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

林聖智 r03223130 at ntu.edu.tw
Sun Sep 22 08:02:45 CEST 2019 

Hi Will, 

Thanks so much for the info. I’ve checked libraries of pw.x and it seems good for them with static addresses. So, I carried out calculations, such as scf and vc_relax, and they worked smoothly. Thus, I think the absence of messages I mentioned in previous e-mail was caused by some of the bins having dynamic addresses. And it could be fixed by replacing their addresses. 

Besides, when I ran test files (make run-tests-pw-serial) in the file--test-suite, the system showed the message below.

env: python2: No such file or directory
make: *** [run-tests-pw-serial] Error 127

I’ve tried several ways to address it. I checked the installation of python2 and its version was 2.7.16. Besides, I also made a symbolic link to direct the system to the location of python 2.7 using the command as follows, but still no joy. Have you ever experienced the situation?

ln -s /opt/local/bin/python2.7 /Users/hayashikiyoshisatoshi/Desktop/q-e-qe-6.4.1/q-e-qe-6.4.1/test-suite/python2


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22日 上午9:52 寫道：
> 
> 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 <mailto: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 <mailto:r03223130 at ntu.edu.tw>
> 
> 
> 
> 
>> Will DeBenedetti <wjd74 at cornell.edu <mailto: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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