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Compilation error with SLEPc

Posted: Thu Oct 03, 2024 9:55 pm
by DmitrySkachkov
Hello,

I am trying to install the GitHub version of Yambo with SLEPc library with the following configuration:

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./configure --enable-memory-profile \
              --enable-dp \
              --enable-slepc-linalg \
              FC=ifort F77=ifort CC=icc MPICC=mpicc MPIFC=mpifort
However I got the following error during compilation:

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make[2]: *** [MATRIX_slepc.o] Error 1
MATRIX_slepc.f90(1527): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [SLEPCEPS]
MATRIX_slepc.f90(1529): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [SLEPCEPSDEF]
MATRIX_slepc.f90(1870): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [SLEPCEPS]
MATRIX_slepc.f90(1871): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [SLEPCEPSDEF]
\t[driver] yambo (setup)
yambo linking failed. Check log/compile_yambo.log
MATRIX_slepc.f90(1527): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [SLEPCEPS]
MATRIX_slepc.f90(1529): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [SLEPCEPSDEF]
MATRIX_slepc.f90(1870): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [SLEPCEPS]
MATRIX_slepc.f90(1871): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [SLEPCEPSDEF]
make[1]: *** [yambo] Error 1
yambo build failed
Could you please explain how to correct these paths.

Configuration script made the following configuration:

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#
# [VER] 5.2
#
# Legend: [E]=external library [C]=internal lib to be compiled [I]=internal lib already compiled [X]=used [-]=not used
# 
# - GENERAL CONFIGURATIONS -
# 
# [SYS] linux@x86_64
# [SRC] /home/3811/yambo-5.2.1_2
# [BRN] master
# [CMP] /home/3811/yambo-5.2.1_2
# [TGT] /home/3811/yambo-5.2.1_2
# [BIN] /home/3811/yambo-5.2.1_2/bin
# [LIB] /home/3811/yambo-5.2.1_2/lib/external/intel/mpifort
#
# [EDITOR] vim
# [ MAKE ] make
#
# [X] Double precision
# [X] Keep object files
# [X] Run-Time timing profile 
# [X] Run-Time memory profile 
#
# - SCRIPTS -
#
# [-] YDB: Yambo DataBase
# [-] YAMBOpy: Yambo Python scripts
# 
# - PARALLEL/CUDA SUPPORT -
#
# [-] CUDA
# [E] MPI
# [-] OpenMP
# [X] Parallel I/O
# 
# - LIBRARIES - 
# 
# > I/O: NETCDF Large Files Support enabled, Version 4, HDF5 Parallel_lib
#
# [C] IOTK      : (LIB)/lib/libiotk.a (QE hdf5-support)
#                 -I(LIB)/include/
# [-] ETSF_IO   : 
#                 
# [I] NETCDFF   : (LIB)/v4/parallel/lib/libnetcdff.a
#                 -I(LIB)/v4/parallel/include
# [I] NETCDF    : (LIB)/v4/parallel/lib/libnetcdf.a
#                 -I(LIB)/v4/parallel/include
# [I] HDF5      : (LIB)/v4/parallel/lib/libhdf5_hl_fortran.a (LIB)/v4/parallel/lib/libhdf5_fortran.a (LIB)/v4/parallel/lib/libhdf5_hl.a (LIB)/v4/parallel/lib/libhdf5.a -lz -lm -ldl -lcurl
#                 -I(LIB)/v4/parallel/include
#
# > MATH: (FFTW MKL) 
#
# [E] BLAS      : -L/opt/shared/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm (for petsc: -L/opt/shared/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm)
# [E] LAPACK    :  (for petsc: )
# [-] SCALAPACK :  
# [-] BLACS     : 
# [E] FFT       : -L/opt/shared/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm
#                 -I/opt/shared/intel/2020u4/compilers_and_libraries_2020.4.304/linux/mkl/include
# [C] PETSC     : (LIB)/double/lib/libpetsc.a -ldl
#                 -I(LIB)/double/include 
# [C] SLEPC     : (LIB)/double/lib/libslepc.a
#                 -I(LIB)/double/include 
#
# > OTHERs
#
# [D] Ydriver   : Download
#
# [I] LibXC     : (LIB)/lib/libxcf90.a (LIB)/lib/libxcf03.a (LIB)/lib/libxc.a
#                 -I(LIB)/include
# [E] MPI       : -L/opt/shared/openmpi/4.1.5-intel-2020/lib -Wl,-rpath -Wl,/opt/shared/openmpi/4.1.5-intel-2020/lib -Wl,--enable-new-dtags -lmpi 
#                 -I/opt/shared/openmpi/4.1.5-intel-2020/include 
# [-] FUTILE    : 
#                  
# [-] YAML      : 
#                 
#
# - COMPILERS -
#
# FC kind = intel ifort version 19.1.3.304
# MPI kind= Open MPI v4.1.5, package: Open MPI frey@r0login1.localdomain.hpc.udel.edu Distribution, ident: 4.1.5, repo rev: v4.1.5, Feb 23, 2023
#
# [ CPP ] icc -std=gnu11 -E -ansi -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP -D_SLEPC   -D_DOUBLE   -D_TIMING     -D_P2Y_QEXSD_HDF5
# [ FPP ] fpp -free -P -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP -D_SLEPC   -D_DOUBLE   -D_TIMING    
# [ CC  ] mpicc -O2 -std=gnu99 -no-multibyte-chars -D_C_US -D_FORTRAN_US
# [ FC  ] mpifort -assume bscc -O3 -g -ip      
# [ FCUF] -assume bscc -O0 -g   
# [ F77 ] mpifort -assume bscc -O3 -g -ip   
# [ F77U] -assume bscc -O0 -g   
# [Cmain] -nofor_main
#
# You can modify compilers and flags by editing the file "config/setup"
#
Thank you,
Dmitry

Re: Compilation error with SLEPc

Posted: Fri Oct 04, 2024 4:44 pm
by Daniele Varsano
Dear Dimitry,

can you attach the log/compile_yambo.log file?

Best,
Daniele

Re: Compilation error with SLEPc

Posted: Sun Oct 06, 2024 1:40 am
by DmitrySkachkov
Dear Daniele,

Here is the log file

Re: Compilation error with SLEPc

Posted: Sun Oct 06, 2024 3:12 am
by DmitrySkachkov
Hi Daniele,

I also tried another cluster to compile with SLEPc, but got another error:

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mod_interfaces.F(11): #error: can't find include file: petsc/finclude/petscsys.h
mod_interfaces.F(12): #error: can't find include file: petsc/finclude/petscvec.h
mod_interfaces.F(13): #error: can't find include file: petsc/finclude/petscmat.h
mod_interfaces.F(14): #error: can't find include file: slepc/finclude/slepcsys.h
mod_interfaces.F(15): #error: can't find include file: slepc/finclude/slepceps.h
mod_interfaces.F(154): #error: can't find include file: petsc/finclude/petscsys.h
mod_interfaces.F(155): #error: can't find include file: petsc/finclude/petscmat.h
make[2]: *** [/p/home/dmitrysk/yambo-5.2.1/config/mk/local/rules.mk:15: mod_interfaces.o] Error 7
\t[driver] yambo (setup)
yambo linking failed. Check log/compile_yambo.log
make[1]: *** [config/mk/global/actions/compile_yambo.mk:44: yambo] Error 1
yambo build failed

Re: Compilation error with SLEPc

Posted: Mon Oct 07, 2024 9:20 am
by Davide Sangalli
Dear Dimitry,
probably the fail is due to a previous fail in compiling either the petsc or the slepc library.

Check the content of the files

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log/configure_petsc*.log
log/compile_petsc*.log
log/configure_slepc*.log
log/compile_slepc*.log
Notice that the automatic compilation of slepc and petsc is a fallback. Especially in clusters, it is suggested to link available libraries. Check with the cluster admin if they have slpc and petsc with support for complex numbers.

Last, please use yambo 5.2.3, not 5.2.1 (e.g. always use the latest available patch level):
https://github.com/yambo-code/yambo/wik ... gz-format)

Best,
D.