Yambo compilation error on lonestar 6 super computer

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
Post Reply
ndimakis
Posts: 2
Joined: Tue Aug 02, 2022 6:18 am

Yambo compilation error on lonestar 6 super computer

Post by ndimakis » Tue Aug 02, 2022 10:21 am

Hello

I am trying to compile Yambo at lonestar 6 supercomputer. I get the following errors

Code: Select all

login1.ls6(1032)$ make core
	[yambo] Compilation Precision check
	           to compile in SINGLE
	[lib/qe_pseudo] qe_pseudo (checking work to be done)
	[lib/slatec] slatec (checking work to be done)
	[lib/math77] math77 (checking work to be done)
	[lib/local] local (checking work to be done)
	[lib/yambo/driver/src/interface] interface (checking work to be done)
	[lib/yambo/driver/src/main] main (checking work to be done)
	[lib/yambo/driver/src/options] options (checking work to be done)
	[src/driver] driver (checking work to be done)
	[src/tools] tools (checking work to be done)
	[src/modules] modules (checking work to be done)
	[src/memory] memory (checking work to be done)
	[src/allocations] allocations (checking work to be done)
	[src/matrices] matrices (checking work to be done)
	[src/linear_algebra] linear_algebra (checking work to be done)
	[src/parallel] parallel (checking work to be done)
	[src/parser] parser (checking work to be done)
	[src/communicate] communicate (checking work to be done)
	[src/output] output (checking work to be done)
	[src/common] common (checking work to be done)
	[src/timing] timing (checking work to be done)
	[src/Yio] Yio (checking work to be done)
	[src/io] io (checking work to be done)
	[src/io_parallel] io_parallel (checking work to be done)
	[src/xc_functionals] xc_functionals (checking work to be done)
	[src/interface] interface (checking work to be done)
	[src/stop_and_restart] stop_and_restart (checking work to be done)
	[src/wf_and_fft] wf_and_fft (checking work to be done)
	[src/bz_ops] bz_ops (checking work to be done)
	[src/coulomb] coulomb (checking work to be done)
	[src/interpolate] interpolate (checking work to be done)
	[src/qp_control] qp_control (checking work to be done)
	[src/setup] setup (checking work to be done)
	[src/tddft] tddft (checking work to be done)
	[src/dipoles] dipoles (checking work to be done)
	[src/pol_function] pol_function (checking work to be done)
	[src/qp] qp (checking work to be done)
	[src/acfdt] acfdt (checking work to be done)
	[src/bse] bse (checking work to be done)
make[2]: *** [/scratch/00657/dimakis/yambo/config/mk/local/rules.mk:9: mod_pseudo.o] Error 1
	[driver] yambo (checking work to be done)
yambo linking failed. Check log/compile_yambo.log
make[1]: *** [config/mk/global/actions/compile_yambo.mk:42: yambo] Error 1
yambo build failed
However, make libs works

Code: Select all

login1.ls6(1033)$ make libs
	[lib/qe_pseudo] qe_pseudo (checking work to be done)
	[lib/slatec] slatec (checking work to be done)
	[lib/math77] math77 (checking work to be done)
	[lib/local] local (checking work to be done)
My ./configure is shown below

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login1.ls6(1034)$ ./configure -enable-hdf5-par-io --with-lapack-libs="-L$MKLROOT -lmkl_intel_lp64  -lmkl_sequential -lmkl_core " -with-scalapack-libs="-L$MKLROOT -lmkl_scalapack_lp64 "  --enable-open-mp --with-fft-libs="-mkl"

#
# [VER] 5.1
#
# 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] /scratch/00657/dimakis/yambo
# [BRN] master
# [CMP] /scratch/00657/dimakis/yambo
# [TGT] /scratch/00657/dimakis/yambo
# [BIN] /scratch/00657/dimakis/yambo/bin
# [LIB] /scratch/00657/dimakis/yambo/lib/external
#
# [EDITOR] vim
# [ MAKE ] make
#
# [-] Double precision
# [X] Keep object files
# [X] Run-Time timing profile 
# [-] Run-Time memory profile 
#
# - SCRIPTS -
#
# [-] YDB: Yambo DataBase
# [-] YAMBOpy: Yambo Python scripts
# 
# - PARALLEL/CUDA SUPPORT -
#
# [-] CUDA
# [E] MPI
# [X] OpenMP
# 
# - I/O -
#
# [X]: Parallel I/O (via HDF5)
# [I]: HDF5 Parallel_lib
# [I]: NETCDF Large Files Support enabled, Version 4
# [-]: Parallel NETCDF 
# [X]: Parallel HDF5 NO Data Compression
# 
# - LIBRARIES - 
#
# [-] FUTILE  :  
#                  
# [-] YAML    :  
#                  
# [I] IOTK    : /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/lib/libiotk.a (QE hdf5-support)
#                 -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/include/
# [-] ETSF_IO :  
#                  
# [I] NETCDF  : /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/lib/libnetcdff.a /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/lib/libnetcdf.a 
#                 -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/include -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/include 
# [I] HDF5    : /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/lib/libhdf5_hl_fortran.a /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/lib/libhdf5_fortran.a /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/lib/libhdf5_hl.a /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/lib/libhdf5.a -lz -lm -ldl -lcurl
#                 -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/include
#
# > MATH: (FFTW MKL) 
#
# [E] FFT       : -mkl
#                 
# [E] BLAS      : -L/opt/intel/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread -lm
# [E] LAPACK    : -L/opt/intel/compilers_and_libraries_2020.1.217/linux/mkl -lmkl_intel_lp64  -lmkl_sequential -lmkl_core 
# [-] SCALAPACK :  
# [-] BLACS     : 
# [-] PETSC     :  
#                  
# [-] SLEPC     :  
#                  
#
# > OTHERs
#
# [I] LibXC     : /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/lib/libxcf90.a /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/lib/libxcf03.a  /scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/lib/libxc.a
#                 -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/include
# [E] MPI       : -L/opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -lmpifort -lmpi -ldl -lrt -lpthread 
#                 -I/opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/include 
#
# - COMPILERS -
#
# FC kind = gfortran GNU Fortran (GCC) 9.4.0
# MPI kind= Intel(R) MPI Library 2019 Update 9 for Linux* OS
#
# [ CPP ] gcc -E -P -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP     -D_OPENMP -D_TIMING     -D_P2Y_QEXSD_HDF5
# [ FPP ] gfortran -E -P -cpp -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP     -D_OPENMP -D_TIMING    
# [ CC  ] mpiicc -O2 -D_C_US -D_FORTRAN_US
# [ FC  ] mpiifort -O3 -g -mtune=native  -fopenmp 
# [ FCUF] -O0 -g -mtune=native 
# [ F77 ] mpiifort -O3 -g -mtune=native 
# [ F77U] -O0 -g -mtune=native 
# [Cmain] 
#
# You can modify compilers and flags by editing the file "config/setup"
#
The compile_yambo.log file is shown below

Code: Select all

login1.ls6(1041)$ more compile_yambo.log 
gfortran -E -P -cpp -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP -D_OPENMP -D_TIMING -D_linux -I/scratch/00657/dimakis/yambo/include -I/scratch/0065
7/dimakis/yambo/include/headers/common -I/scratch/00657/dimakis/yambo/include/headers/parser -I/scratch/00657/dimakis/yambo/lib/yambo/driver/include -I/scratch/006
57/dimakis/yambo/include/driver -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/include/  -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifo
rt/v4/parallel/include -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/include   -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpi
ifort/v4/parallel/include -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/include    -I/scratch/00657/dimakis/yambo/lib/yambo/driver/include -I/scrat
ch/00657/dimakis/yambo/include/driver /scratch/00657/dimakis/yambo/src/modules/mod_pseudo.F >> mod_pseudo.tmp_source
mpiifort -c -O3 -g -mtune=native   -fopenmp  -I/scratch/00657/dimakis/yambo/include -I/scratch/00657/dimakis/yambo/include/headers/common -I/scratch/00657/dimakis/
yambo/include/headers/parser -I/scratch/00657/dimakis/yambo/lib/yambo/driver/include -I/scratch/00657/dimakis/yambo/include/driver -I/scratch/00657/dimakis/yambo/l
ib/external/gfortran/mpiifort/include/  -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/include -I/scratch/00657/dimakis/yambo/lib/extern
al/gfortran/mpiifort/v4/parallel/include   -I/scratch/00657/dimakis/yambo/lib/external/gfortran/mpiifort/v4/parallel/include -I/scratch/00657/dimakis/yambo/lib/ext
ernal/gfortran/mpiifort/include    -I/scratch/00657/dimakis/yambo/lib/yambo/driver/include -I/scratch/00657/dimakis/yambo/include/driver mod_pseudo.f90
mod_pseudo.f90(32): error #7013: This module file was not generated by any release of this compiler.   [QE_PSEUDO_M]
 use qe_pseudo_m, ONLY:qe_pseudo_deallocate, qe_pseudo_allocate,&
-----^
mod_pseudo.f90(107): error #6406: Conflicting attributes or multiple declaration of name.   [BEC_TYPE]
 type(bec_type), allocatable:: becp(:,:)
------^
mod_pseudo.f90(32): error #6580: Name in only-list does not exist or is not accessible.   [QE_PSEUDO_DEALLOCATE]
 use qe_pseudo_m, ONLY:qe_pseudo_deallocate, qe_pseudo_allocate,&
-----------------------^
mod_pseudo.f90(32): error #6580: Name in only-list does not exist or is not accessible.   [QE_PSEUDO_ALLOCATE]
 use qe_pseudo_m, ONLY:qe_pseudo_deallocate, qe_pseudo_allocate,&
---------------------------------------------^
mod_pseudo.f90(33): error #6580: Name in only-list does not exist or is not accessible.   [BEC_TYPE]
&                      bec_type, deallocate_bec_type
-----------------------^
mod_pseudo.f90(33): error #6580: Name in only-list does not exist or is not accessible.   [DEALLOCATE_BEC_TYPE]
&                      bec_type, deallocate_bec_type
---------------------------------^
mod_pseudo.f90(35): error #6580: Name in only-list does not exist or is not accessible.   [MEM_ERR]
 use memory,     ONLY:MEM_err,MEM_msg,MEM_count,MEM_global_mesg,IPL
----------------------^
mod_pseudo.f90(35): error #6580: Name in only-list does not exist or is not accessible.   [MEM_MSG]
 use memory,     ONLY:MEM_err,MEM_msg,MEM_count,MEM_global_mesg,IPL
------------------------------^
mod_pseudo.f90(35): error #6580: Name in only-list does not exist or is not accessible.   [MEM_COUNT]
 use memory,     ONLY:MEM_err,MEM_msg,MEM_count,MEM_global_mesg,IPL
--------------------------------------^
mod_pseudo.f90(35): error #6580: Name in only-list does not exist or is not accessible.   [MEM_GLOBAL_MESG]
 use memory,     ONLY:MEM_err,MEM_msg,MEM_count,MEM_global_mesg,IPL
------------------------------------------------^
mod_pseudo.f90(35): error #6580: Name in only-list does not exist or is not accessible.   [IPL]
 use memory,     ONLY:MEM_err,MEM_msg,MEM_count,MEM_global_mesg,IPL
----------------------------------------------------------------^
mod_pseudo.f90(119): error #6404: This name does not have a type, and must have an explicit type.   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(119): error #6385: The highest data type rank permitted is INTEGER(KIND=8).   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(119): error #6404: This name does not have a type, and must have an explicit type.   [MEM_MSG]
 & stat=MEM_err,errmsg=MEM_msg)
-----------------------^
mod_pseudo.f90(125): error #6385: The highest data type rank permitted is INTEGER(KIND=8).   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(131): error #6385: The highest data type rank permitted is INTEGER(KIND=8).   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(145): error #6385: The highest data type rank permitted is INTEGER(KIND=8).   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(147): error #6406: Conflicting attributes or multiple declaration of name.   [MEM_COUNT]
 & call MEM_count("pp_kbs",pp_kbs)
--------^
mod_pseudo.f90(151): error #6385: The highest data type rank permitted is INTEGER(KIND=8).   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(153): error #6406: Conflicting attributes or multiple declaration of name.   [MEM_COUNT]
 & call MEM_count("pp_kb",pp_kb)
--------^
mod_pseudo.f90(157): error #6385: The highest data type rank permitted is INTEGER(KIND=8).   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(159): error #6406: Conflicting attributes or multiple declaration of name.   [MEM_COUNT]
 & call MEM_count("pp_kbd",pp_kbd)
--------^
mod_pseudo.f90(171): error #6385: The highest data type rank permitted is INTEGER(KIND=8).   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(173): error #6406: Conflicting attributes or multiple declaration of name.   [MEM_COUNT]
 & call MEM_count("pp_kbs",pp_kbs)
--------^
mod_pseudo.f90(177): error #6385: The highest data type rank permitted is INTEGER(KIND=8).   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(179): error #6406: Conflicting attributes or multiple declaration of name.   [MEM_COUNT]
 & call MEM_count("pp_kb",pp_kb)
--------^
mod_pseudo.f90(183): error #6385: The highest data type rank permitted is INTEGER(KIND=8).   [MEM_ERR]
 & stat=MEM_err,errmsg=MEM_msg)
--------^
mod_pseudo.f90(185): error #6406: Conflicting attributes or multiple declaration of name.   [MEM_COUNT]
 & call MEM_count("pp_kbd",pp_kbd)
--------^
mod_pseudo.f90(195): error #6683: A kind type parameter must be a compile-time constant.   [IPL]
 & call MEM_free("pp_kbs_old",int(-1,KIND=IPL))
------------------------------------------^
mod_pseudo.f90(195): warning #7319: This argument's data type is incompatible with this intrinsic procedure; procedure assumed EXTERNAL.   [INT]
 & call MEM_free("pp_kbs_old",int(-1,KIND=IPL))
------------------------------------------^
mod_pseudo.f90(195): error #6404: This name does not have a type, and must have an explicit type.   [INT]
 & call MEM_free("pp_kbs_old",int(-1,KIND=IPL))
------------------------------^
mod_pseudo.f90(314): catastrophic error: Too many errors, exiting
compilation aborted for mod_pseudo.f90 (code 1)
Thank you,

Nick

User avatar
Nicola Spallanzani
Posts: 62
Joined: Thu Nov 21, 2019 10:15 am

Re: Yambo compilation error on lonestar 6 super computer

Post by Nicola Spallanzani » Tue Aug 02, 2022 11:18 am

Dear Nick,
try to set these variables before the configure:

Code: Select all

export FC=ifort 
export F77=ifort
export CPP="icc -E -ansi"
export CC=icc 
export FPP="fpp -free -P"
export F90SUFFIX=".f90"
export MPIFC=mpiifort
export MPIF77=mpiifort
export MPICC=mpiicc
export MPICXX=mpiicpc
But please, delete the folder that you are using in order to be sure to restart the compilation from scratch.

Best regards,
Nicola
Nicola Spallanzani, PhD
S3 Centre, Istituto Nanoscienze CNR and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu

ndimakis
Posts: 2
Joined: Tue Aug 02, 2022 6:18 am

Re: Yambo compilation error on lonestar 6 super computer

Post by ndimakis » Tue Aug 02, 2022 12:37 pm

Hello

Thank you for your email. I still have errors such as

Code: Select all

login2.ls6(1037)$ make libs
	[lib/qe_pseudo] qe_pseudo (checking work to be done)
make[2]: *** [/scratch/00657/dimakis/yambo-5.1.1/config/mk/local/rules.mk:9: atom.o] Error 1
atom.f90(14): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [RADIAL_GRIDS]
atom.f90(14): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [RADIAL_GRIDS]
	[lib/slatec] slatec (checking work to be done)
	[lib/math77] math77 (checking work to be done)
	[lib/local] local (checking work to be done)
login2.ls6(1038)$ make core
	[yambo] Compilation Precision check
	           to compile in SINGLE
	[SETUP] Modules detection [ ################################################################ ] 63/63  
	[SETUP] Dependencies [ ################################################################ ] 63/63  
	[lib/qe_pseudo] qe_pseudo (checking work to be done)
	[lib/qe_pseudo] kind
	[lib/qe_pseudo] constants
	[lib/qe_pseudo] radial_grids
	[lib/qe_pseudo] atom
	[lib/qe_pseudo] parameters
	[lib/qe_pseudo] qe_auxdata
	[lib/qe_pseudo] recvec
	[lib/qe_pseudo] becmod
	[lib/qe_pseudo] pseudo_types
	[lib/qe_pseudo] spin_orb
	[lib/qe_pseudo] invmat
	[lib/qe_pseudo] uspp
	[lib/qe_pseudo] s_psi
	[lib/qe_pseudo] us_module
	[lib/qe_pseudo] init_us_1
	[lib/qe_pseudo] init_us_2
	[lib/qe_pseudo] ylmr2
	[lib/qe_pseudo] simpsn
	[lib/qe_pseudo] upf_to_internal
	[lib/qe_pseudo] read_upf_v1
	[lib/qe_pseudo] read_upf_v2
	[lib/qe_pseudo] upf
	[lib/qe_pseudo] read_uspp
	[lib/qe_pseudo] read_pseudo
	[lib/qe_pseudo] read_ncpp
	[lib/qe_pseudo] struct_fact
	[lib/qe_pseudo] sph_ind
	[lib/qe_pseudo] spinor
	[lib/qe_pseudo] sph_bes
	[lib/qe_pseudo] qvan2
	[lib/qe_pseudo] setqf
	[lib/qe_pseudo] matches
	[lib/qe_pseudo] erf
	[lib/qe_pseudo] allocate_nlpot
	[lib/qe_pseudo] init_run
	[lib/qe_pseudo] qe_pseudo_module
	[lib/qe_pseudo] qe_errore
	[lib/qe_pseudo] addusdens
	[lib/qe_pseudo] sum_bec
	[lib/qe_pseudo] d_matrix
	[lib/qe_pseudo] libqe_pseudo.a (lib)
	[lib/slatec] slatec (checking work to be done)
	[lib/math77] math77 (checking work to be done)
	[lib/local] local (checking work to be done)
	[lib/yambo/driver/src/interface] interface (checking work to be done)
	[lib/yambo/driver/src/main] main (checking work to be done)
	[lib/yambo/driver/src/options] options (checking work to be done)
	[lib/yambo/driver/src/interface] get_running_tool
	[lib/yambo/driver/src/interface] get_running_project
	[lib/yambo/driver/src/interface] get_runlevel
	[lib/yambo/driver/src/interface] get_libraries
	[lib/yambo/driver/src/interface] get_version
	[lib/yambo/driver/src/interface] mod_C_driver
	[lib/yambo/driver/src/interface] C_driver_transfer
	[lib/yambo/driver/src/interface] libyambo_Ydriver_interface.a (lib)
	[lib/yambo/driver/src/main] launcher
	[lib/yambo/driver/src/main] command_line
	[lib/yambo/driver/src/main] input_file
	[lib/yambo/driver/src/main] load_environments
	[lib/yambo/driver/src/main] options_maker
	[lib/yambo/driver/src/main] title
	[lib/yambo/driver/src/main] tool_init
	[lib/yambo/driver/src/main] usage
	[lib/yambo/driver/src/main] use_me
	[lib/yambo/driver/src/main] libyambo_Ydriver_main.a (lib)
	[lib/yambo/driver/src/options] options_help
	[lib/yambo/driver/src/options] libyambo_Ydriver_options.a (lib)
	[src/driver] driver (checking work to be done)
	[src/tools] tools (checking work to be done)
	[src/modules] modules (checking work to be done)
	[src/memory] memory (checking work to be done)
	[src/matrices] matrices (checking work to be done)
	[src/linear_algebra] linear_algebra (checking work to be done)
	[src/parallel] parallel (checking work to be done)
	[src/parser] parser (checking work to be done)
	[src/communicate] communicate (checking work to be done)
	[src/common] common (checking work to be done)
	[src/timing] timing (checking work to be done)
	[src/Yio] Yio (checking work to be done)
	[src/io] io (checking work to be done)
	[src/xc_functionals] xc_functionals (checking work to be done)
	[src/interface] interface (checking work to be done)
	[src/stop_and_restart] stop_and_restart (checking work to be done)
	[src/wf_and_fft] wf_and_fft (checking work to be done)
	[src/bz_ops] bz_ops (checking work to be done)
	[src/coulomb] coulomb (checking work to be done)
	[src/interpolate] interpolate (checking work to be done)
	[src/qp_control] qp_control (checking work to be done)
	[src/setup] setup (checking work to be done)
	[src/tddft] tddft (checking work to be done)
	[src/dipoles] dipoles (checking work to be done)
	[src/pol_function] pol_function (checking work to be done)
	[src/qp] qp (checking work to be done)
	[src/acfdt] acfdt (checking work to be done)
	[src/bse] bse (checking work to be done)
	[src/driver] options_control
	[src/driver] options_interfaces
	[src/driver] options_projects
	[src/driver] options_yambo
	[src/driver] options_ypp
	[src/driver] libdriver.a (lib)
	[src/tools] ct_cptimer
	[src/tools] c_printing
	[src/tools] io
	[src/tools] stack
	[src/tools] memstat
	[src/tools] libtools.a (lib)
	[src/modules] mod_pars
	[src/modules] mod_units
	[src/modules] mod_lexical_sort
	[src/modules] mod_stderr
	[src/modules] mod_openmp
	[src/modules] mod_memory
	[src/modules] mod_parallel
	[src/modules] mod_com_interfcs
	[src/modules] mod_electrons
	[src/modules] mod_com
	[src/modules] mod_cusolverdn_y
	[src/modules] mod_cuda
	[src/modules] mod_matrix_operate
	[src/modules] mod_D_lattice
	[src/modules] mod_descriptors
	[src/modules] mod_R_lattice
	[src/modules] mod_DIPOLES
	[src/modules] mod_matrix
	[src/modules] mod_X
	[src/modules] mod_parallel_interface
	[src/modules] mod_SLK
	[src/modules] mod_drivers
	[src/modules] mod_linear_algebra
	[src/modules] mod_wrapper
	[src/modules] mod_wrapper_omp
	[src/modules] mod_FFT
	[src/modules] mod_LIVE_t
	[src/modules] mod_logo
	[src/modules] mod_cutoff_ws
	[src/modules] mod_timing
	[src/modules] mod_wave_func
	[src/modules] mod_xc_functionals
	[src/modules] mod_global_XC
	[src/modules] mod_frequency
	[src/modules] mod_vec_operate
	[src/modules] mod_functions
	[src/modules] mod_zeros
	[src/modules] mod_atom_proj
	[src/modules] mod_pseudo
	[src/modules] mod_QP
	[src/modules] mod_collision_el
	[src/modules] mod_BS
	[src/modules] mod_BS_solvers
	[src/modules] mod_QP_CTL
	[src/modules] mod_TDDFT
	[src/modules] mod_ACFDT
	[src/modules] mod_MAGNONS
	[src/modules] mod_DICHROISM
	[src/modules] mod_PHOTOLUM
	[src/modules] mod_IO_interfaces
	[src/modules] mod_IO
	[src/modules] mod_ELPH
	[src/modules] mod_PHEL
	[src/modules] mod_interfaces
	[src/modules] mod_X_output
	[src/modules] mod_OUTPUT_simple
	[src/modules] mod_POL_FIT
	[src/modules] mod_RT_lifetimes
	[src/modules] mod_RT_occupations
	[src/modules] mod_real_time
	[src/modules] mod_hamiltonian
	[src/modules] mod_debug
	[src/modules] mod_interpolate
	[src/modules] mod_interpolate_tools
	[src/modules] SET_logicals
	[src/modules] mod_RT_control
	[src/modules] mod_RT_output
	[src/modules] mod_SC
	[src/modules] mod_collision_ext
	[src/modules] mod_electric
	[src/modules] mod_fields
	[src/modules] mod_magnetic
	[src/modules] mod_nl_optics
	[src/modules] mod_plasma
	[src/modules] SET_defaults
	[src/modules] libmodules.a (lib)
	[src/memory] MEM_defaults
	[src/memory] MEM_manager_init
	[src/memory] MEM_library
	[src/memory] MEM_bits
	[src/memory] MEM_report
	[src/memory] MEM_treshold_estimate
	[src/memory] MEM_error
	[src/memory] MEM_free
	[src/memory] MEM_global_mesg
	[src/memory] MEM_manager_alloc
	[src/memory] MEM_manager_messages
	[src/memory] libmemory.a (lib)
	[src/matrices] MATRIX_init
	[src/matrices] MATRIX_duplicate
	[src/matrices] MATRIX_transfer_side_crop
	[src/matrices] MATRIX_BSE_to_PAR
	[src/matrices] MATRIX_PAR_to_from_PAR
	[src/matrices] MATRIX_transfer
	[src/matrices] libmatrices.a (lib)
	[src/linear_algebra] LINEAR_ALGEBRA_driver
	[src/linear_algebra] SERIAL_SVD_inversion
	[src/linear_algebra] SERIAL_inversion
	[src/linear_algebra] SERIAL_diagonalization
	[src/linear_algebra] SERIAL_HERMITIAN_diagonalization
	[src/linear_algebra] SERIAL_lin_system
	[src/linear_algebra] liblinear_algebra.a (lib)
	[src/parallel] check_for_a_redundant_IO
	[src/parallel] PARALLEL_live_message
	[src/parallel] PARALLEL_set_the_active_structures
	[src/parallel] PARALLEL_check_phase_space
	[src/parallel] PARALLEL_Transitions_grouping
	[src/parallel] PARALLEL_add_Q_to_K_list
	[src/parallel] PARALLEL_minimal_index_from_overlaping
	[src/parallel] PARALLEL_get_ENVIRONMENT_structure
	[src/parallel] PARALLEL_get_user_structure
	[src/parallel] PARALLEL_assign_chains_and_COMMs
	[src/parallel] SLK_communicators
	[src/parallel] PARALLEL_scheme_initialize
	[src/parallel] PARALLEL_SETUP_K_scheme
	[src/parallel] PARALLEL_PAR_to_PAR_comms_init
	[src/parallel] PARALLEL_assign_LA_COMMs
	[src/parallel] PARALLEL_WF_index
	[src/parallel] PARALLEL_SND_RCV_plan
	[src/parallel] PARALLEL_structure
	[src/parallel] PARALLEL_build_up_child_INTER_chains
	[src/parallel] PARALLEL_distribute_BZk_using_IBZk
	[src/parallel] PARALLEL_MATRIX_distribute
	[src/parallel] PARALLEL_global_BZINDX
	[src/parallel] PARALLEL_global_defaults
	[src/parallel] PARALLEL_global_reset
	[src/parallel] PARALLEL_global_dimensions
	[src/parallel] PARALLEL_global_ScaLapacK
	[src/parallel] PARALLEL_global_Response_G
	[src/parallel] PARALLEL_global_Self_Energy
	[src/parallel] PARALLEL_global_Response_T
	[src/parallel] PARALLEL_global_Response_IO
	[src/parallel] PARALLEL_global_DIPOLES
	[src/parallel] PARALLEL_global_indexes
	[src/parallel] PARALLEL_index
	[src/parallel] PARALLEL_WF_distribute
	[src/parallel] PARALLEL_Haydock_VEC_COMMs
	[src/parallel] PARALLEL_FREQS_setup
	[src/parallel] libparallel.a (lib)
	[src/parser] PARSER_math
	[src/parser] PARSER_interface
	[src/parser] PARSER
	[src/parser] PARSER_exp
	[src/parser] PARSER_symbols
	[src/parser] PARSER_lib
	[src/parser] mod_parser_m
	[src/parser] mod_itm
	[src/parser] mod_it_tools
	[src/parser] PARSER_close_G
	[src/parser] PARSER_convert_INT
	[src/parser] PARSER_convert_REAL
	[src/parser] PARSER_array
	[src/parser] PARSER_dump_the_additional_lines
	[src/parser] initinfio
	[src/parser] initactivate
	[src/parser] initverbosity
	[src/parser] libparser.a (lib)
	[src/communicate] acknowledge_yambo
	[src/communicate] REPORT_Occupations
	[src/communicate] section
	[src/communicate] REPORT_Energies
	[src/communicate] com_compose_msg
	[src/communicate] com_utilities_subroutines
	[src/communicate] com_utilities_functions
	[src/communicate] com_utilities_netcdf
	[src/communicate] msg_manager
	[src/communicate] msg_characters_vector_int
	[src/communicate] msg_integers_vector_int
	[src/communicate] msg_reals_vector_int
	[src/communicate] DESC_write
	[src/communicate] OUTPUT_unit_conversion
	[src/communicate] OUTPUT_add_column
	[src/communicate] libcommunicate.a (lib)
	[src/common] eval_G_minus_G
	[src/common] G_rot_grid
	[src/common] G_index
	[src/common] G_index_energy_factor
	[src/common] eval_Gradient
	[src/common] FREQUENCIES_damping
	[src/common] FREQUENCIES_setup
	[src/common] FREQUENCIES_coarse_grid
	[src/common] FREQUENCIES_Green_Function
	[src/common] FREQUENCIES_reset
	[src/common] FREQUENCIES_set_reference_point
	[src/common] FREQUENCIES_merge
	[src/common] Kramers_Kronig
	[src/common] Convolve
	[src/common] RIntegrate
	[src/common] Laplace_transform
	[src/common] CIntegrate
	[src/common] QPartilize
	[src/common] Lorentzian_FT
	[src/common] OCCUPATIONS_Fermi
	[src/common] OCCUPATIONS_Extend
	[src/common] OCCUPATIONS_Gaps
	[src/common] OCCUPATIONS_Extend_Double_Grid
	[src/common] LEVELS_respect_degenerations
	[src/common] crystal_lattice
	[src/common] QP_state_print
	[src/common] QP_state_group
	[src/common] spline_fit
	[src/common] OBS_rotate
	[src/common] device_memcpy
	[src/common] device_memcpy_mod
	[src/common] device_auxfunc
	[src/common] device_auxfunc_mod
	[src/common] device_fbuff
	[src/common] device_fbuff_mod
	[src/common] deviceXlib_mod
	[src/common] libcommon.a (lib)
	[src/timing] TIMING_clock_write
	[src/timing] TIMING_overview
mv: cannot move 'libtiming.a' to '/scratch/00657/dimakis/yambo-5.1.1/lib/libtiming.a': Device or resource busy
make[2]: *** [/scratch/00657/dimakis/yambo-5.1.1/config/mk/local/operations.mk:9: lib] Error 1
	[driver] yambo (checking work to be done)
yambo linking failed. Check log/compile_yambo.log
make[1]: *** [config/mk/global/actions/compile_yambo.mk:42: yambo] Error 1
yambo build failed
My ./configure was as follows

Code: Select all

login2.ls6(1039)$ ./configure -enable-hdf5-par-io --with-lapack-libs="-L$MKLROOT -lmkl_intel_lp64  -lmkl_sequential -lmkl_core " -with-scalapack-libs="-L$MKLROOT -lmkl_scalapack_lp64 "  --enable-open-mp --with-fft-libs="-mkl"

# [VER] 5.1
#
# 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] /scratch/00657/dimakis/yambo-5.1.1
# [BRN] 
# [CMP] /scratch/00657/dimakis/yambo-5.1.1
# [TGT] /scratch/00657/dimakis/yambo-5.1.1
# [BIN] /scratch/00657/dimakis/yambo-5.1.1/bin
# [LIB] /scratch/00657/dimakis/yambo-5.1.1/lib/external
#
# [EDITOR] vim
# [ MAKE ] make
#
# [-] Double precision
# [X] Keep object files
# [X] Run-Time timing profile 
# [-] Run-Time memory profile 
#
# - SCRIPTS -
#
# [-] YDB: Yambo DataBase
# [-] YAMBOpy: Yambo Python scripts
# 
# - PARALLEL/CUDA SUPPORT -
#
# [-] CUDA
# [E] MPI
# [X] OpenMP
# 
# - I/O -
#
# [X]: Parallel I/O (via HDF5)
# [I]: HDF5 Parallel_lib
# [I]: NETCDF Large Files Support enabled, Version 4
# [-]: Parallel NETCDF 
# [X]: Parallel HDF5 NO Data Compression
# 
# - LIBRARIES - 
#
# [-] FUTILE  :  
#                  
# [-] YAML    :  
#                  
# [I] IOTK    : /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/lib/libiotk.a (QE hdf5-support)
#                 -I/scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/include/
# [-] ETSF_IO :  
#                  
# [I] NETCDF  : /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/lib/libnetcdff.a /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/lib/libnetcdf.a 
#                 -I/scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/include -I/scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/include 
# [I] HDF5    : /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/lib/libhdf5_hl_fortran.a /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/lib/libhdf5_fortran.a /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/lib/libhdf5_hl.a /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/lib/libhdf5.a -lz -lm -ldl -lcurl
#                 -I/scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/include
#
# > MATH: (FFTW MKL) 
#
# [E] FFT       : -mkl
#                 
# [E] BLAS      : -L/opt/intel/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm
# [E] LAPACK    : -L/opt/intel/compilers_and_libraries_2020.1.217/linux/mkl -lmkl_intel_lp64  -lmkl_sequential -lmkl_core 
# [-] SCALAPACK :  
# [-] BLACS     : 
# [-] PETSC     :  
#                  
# [-] SLEPC     :  
#                  
#
# > OTHERs
#
# [I] LibXC     : /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/lib/libxcf90.a /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/lib/libxcf03.a  /scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/lib/libxc.a
#                 -I/scratch/00657/dimakis/yambo-5.1.1/lib/external/intel/mpiifort/include
# [E] MPI       : -L/opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release -Xlinker -rpath -Xlinker /opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib -lmpifort -lmpi -ldl -lrt -lpthread 
#                 -I/opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/include 
#
# - COMPILERS -
#
# FC kind = intel ifort version 19.1.1.217
# MPI kind= Intel(R) MPI Library 2019 Update 9 for Linux* OS
#
# [ CPP ] icc -E -ansi -ansi -D_HDF5_LIB -D_HDF5_IO -D_PAR_IO -D_MPI -D_FFTW -D_FFTW_OMP     -D_OPENMP -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_OPENMP -D_TIMING    
# [ CC  ] mpiicc -O2 -std=gnu99 -no-multibyte-chars -D_C_US -D_FORTRAN_US
# [ FC  ] mpiifort -assume bscc -O3 -g -ip    -qopenmp 
# [ FCUF] -assume bscc -O0 -g   
# [ F77 ] mpiifort -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"
#
login2.ls6(1040)$ 
I haver used the following before calling ./configure

Code: Select all

login2.ls6(1025)$ export FC=ifort 
login2.ls6(1026)$ export F77=ifort
login2.ls6(1027)$ export CPP="icc -E -ansi"
login2.ls6(1028)$ export CC=icc 
login2.ls6(1029)$ export FPP="fpp -free -P"
login2.ls6(1030)$ 
login2.ls6(1030)$ 
login2.ls6(1030)$ 
login2.ls6(1030)$ export F90SUFFIX=".f90"
login2.ls6(1031)$ export MPIFC=mpiifort
login2.ls6(1032)$ export MPIF77=mpiifort
login2.ls6(1033)$ export MPICC=mpiicc
login2.ls6(1034)$ export MPICXX=mpiicpc
Thanks-Nick
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User avatar
Nicola Spallanzani
Posts: 62
Joined: Thu Nov 21, 2019 10:15 am

Re: Yambo compilation error on lonestar 6 super computer

Post by Nicola Spallanzani » Mon Aug 08, 2022 6:54 pm

Dear Nick,
try also this configure:

Code: Select all

export FC=ifort 
export F77=ifort
export CPP="icc -E -ansi"
export CC=icc 
export FPP="fpp -free -P"
export F90SUFFIX=".f90"
export MPIFC=mpiifort
export MPIF77=mpiifort
export MPICC=mpiicc
export MPICXX=mpiicpc

./configure \
    --enable-open-mp --enable-mpi --enable-hdf5-par-io \
    --enable-msgs-comps --enable-time-profile --enable-memory-profile \
    --with-blas-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
    --with-lapack-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
    --with-scalapack-libs="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64" \
    --with-blacs-libs="-L${MKLROOT}/lib/intel64 -lmkl_blacs_intelmpi_lp64" \
    --with-fft-includedir="${MKLROOT}/include" \
    --with-fft-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
    --with-extlibs-path=${HOME}/opt/yambo-ext-libs

make -j4 core
Best,
Nicola
Nicola Spallanzani, PhD
S3 Centre, Istituto Nanoscienze CNR and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu

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