Elk / Discussion / Elk Users: Help request: Library management to install elk on Linux Sub-system for Windows

Hi all,

I would like to install elk on Window's Ubuntu sub-system and I would like to use it in parallel. The problem is I don't completely understand the library management. Can you help me figure this out? Please correct me if I did something wrong and tell me if I need to provide more details.

This is what I added to the make.inc apart from copying the libxc.a and libxcf90.a files to elk/src:

F90 = mpifort
F77 = mpifort
SRC_MPI = /usr/lib/x86_64-linux-gnu/libmpi.so /usr/lib/x86_64-linux-gnu/libmpi.so.20
SRC_OBLAS = /usr/lib/x86_64-linux-gnu/openblas/libblas.so /usr/lib/x86_64-linux-gnu/openblas/libblas.so /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LIB_libxc = libxcf90.a libxc.a
SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90

I didn't change the LIB_LPK variable that says is for LAPACK and BLAS.

This is the error I had:

...
libxcifc.o: In function `__libxcifc_MOD_xcifc_libxc':
libxcifc.f90:(.text+0x2a55): undefined reference to `xc_f90_func_set_ext_params_'
libxcifc.f90:(.text+0x2cae): undefined reference to `xc_f90_func_set_ext_params_'
oblas_init.o: In function `oblas_init_':
oblas_init.f90:(.text+0xa): undefined reference to `openblas_set_num_threads_'
collect2: error: ld returned 1 exit status
Makefile:200: recipe for target 'elk' failed
make[1]: *** [elk] Error 1
make[1]: Leaving directory '/home/oscar/elk-6.3.2/src'
Makefile:7: recipe for target 'all' failed
make: *** [all] Error 2

I also include sone ldconfig information:

$ ldconfig -p | grep openblas
    libopenblas.so.0 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libopenblas.so.0
    libopenblas.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libopenblas.so
    liblapack.so.3 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/openblas/liblapack.so.3
    liblapack.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/openblas/liblapack.so
    libblas.so.3 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
    libblas.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/openblas/libblas.so
$ ldconfig -p | grep lapack
    libscalapack-openmpi.so.2.0 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so.2.0
    libscalapack-mpich.so.2.0 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libscalapack-mpich.so.2.0
    libscalapack-mpich.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libscalapack-mpich.so
    liblapack.so.3 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/openblas/liblapack.so.3
    liblapack.so.3 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/liblapack.so.3
    liblapack.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/openblas/liblapack.so
    liblapack.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/liblapack.so
$ ldconfig -p | grep blacs
    libblacsF77init-openmpi.so.1 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libblacsF77init-openmpi.so.1
    libblacsF77init-openmpi.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libblacsF77init-openmpi.so
    libblacsCinit-openmpi.so.1 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libblacsCinit-openmpi.so.1
    libblacsCinit-openmpi.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libblacsCinit-openmpi.so
    libblacs-openmpi.so.1 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libblacs-openmpi.so.1
    libblacs-openmpi.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libblacs-openmpi.so
$ ldconfig -p | grep libxc
libxcf90.so.4 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcf90.so.4
    libxcf90.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcf90.so
    libxcf03.so.4 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcf03.so.4
    libxcf03.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcf03.so
    libxcb.so.1 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcb.so.1
    libxcb-sync.so.1 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcb-sync.so.1
    libxcb-shape.so.0 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcb-shape.so.0
    libxcb-present.so.0 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcb-present.so.0
    libxcb-glx.so.0 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0
    libxcb-dri3.so.0 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcb-dri3.so.0
    libxcb-dri2.so.0 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0
    libxc.so.4 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxc.so.4
    libxc.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libxc.so

Dear Oscar,

Building make.inc can be tricky, I had some headackes with it.

Do you have an Ubuntu in a virtual machine?
If so, you just follow Ubuntu instructions for compilation, linking and stuff, in general.

General note: gcc is better for elk, and MKL is better on Intel processors (surprisingly).

SRC_MPI and SRC_OBLAS are source flags, they point to f90 files and are usually used with stubs (i.e. to disable the respective feature).

Here is a pure gcc make.inc (without libwannier)

MAKE = make
F90 = mpifort
CC = mpicc
F90_OPTS = -O3 -ffast-math -funroll-loops -fopenmp 
F77 = mpifort
F77_OPTS = -O3 -ffast-math -funroll-loops -fopenmp 
AR = ar
LIB_SYS = 

LIB_LPK = lapack.a blas.a
SRC_OBLAS = oblas_stub.f90

SRC_OMP = 

SRC_MKL = mkl_stub.f90
SRC_BLIS = blis_stub.f90

SRC_W90S = w90_stub.f90

SRC_MPI =

LIB_libxc = libxcf90.a libxc.a
SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90

SRC_FFT = zfftifc.f90
LIB_FFT = fftlib.a

Here is a make.inc of my workhorse with gcc 7.4 and MKL, openMP + MPI (note that I use libwannier):

MAKE = make
F90 = mpifort
CC = mpicc

F90_OPTS = -O3 -ffast-math -funroll-loops -fopenmp -L$(MKLROOT)lib/intel64 -Wl,-lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl 

F77 = mpifort
F77_OPTS = -O3 -ffast-math -funroll-loops -fopenmp -L$(MKLROOT)/lib/intel64 -Wl,-lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl
AR = ar
LIB_SYS = 

MKLROOT=/usr/local/intel/15.0.1.133/composer_xe_2015.1.133/mkl
LIB_LPK = -L$(MKLROOT)/lib/intel64 -Wl,-lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl
SRC_MKL =


SRC_OMP = 
SRC_OBLAS = oblas_stub.f90
SRC_BLIS = blis_stub.f90

SRC_W90S =
LIB_W90 = libwannier.a

SRC_MPI =

LIB_libxc = libxcf90.a libxc.a
SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90

LIB_FFT = -lfftw3
SRC_FFT = zfftifc_fftw.f90

Best regards.
Andrew

Hi Andrew,

I don't have a virtual machine, I have Ubuntu as a Linux Sub-system for Windows. I followed the installation instructions from the manual, I only followed the linking instructions for libxc because it's the only one mentioned. Do I have to special file handlings for other libraries?

I have AMD, so I am not using MKL. Here's more information on my computer:

model name      : AMD FX(tm)-8320 Eight-Core Processor

$ gcc --version
gcc (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0

And here's my make.inc, I deleted the BLAS and LAPACK stubs:

MAKE = make
F90 = mpifort
CC = mpicc
F90_OPTS = -O3 -ffast-math -funroll-loops -fopenmp
F77 = mpifort
F77_OPTS = -O3 -ffast-math -funroll-loops -fopenmp
AR = ar
LIB_SYS =
 # LAPACK and BLAS libraries
LIB_LPK = -L/usr/lib/x86_64-linux-gnu/openblas -lblas -L/usr/lib/x86_64-linux-gnu/openblas -llapack
LIB_FFT = fftlib.a
SRC_OMP =

SRC_MPI = /usr/lib/x86_64-linux-gnu/libmpi.so
SRC_MKL = mkl_stub.f90
SRC_OBLAS = /usr/lib/x86_64-linux-gnu/openblas/libblas.so
SRC_BLIS = blis_stub.f90
SRC_libxc = libxcifc_stub.f90
LIB_libxc = libxcf90.a libxc.a
SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90
SRC_FFT = zfftifc.f90
SRC_W90S = w90_stub.f90

And here's te error I got:

... 
 /usr/bin/ld: oblas_init.o: undefined reference to symbol 'openblas_set_num_threads_'    
//usr/lib/x86_64-linux-gnu/libopenblas.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Makefile:200: recipe for target 'elk' failed
make[1]: *** [elk] Error 1
make[1]: Leaving directory '/home/izxle/elk-6.3.2/src'
Makefile:7: recipe for target 'all' failed
make: *** [all] Error 2

Thank you for your help

Best regards,

Oscar X. Guerrero

Anton F. - 2020-02-22

Hi, Oscar,
If you have a single machine, you don't have to use MPI, just OpenMP parallelism, as far as I know, is required.
Best regards,
Anton.

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Andrew Shyichuk - 2020-02-23

Dear Oscar,

SRC_MPI should point to a stub or be empty:

SRC_MPI =

Same goes for SRC_OBLAS. Youl LIB_LPK line should be enouch to link OBLAS.

Generally, I do not think you should link .so like that.

As Anton F. correctly said, you do not need MPI on a single machine.

And, gcc is definitely better on an AMD machine.

Finally, try compiling elk with the included LAPACK and BLAS, with mpicc, just to get it running. Once that is done, you may consider adding external linear algebra libs and check the performance gain.

Best regards.
Andrew
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Help request: Library management to install elk on Linux Sub-system for Windows

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Help request: Library management to install elk on Linux Sub-system for Windows