../clib/clib.a(md5_from_file.o): relocation R_X86_64_32
> against `.rodata.str1.8' can not be used when making a PIE object;
> recompile with -fPIC
>
> /usr/bin/ld: ../../clib/clib.a(md5.o): relocation R_X86_64_32 against
> `.rodata' can not be used when making a PIE object; recompile with -fPIC
>
> /usr/bin/ld: final link failed: Nonrepresentable section on output
>
> collect2: error: ld returned 1 exit status
>
> Makefile:256: recipe for target 'pw.x' failed
>
> make[2]: *** [pw.x] Error 1
>
> make[2]: Leaving directory
> '/home/jorge/20191226-qe51-compilations/26/espresso.5.1.r11289.pybeef/espresso/PW/src'
>
> Makefile:9: recipe for target 'pw' failed
>
> make[1]: *** [pw] Error 1
>
> make[1]: Leaving directory
> '/home/jorge/20191226-qe51-compilations/26/espresso.5.1.r11289.pybeef/espresso/PW'
>
> Makefile:47: recipe for target 'pw' failed
>
>
>
>
>
> Both, the lbeef and the qe were compiled using gcc-4.8. The code lines
> used are described below:
>
>
>
> Installation of lbeef library:
>
> ./configure CC=gcc-4.8
> --prefix=/home/jorge/20191226-qe51-compilations/26/libbeef
>
> make
>
> make install
>
>
>
> Compilation of qe:
>
> ./configure CC_gcc=4.8
> BEEF_LIBS="-L/home/jorge/20191226-qe51-compilations/26/libbeef/lib -lbeef"
>
> make pw
>
>
>
> So the error this time is basically related to: “/usr/bin/ld:
> ../../clib/clib.a(c_mkdir.o): relocation R_X86_64_32 against
> `.rodata.str1.8' can not be used when making a PIE object; recompile with
> -fPIC”.
>
> I wonder if this is still related to the compiler used. If so, should I
> try icc compilers instead?
>
> I have to mentioned that I also installed separately gfortran-4.8 (v
> 4.8.5), and did the same as described for gcc-4.8 (installed lbeef and
> tried to compile qe), but the error was exactly the same.
>
>
>
> Let me recall the specification of the environment I’m working on:
>
> OS: Ubuntu v.18.04.1 (64bit Virtual machine guest on Windows 10 host –
> VirtualBox6.0)
>
> Processor: Intel® Core™ i7-8550U CPU @ 1.80GHz × 4
>
> Graphics: SVGA3D; build: RELEASE; LLVM;
> Compiller: gcc, GNU Fortran (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 (also
> installed separately gcc-4.8.5 and gfortran-4.8.5)
>
>
>
> Last time I forgot to mentioned that I’m trying to do the installation on
> a ubuntu virtual machine. Before of attempting the specific compilation I’m
> describing here (qe5.1-patched/lbeef), I managed to compile normal qe5.1 or
> qe6.4 source codes in the standard manner (./configure; make pw), without
> any issue. The problems appeared at the moment of using the pair
> qe5.1-patched/lbeef, with the particularities that demand this
> installation. To double check that the issue was not related to my ubuntu
> virtual machine, I tested the described above using the Quantum Mobile
> 19.09.0 (Ubuntu 18.04.3 LTS) , but the obtained errors were exactly the
> same. If for some reason the use of a ubuntu as a virtual machine is not
> suitable for this compilation, please let me know.
>
>
>
> I would appreciate further guidance with this issue.
>
>
>
> Regards
>
> Jorge
>
>
>
> -----
> Jorge A. Delgado, Ph.D.
> Research Scientist - Catalysis and Nanomaterials
> National Institute of Advanced Industrial Science and Technology (AIST)
> Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
>
> <ayada at sbchem.kyoto-u.ac.jp>
>
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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