[QE-users] Error during compilation in the step of make all command

[Will DeBenedetti]

Hi Sheng-Chinh,

Have you looked to see if you have made QE binaries? These will be in the
/qe/bin On my machine these are located here:  /Users/wjid/qe/bin

Using ls shows the following after running `make all`:

wjid$ ls

alpha2f.x neb.x

average.x open_grid.x

band.eps path_interpolation.x

bands.x ph.x

bse_main.x phcg.x

cell2ibrav.x plan_avg.x

cp.x plotband.x

dist.x plotproj.x

dos.x plotrho.x

dynmat.x pmw.x

epa.x pp.x

epsilon.x ppacf.x

ev.x projwfc.x

fd.x pw.x

fd_ef.x pw2bgw.x

fd_ifc.x pw2critic.x

fermi_proj.x pw2gw.x

fermi_velocity.x pw2wannier90.x

fqha.x pw4gww.x

fs.x pwcond.x

generate_rVV10_kernel_table.x pwi2xsf.x

generate_vdW_kernel_table.x q2qstar.x

gww.x q2r.x

gww_fit.x q2trans.x

head.x q2trans_fd.x

hp.x simple.x

ibrav2cell.x simple_bse.x

initial_state.x simple_ip.x

iotk spectra_correction.x

iotk.x sumpdos.x

iotk_print_kinds.x turbo_davidson.x

kpoints.x turbo_eels.x

lambda.x turbo_lanczos.x

ld1.x turbo_spectrum.x

manycp.x wannier_ham.x

manypw.x wannier_plot.x

matdyn.x wfck2r.x

molecularnexafs.x wfdd.x

molecularpdos.x xspectra.x

Then you should verify that your binaries are linked properly by using
otool, which is the linux equivalent of ldd.

The command to show which shared libraries are linked with this binary use
otool -L (in terminal)

wjid$ otool -L pw.x

pw.x:

/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_scalapack_lp64.dylib
(compatibility version 0.0.0, current version 0.0.0)

/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_intel_lp64.dylib
(compatibility version 0.0.0, current version 0.0.0)

/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_intel_thread.dylib
(compatibility version 0.0.0, current version 0.0.0)

/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_core.dylib
(compatibility version 0.0.0, current version 0.0.0)

/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_blacs_mpich_lp64.dylib
(compatibility version 0.0.0, current version 0.0.0)

/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
1252.50.4)

/usr/local/bin/mpich-install/lib/libmpifort.12.dylib (compatibility version
14.0.0, current version 14.7.0)

/usr/local/bin/mpich-install/lib/libmpi.12.dylib (compatibility version
14.0.0, current version 14.7.0)

/usr/local/bin/mpich-install/lib/libpmpi.12.dylib (compatibility version
14.0.0, current version 14.7.0)

The output shows which MKL and mpich libraries are linked to the pw.x
binary.

Like I said in my previous email, if you have system integrity protection
enabled (it is by default) linking to dynamic libraries is disabled by
default. These binaries will look like plotrho.x as below:

wjid$ otool -L plotrho.x

plotrho.x:

@rpath/libmkl_scalapack_ilp64.dylib (compatibility version 0.0.0, current
version 0.0.0)

@rpath/libmkl_intel_ilp64.dylib (compatibility version 0.0.0, current
version 0.0.0)

@rpath/libmkl_intel_thread.dylib (compatibility version 0.0.0, current
version 0.0.0)

@rpath/libmkl_core.dylib (compatibility version 0.0.0, current version
0.0.0)

@rpath/libmkl_blacs_mpich_ilp64.dylib (compatibility version 0.0.0, current
version 0.0.0)

/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
1252.50.4)

/usr/local/bin/mpich-install/lib/libmpifort.12.dylib (compatibility version
14.0.0, current version 14.7.0)

/usr/local/bin/mpich-install/lib/libmpi.12.dylib (compatibility version
14.0.0, current version 14.7.0)

/usr/local/bin/mpich-install/lib/libpmpi.12.dylib (compatibility version
14.0.0, current version 14.7.0)


To get around this, you can replace the dynamic link with a static address
using install_name_tool command as below. For my setup this looks like the
following:

 install_name_tool -change "@rpath at rpath/libmkl_scalapack_ilp64.dylib" "
/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/
lib/libmkl_scalapack_lp64.dylib" </Path/To/Binary>

Note that the above command is a one-liner. Repeat this until all of
the @rpath/..../ are gone.

Will DeBenedetti
Cornell University



On Sat, Sep 21, 2019 at 9:14 PM 林聖智 <r03223130 at ntu.edu.tw> wrote:

> Hi Will,
>
> Thanks for reaching out to me. But, I am really new to QE and do not
> understand what files I need to identify. Can you give me more details?
>
> Also, I leave the message, as follows, I got in the end of the ‘'make
> all'' command. Hope this can help identify the problem.
>
> ld: warning: text-based stub file
> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory.tbd
> and library file
> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
> are out of sync. Falling back to library file for linking.
> ld: warning: text-based stub file
> /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS.tbd and
> library file
> /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS are out of
> sync. Falling back to library file for linking.
> ( cd ../../bin ; ln -fs ../GWW/bse/bse_main.x . )
>
> Thank you for considering my request.
> Sheng-Chih Lin
> r03223130 at ntu.edu.tw
>
>
>
>
> Will DeBenedetti <wjd74 at cornell.edu> 於 2019年9月21日 下午10:28 寫道：
>
> Path/To/QE/Binaries
>
>
> _______________________________________________
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