Compilation error with SLEPc

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? Problems in GPU architectures? This is the place to look.

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If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
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DmitrySkachkov
Posts: 9
Joined: Mon Dec 13, 2021 8:52 pm
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Compilation error with SLEPc

Post by DmitrySkachkov » Thu Oct 03, 2024 9:55 pm

Hello,

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

Code: Select all

./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:

Code: Select all

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:

Code: Select all

#
# [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
Dmitry Skachkov
University of Central Florida
https://github.com/Dmitry-Skachkov

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Daniele Varsano
Posts: 4003
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Compilation error with SLEPc

Post by Daniele Varsano » Fri Oct 04, 2024 4:44 pm

Dear Dimitry,

can you attach the log/compile_yambo.log file?

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

DmitrySkachkov
Posts: 9
Joined: Mon Dec 13, 2021 8:52 pm
Contact:

Re: Compilation error with SLEPc

Post by DmitrySkachkov » Sun Oct 06, 2024 1:40 am

Dear Daniele,

Here is the log file
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Dmitry Skachkov
University of Central Florida
https://github.com/Dmitry-Skachkov

DmitrySkachkov
Posts: 9
Joined: Mon Dec 13, 2021 8:52 pm
Contact:

Re: Compilation error with SLEPc

Post by DmitrySkachkov » Sun Oct 06, 2024 3:12 am

Hi Daniele,

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

Code: Select all

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
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Dmitry Skachkov
University of Central Florida
https://github.com/Dmitry-Skachkov

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Davide Sangalli
Posts: 622
Joined: Tue May 29, 2012 4:49 pm
Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
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Re: Compilation error with SLEPc

Post by Davide Sangalli » Mon Oct 07, 2024 9:20 am

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

Code: Select all

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.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

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