[QE-users] Installing QE 670 on AMD EPYC

[Tobias Klöffel]

Dear Chandan,
you are missing the threaded fftw library. If you compiled with openmp 
there should be something like fftw_threads in your fftw lib folder.
However, you can also just use the precompiled fftw + blis, from AMD, 
called AOCL
https://developer.amd.com/amd-aocl/
https://developer.amd.com/amd-aocc/

Best,
Tobias

On 3/11/21 6:58 PM, Chandan Kumar Choudhury wrote:
> Hi Pietro,
>
> This did help. I guess I am getting closer!!
>  I could proceed further, but still got some error.
> Can you please suggest a workaround?
> I have compiled FFTW, openmpi, and QE with CC=clang, CPP=clang-cpp 
> CXX=clang++ and F90=flang.
>
>
>
>    pwscf.o  libpw.a ../../Modules/libqemod.a 
> ../../KS_Solvers/libks_solvers.a ../../upflib/libupf.a 
> ../../FFTXlib/libqefft.a ../../LAXlib/libqela.a 
> ../../UtilXlib/libutil.a ../../dft-d3/libdftd3qe.a 
> /home/chandan_prescience_in/softwares/q-e-qe-6.7.0//clib/clib.a 
> /home/chandan_prescience_in/softwares/q-e-qe-6.7.0//LIBBEEF/libbeef.a 
> /home/chandan_prescience_in/apps/scalapack/libscalapack.a 
> /home/chandan_prescience_in/apps/libFLAME/lib/libflame.a 
> -L/home/chandan_prescience_in/softwares/q-e-qe-6.7.0//FoX/lib 
> -lFoX_dom -lFoX_sax -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys 
> /home/chandan_prescience_in/apps/amd-fftw/double/lib/libfftw3.a 
> /home/chandan_prescience_in/apps/blis/lib/libblis.a 
> -L/home/chandan_prescience_in/apps/openmpi/410/lib
> ld.lld: error: undefined symbol: dfftw_cleanup_threads_
> >>> referenced by fft_scalar.FFTW3.f90:148
> >>>              fft_scalar.FFTW3.o:(fft_scalar_fftw3_cft_1z_) in archive 
> ../../FFTXlib/libqefft.a
> >>> referenced by fft_scalar.FFTW3.f90:301
> >>>              fft_scalar.FFTW3.o:(fft_scalar_fftw3_cft_2xy_) in archive 
> ../../FFTXlib/libqefft.a
> >>> referenced by fft_scalar.FFTW3.f90:447
> >>>              fft_scalar.FFTW3.o:(fft_scalar_fftw3_cfft3d_) in archive 
> ../../FFTXlib/libqefft.a
> >>> referenced 1 more times
>
> ld.lld: error: undefined symbol: fftw_init_threads
> >>> referenced by fft_scalar.FFTW3.f90:149
> >>>              fft_scalar.FFTW3.o:(fft_scalar_fftw3_cft_1z_) in archive 
> ../../FFTXlib/libqefft.a
> >>> referenced by fft_scalar.FFTW3.f90:302
> >>>              fft_scalar.FFTW3.o:(fft_scalar_fftw3_cft_2xy_) in archive 
> ../../FFTXlib/libqefft.a
> >>> referenced by fft_scalar.FFTW3.f90:448
> >>>              fft_scalar.FFTW3.o:(fft_scalar_fftw3_cfft3d_) in archive 
> ../../FFTXlib/libqefft.a
> >>> referenced 1 more times
>
> ld.lld: error: undefined symbol: dfftw_plan_with_nthreads_
> >>> referenced by fft_scalar.FFTW3.f90:150
> >>>              fft_scalar.FFTW3.o:(fft_scalar_fftw3_cft_1z_) in archive 
> ../../FFTXlib/libqefft.a
> >>> referenced by fft_scalar.FFTW3.f90:303
> >>>              fft_scalar.FFTW3.o:(fft_scalar_fftw3_cft_2xy_) in archive 
> ../../FFTXlib/libqefft.a
> >>> referenced by fft_scalar.FFTW3.f90:449
> >>>              fft_scalar.FFTW3.o:(fft_scalar_fftw3_cfft3d_) in archive 
> ../../FFTXlib/libqefft.a
> >>> referenced 1 more times
> clang-11: error: linker command failed with exit code 1 (use -v to see 
> invocation)
> make[2]: *** [Makefile:262: pw.x] Error 1
> make[2]: Leaving directory 
> '/home/chandan_prescience_in/softwares/q-e-qe-6.7.0/PW/src'
> make[1]: *** [Makefile:9: pw] Error 1
> make[1]: Leaving directory 
> '/home/chandan_prescience_in/softwares/q-e-qe-6.7.0/PW'
> make: *** [Makefile:66: pw] Error 1
>
>
> Thank you!
>
> Chandan
> --
> Chandan Kumar Choudhury, PhD
> Senior Scientist (Computational Science)
> Prescience.in
>
>> On Mar 11, 2021, at 8:52 PM, Pietro Delugas <pdelugas at sissa.it 
>> <mailto:pdelugas at sissa.it>> wrote:
>>
>> Dear Chandan
>> Fox is probably compiling using a different compiler.
>> Check the make.inc file and see if F90 is set to the same compiler 
>> used by mpif90
>> The command
>> mpif90  --show
>> will tell you  which compiler is used by mpif90
>> set F90 to the same compiler do make clean and then make pw again.
>> Removing mod files in never effective because tha make command does 
>> not check them It check .o files only.
>> Do make clean.
>> Pietro
>> Sent fromMail <https://go.microsoft.com/fwlink/?LinkId=550986>for 
>> Windows 10
>> *From:*Chandan Kumar Choudhury <mailto:ckchoud at g.clemson.edu>
>> *Sent:*Thursday, March 11, 2021 3:45 PM
>> *To:*Quantum ESPRESSO users Forum 
>> <mailto:users at lists.quantum-espresso.org>
>> *Subject:*Re: [QE-users] Installing QE 670 on AMD EPYC
>> Thank you Paolo!
>>
>>
>> I did the following steps:
>> make pw
>> rm  FoX/finclude/m_common_io.mod
>> make clean
>> make pw
>>
>>
>> make clean removes the FoX directory and it recreates when we do 
>> 'make pw’
>> So, I still the same error
>> mpif90 -O3 -g -fopenmp -cpp -fopenmp -D__FFTW3 -D__MPI -D__SCALAPACK 
>> -I/home/chandan_prescience_in/apps/blis/include 
>> -I/home/chandan_prescience_in/apps/libFLAME/include 
>> -I/home/chandan_prescience_in/apps/amd-fftw/double/include 
>> -I/home/chandan_prescience_in/softwares/q-e-qe-6.7.0/FoX/finclude 
>> -I/home/chandan_prescience_in/softwares/q-e-qe-6.7.0/include 
>> -I/home/chandan_prescience_in/softwares/q-e-qe-6.7.0//upflib 
>> -I/home/chandan_prescience_in/softwares/q-e-qe-6.7.0//Modules 
>> -I/home/chandan_prescience_in/softwares/q-e-qe-6.7.0//FFTXlib 
>> -I/home/chandan_prescience_in/softwares/q-e-qe-6.7.0//LAXlib 
>> -I/home/chandan_prescience_in/softwares/q-e-qe-6.7.0//UtilXlib 
>> -I/home/chandan_prescience_in/softwares/q-e-qe-6.7.0//FoX/finclude 
>> -I../ELPA/src -c fox_init_module.f90
>> F90-F-0004-Corrupt or Old Module file 
>> /home/chandan_prescience_in/softwares/q-e-qe-6.7.0/FoX/finclude/m_common_io.mod 
>> (fox_init_module.f90: 4)
>> F90/x86-64 Linux Flang - 1.5 2017-05-01: compilation aborted
>> make[1]: *** [../make.inc:16: fox_init_module.o] Error 1
>> make[1]: Leaving directory 
>> '/home/chandan_prescience_in/softwares/q-e-qe-6.7.0/Modules'
>> make: *** [Makefile:179: mods] Error 1
>>
>>
>> --
>> Chandan Kumar Choudhury, PhD
>> Senior Scientist (Computational Science)
>> Prescience.in
>>
>>     On Mar 11, 2021, at 7:40 PM, Paolo Giannozzi
>>     <p.giannozzi at gmail.com <mailto:p.giannozzi at gmail.com>> wrote:
>>     rm FoX/include/delete m_commom_io.mod
>>     Not enough? "make clean", then "make [what-you-need]"
>>
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-- 
M.Sc. Tobias Klöffel
=======================================================
HPC (High Performance Computing) group
Erlangen Regional Computing Center(RRZE)
Friedrich-Alexander-Universität Erlangen-Nürnberg
Martensstr. 1
91058 Erlangen

Room: 1.133
Phone: +49 (0) 9131 / 85 - 20101

=======================================================

E-mail: tobias.kloeffel at fau.de

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