error while executing make for abinit-9.2.1 on NIC4 cluster  [SOLVED]

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Gang Tang
Posts: 6
Joined: Mon Dec 02, 2019 10:43 am

error while executing make for abinit-9.2.1 on NIC4 cluster  [SOLVED]

Post by Gang Tang » Tue Oct 06, 2020 11:59 pm

Dear All Abinit users,

I have loaded all mandatory libraries for abinit-9.2.1

Code: Select all

module load intel/2018b
module load HDF5/1.10.2-intel-2018b
module load libxc/3.0.1-intel-2018b
module load netCDF/4.6.1-intel-2018b
module load netCDF-Fortran/4.4.4-intel-2018b
module load Wannier90/2.0.1.1-intel-2018b-abinit
and I have used the following file to configure it.

Code: Select all

prefix="/home/ulg/phythema/gtang/software/abinit-9.2.1/build"
FC="mpif90"
CC="mpicc"
CXX="mpicxx"

with_mpi="yes"

with_linalg="yes"
with_linalg_flavor="mkl"
LINALG_CPPFLAGS="-I${MKLROOT}/include"
LINALG_FCFLAGS="-I${MKLROOT}/include"
LINALG_LIBS="-L${MKLROOT}/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group"

with_fft="/home/ulg/phythema/gtang/software/fftw-3.3.8/build"
FFT_CPPFLAGS="-I/home/ulg/phythema/gtang/software/fftw-3.3.8/build/include"
FFT_FCFLAGS="-I/home/ulg/phythema/gtang/software/fftw-3.3.8/build/include"
FFT_LIBS="-L/home/ulg/phythema/gtang/software/fftw-3.3.8/build/lib -lfftw3f -lfftw3"

with_libxc="yes"
LIBXC_CPPFLAGS="-I/home/easybuild/.local/easybuild/software/libxc/3.0.1-intel-2018b/include"
LIBXC_FCFLAGS="-I/home/easybuild/.local/easybuild/software/libxc/3.0.1-intel-2018b/include"
LIBXC_LIBS="-L/home/easybuild/.local/easybuild/software/libxc/3.0.1-intel-2018b/lib -lxcf90 -lxc"

with_hdf5="yes"
HDF5_CPPFLAGS="-I/home/easybuild/.local/easybuild/software/HDF5/1.10.2-intel-2018b/include"
HDF5_FCFLAGS="-I/home/easybuild/.local/easybuild/software/HDF5/1.10.2-intel-2018b/include"
HDF5_LIBS="-L/home/easybuild/.local/easybuild/software/HDF5/1.10.2-intel-2018b/lib -lhdf5 -lhdf5_hl"

with_netcdf="yes"
NETCDF_CPPFLAGS="-I/home/easybuild/.local/easybuild/software/netCDF/4.6.1-intel-2018b/include"
NETCDF_FCFLAGS="-I/home/easybuild/.local/easybuild/software/netCDF/4.6.1-intel-2018b/include"
NETCDF_LIBS="-L/home/easybuild/.local/easybuild/software/netCDF/4.6.1-intel-2018b/lib64 -lnetcdf"

with_netcdf_fortran="/home/ulg/phythema/gtang/software/netcdf-fortran-4.5.2/build"
NETCDF_FORTRAN_CPPFLAGS="-I/home/ulg/phythema/gtang/software/netcdf-fortran-4.5.2/build/include"
NETCDF_FORTRAN_FCFLAGS="-I/home/ulg/phythema/gtang/software/netcdf-fortran-4.5.2/build/include"
NETCDF_FORTRAN_LIBS="-L/home/ulg/phythema/gtang/software/netcdf-fortran-4.5.2/build/lib -lnetcdff"

with_wannier90="yes"
WANNIER90_LIBS="-L/home/easybuild/.local/easybuild/software/Wannier90/2.0.1.1-intel-2018b-abinit/lib -lwannier90"
And the result was the following

Core build parameters
---------------------

* C compiler : gnu version 7.3
* Fortran compiler : gnu version 7.3
* architecture : intel xeon (64 bits)
* debugging : basic
* optimizations : standard

* OpenMP enabled : no (collapse: ignored)
* MPI enabled : yes (flavor: auto)
* MPI in-place : no
* MPI-IO enabled : yes
* GPU enabled : no (flavor: none)

* LibXML2 enabled : no
* LibPSML enabled : no
* XMLF90 enabled : no
* HDF5 enabled : yes (MPI support: no)
* NetCDF enabled : yes (MPI support: no)
* NetCDF-F enabled : yes (MPI support: no)

* FFT flavor : dfti (libs: auto-detected)
* LINALG flavor : mkl (libs: user-defined)

* Build workflow : monolith

0 deprecated options have been used:.

Configuration complete.
You may now type "make" to build Abinit.
(or "make -j<n>", where <n> is the number of available processors)
---------------------

Since the above result came, I proceeded to execute the make command.

I issued the make command, then the following error occurred,
---------------------
make[5]: *** No rule to make target `m_optim_dumper.o', needed by `lib14_hidewrite.a'. Stop.
make[5]: *** Waiting for unfinished jobs....
make[5]: Leaving directory `/home/users/g/t/gtang/software/abinit-9.2.1/build/shared/common/src/14_hidewrite'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/users/g/t/gtang/software/abinit-9.2.1/build/shared/common/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/users/g/t/gtang/software/abinit-9.2.1/build/shared/common'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/users/g/t/gtang/software/abinit-9.2.1/build/shared'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/users/g/t/gtang/software/abinit-9.2.1/build'
make: *** [all] Error 2
---------------------

Can anyone help me with this?
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jbeuken
Posts: 365
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Re: error while executing make for abinit-9.2.1 on NIC4 cluster

Post by jbeuken » Thu Oct 08, 2020 11:02 am

Hi,

these are the modules used :

Code: Select all

module load EasyBuild
module load Python/3.6.6-intel-2018b
module load intel/2018b
module load iimpi/2018b
module load HDF5/1.10.2-intel-2018b
module load libxc/3.0.1-intel-2018b
module load netCDF/4.6.1-intel-2018b
module load netCDF-Fortran/4.4.4-intel-2018b
module load Wannier90/2.0.1.1-intel-2018b-abinit
and this is the config file :

Code: Select all

FC="mpiifort"
CC="mpiicc"
CXX="mpiicpc"

with_mpi="yes"
enable_openmp="no"

CFLAGS="-O2 -g"
CXXFLAGS="-O2 -g"
FCFLAGS="-O2 -g"

# BLAS/LAPACK with MKL
with_linalg_flavor="mkl"
LINAGL_LIBS="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm -ldl"

# FFT from MKL
with_fft_flavor="dfti"

# libxc
with_libxc="${EBROOTLIBXC}"

# hdf5/netcdf4. Use nc-config and nf-config to get installation directory
with_netcdf="`nc-config --prefix`"
with_netcdf_fortran="`nf-config --prefix`"
with_hdf5="${EBROOTHDF5}"
./configure tested on NIC4

jmb
------
Jean-Michel Beuken
Computer Scientist
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Gang Tang
Posts: 6
Joined: Mon Dec 02, 2019 10:43 am

Re: error while executing make for abinit-9.2.1 on NIC4 cluster

Post by Gang Tang » Thu Oct 08, 2020 3:25 pm

Thank you very much. Your method works. I believe your reply provides a good template that can tell other users how to compile abinit 9.2.1 on the cluster.
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