[QE-users] Error during compilation in the step of make all command
林聖智
r03223130 at ntu.edu.tw
Mon Sep 23 04:14:12 CEST 2019
Dear Will,
Thanks so much for your help. Using the virtual environment by anaconda, now I can run the overall test system smoothly, despite some failed tests.
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 下午8:11 寫道：
>
> Hi Sheng-Chinh,
>
> I also recall having this error at some point. Usually 99.99% of these errors have to do with PATH variables being incorrectly set. For a number of reasons, I do not use the Python that ships with Macs, I instead use virtual environments using Anaconda (not an endorsement, just a much painless way of using software that Apple will soon deprecate). I was able to get the test suite running by creating a virtual environment using Python 2.7.something and activating this environment using condo activate name_of_environment
>
> As per the documentation you will to run make run-tests-foo, then the tests will run serially or in parallel. Keep in mind only PW, CP, PH, and EPW binaries are supported. Make sure you have statically lined these four binaries as per my previous message and verify using otool -L otherwise the tests will crash. I have a 4-core processor and the tests took quite some time running in parallel on the Intel compiler suite. Running on gFortran will be slower.
>
> Will DeBenedetti
>
>
>
> On Sun, Sep 22, 2019 at 2:03 AM 林聖智 <r03223130 at ntu.edu.tw <mailto:r03223130 at ntu.edu.tw>> wrote:
> 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 <mailto:r03223130 at ntu.edu.tw>
>
>
>
>
>> Will DeBenedetti <wjd74 at cornell.edu <mailto: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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