Installation problem

[Vinod Solet]

Hi users, 

I am trying to install BerkeleyGW-3.0.1. But the "stampede.tacc.utexas.edu_threaded_hdf5.mk " file is not present in the config folder. Can anyone help me regarding this?

[Mauro Del Ben]

Hi Vinod,

This is the arch.mk we have used on Frontera at TACC last summer, it should be relatively straightforward to adapt it for stampede.

# You'll need to run:
# module load arpack impi intel/19.0.5 phdf5
#
# Use 'make -j 8' for parallel build on Frontera
#
# Zhenglu Li
# July 2020, Berkeley

COMPFLAG  = -DINTEL
PARAFLAG  = -DMPI -DOMP
MATHFLAG  = -DUSESCALAPACK -DUNPACKED -DUSEFFTW3 -DHDF5
# Only uncomment DEBUGFLAG if you need to develop/debug BerkeleyGW.
# The output will be much more verbose, and the code will slow down by ~20%.
#DEBUGFLAG = -DDEBUG

FCPP    = cpp -C -nostdinc
F90free = mpiifort -xCORE-AVX512 -free -qopenmp -ip -no-ipo
LINK    = mpiifort -xCORE-AVX512 -qopenmp -ip -no-ipo
# We need the -fp-model procise to pass the testsuite.
FOPTS   = -O3 -fp-model source
FNOOPTS = -O2 -fp-model source -no-ip
#FOPTS   = -g -O0 -check all -Warn all -traceback
#FNOOPTS = $(FOPTS)
MOD_OPT = -module
INCFLAG = -I

C_PARAFLAG = -DPARA -DMPICH_IGNORE_CXX_SEEK
CC_COMP = mpiicpc -xCORE-AVX512
C_COMP  = mpiicc -xCORE-AVX512
C_LINK  = mpiicpc -xCORE-AVX512
C_OPTS  = -O3 -ip -no-ipo -qopenmp
C_DEBUGFLAG =

REMOVE  = /bin/rm -f

# Math Libraries
#
MKLPATH      = $(MKLROOT)/lib/intel64

FFTWLIB      = -Wl,--start-group \
$(MKLPATH)/libmkl_intel_lp64.a \
$(MKLPATH)/libmkl_intel_thread.a \
$(MKLPATH)/libmkl_core.a \
-Wl,--end-group -liomp5 -lpthread -lm -ldl
FFTWINCLUDE  = $(MKLROOT)/include/fftw


LAPACKLIB    = -Wl,--start-group \
$(MKLPATH)/libmkl_intel_lp64.a \
$(MKLPATH)/libmkl_intel_thread.a \
$(MKLPATH)/libmkl_core.a \
$(MKLPATH)/libmkl_blacs_intelmpi_lp64.a \
-Wl,--end-group -liomp5 -lpthread -lm -ldl
SCALAPACKLIB = $(MKLPATH)/libmkl_scalapack_lp64.a

HDF5PATH     = $(TACC_HDF5_LIB)
HDF5LIB      = $(HDF5PATH)/libhdf5hl_fortran.a \
$(HDF5PATH)/libhdf5_hl.a \
$(HDF5PATH)/libhdf5_fortran.a \
$(HDF5PATH)/libhdf5.a \
$(HDF5PATH)/libsz.a \
-lz
HDF5INCLUDE  = $(HDF5PATH)/../include

TESTSCRIPT = 

On Wed, May 31, 2023 at 7:35 AM Vinod Solet <vso...@gmail.com> wrote:

Hi users, 

I am trying to install BerkeleyGW-3.0.1. But the "stampede.tacc.utexas.edu_threaded_hdf5.mk " file is not present in the config folder. Can anyone help me regarding this?

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[Vinod Solet]

Thank to you Mauro Del Ben for your reply.

But after your suggestion, i got error like this

hdf5_io_safe.p.f:(.text+0x793): undefined reference to `__h5d_MOD_h5dcreate_f'
/usr/bin/ld: Common/hdf5_io_safe.o: in function `__hdf5_io_safe_m_MOD_safe_h5screate_simple':
hdf5_io_safe.p.f:(.text+0x7d3): undefined reference to `__h5s_MOD_h5screate_simple_f'
collect2: error: ld returned 1 exit status
make[2]: *** [Common/common-rules.mk:212: Common/test_evecs.real.x] Error 1
make[2]: Leaving directory '/home/vinod/programs/BerkeleyGW-3.0.1'
make[1]: *** [Makefile:8: pre] Error 2
make[1]: Leaving directory '/home/vinod/programs/BerkeleyGW-3.0.1'
make: *** [Makefile:115: all] Error 2

This is my arch.mk file

FCPP    = cpp -C -nostdinc

#F90free = /usr/bin/mpif90 -ffree-form -ffree-line-length-none -Wall
F90free = /usr/bin/mpif90 -ffree-form -ffree-line-length-none -fbounds-check -Wintrinsic-shadow -std=gnu -fopenmp
#F90free = /usr/bin/mpif90 -ffree-form -ffree-line-length-none -fbounds-check -Wall -pedantic-errors -std=gnu -fopenmp
#F90free = /usr/bin/mpif90 -ffree-form -ffree-line-length-none -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow
# denormal not supported, according to runtime error
# precision is flagged by cputime: http://gcc.gnu.org/onlinedocs/gcc-4.5.3/gfortran/Debugging-Options.html
# underflow is flagged by dlamch from lapack
LINK    = /usr/bin/mpif90 -fopenmp
FOPTS   = -O3
#FOPTS   = -g -C
FNOOPTS = $(FOPTS)
MOD_OPT = -J

INCFLAG = -I

C_PARAFLAG  = -DPARA

CC_COMP  = /usr/bin/mpiCC
C_COMP  = /usr/bin/mpicc
C_LINK  = /usr/bin/mpiCC
C_OPTS  = -O3

C_DEBUGFLAG =

REMOVE  = /bin/rm -f

# Math Libraries
#
MKLPATH      = $(MKLROOT)/lib/intel64

FFTWLIB      = -Wl,--start-group \
$(MKLPATH)/libmkl_intel_lp64.a \
$(MKLPATH)/libmkl_intel_thread.a \
$(MKLPATH)/libmkl_core.a \
-Wl,--end-group -liomp5 -lpthread -lm -ldl
FFTWINCLUDE  = $(MKLROOT)/include/fftw

# Math Libraries
#
#FFTWLIB      = -L/usr/lib/x86_64-linux-gnu -lfftw3 -lfftw3_threads
#FFTWINCLUDE  = /usr/include
# FHJ: Note: manually compiled threaded LAPACK and ScaLAPACK on tigger
LAPACKLIB    = /usr/lib/x86_64-linux-gnu/liblapack.a -L/usr/lib/x86_64-linux-gnu -lblas
SCALAPACKLIB = /home/vinod/programs/scalapack-2.2.0/libscalapack.a

HDF5LIB      = -L/home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib -lhdf5_hl -lhdf5 -lz
HDF5INCLUDE  = /home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/include

#need to export MPIEXEC=/usr/bin/mpirun if this is not default in `which mpiexec`
TESTSCRIPT = make check-parallel
                                                                                                                                                                                         69,1          Bot

Thank you in advance.

[Mauro Del Ben]

Hi Vinod,

You need to add the fortran HDF5 library wrappers to the HDF5LIB line:

HDF5LIB      = -L/home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz

Best

-M

[Vinod Solet]

Hello Dr. Ben, There is no such file of -lhdf5hl_fortran in my lib folder of hdf5, indeed the different file -lhdf5_hl_fortran is present here. After running this i got this error.

make[2]: Leaving directory '/home/vinod/programs/BerkeleyGW-3.0.1'

make[2]: Entering directory '/home/vinod/programs/BerkeleyGW-3.0.1'
cd ./Common/qhull && make lib
/usr/bin/mpif90 -fopenmp -O3 -o Common/test_evecs.real.x Common/test_evecs.o Common/global.o Common/typedefs.o Common/nrtype.o Common/push_pop.o Common/message.o Common/peinfo.o Common/timing.o Common/scalapack_aux.o Common/os.o Common/os_c.o Common/evecs.o Common/hdf5_io.o Common/wfn_io_hdf5.o Common/hdf5_io_data.o Common/hdf5_io_safe.o -L/home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib -lhdf5_hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz
make[3]: Entering directory '/home/vinod/programs/BerkeleyGW-3.0.1/Common/qhull'
make[3]: Nothing to be done for 'lib'.
make[3]: Leaving directory '/home/vinod/programs/BerkeleyGW-3.0.1/Common/qhull'
/usr/bin/ld: Common/evecs.o: in function `__evecs_m_MOD_evecs_read_local_arrays_par_hdf5':
evecs.p.f:(.text+0x4bc9): undefined reference to `h5pset_dxpl_mpio_f_'
/usr/bin/ld: Common/evecs.o: in function `__evecs_m_MOD_evecs_write_local_arrays_par_hdf5':
evecs.p.f:(.text+0x812a): undefined reference to `h5pset_dxpl_mpio_f_'
/usr/bin/ld: Common/hdf5_io.o: in function `__hdf5_io_m_MOD_hdf5_create_file':
hdf5_io.p.f:(.text+0x408): undefined reference to `h5pset_fapl_mpio_f_'
/usr/bin/ld: hdf5_io.p.f:(.text+0x501): undefined reference to `h5pset_fapl_mpio_f_'
/usr/bin/ld: Common/hdf5_io.o: in function `__hdf5_io_m_MOD_hdf5_open_file':
hdf5_io.p.f:(.text+0x772): undefined reference to `h5pset_fapl_mpio_f_'
/usr/bin/ld: hdf5_io.p.f:(.text+0x923): undefined reference to `h5pset_fapl_mpio_f_'
/usr/bin/ld: Common/wfn_io_hdf5.o: in function `__wfn_io_hdf5_m_MOD_read_hdf5_bands_block':
wfn_io_hdf5.p.f:(.text+0x32ee): undefined reference to `h5pset_dxpl_mpio_f_'
/usr/bin/ld: wfn_io_hdf5.p.f:(.text+0x3593): undefined reference to `h5pset_dxpl_mpio_f_'
/usr/bin/ld: Common/hdf5_io_safe.o: in function `__hdf5_io_safe_m_MOD_safe_h5pset_dxpl_mpio':
hdf5_io_safe.p.f:(.text+0x603): undefined reference to `h5pset_dxpl_mpio_f_'
/usr/bin/ld: /home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib/libhdf5.so: undefined reference to `stat64@GLIBC_2.33'
/usr/bin/ld: /home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib/libhdf5.so: undefined reference to `fstat64@GLIBC_2.33'
/usr/bin/ld: /home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib/libhdf5.so: undefined reference to `dlclose@GLIBC_2.34'
/usr/bin/ld: /home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib/libhdf5.so: undefined reference to `dlerror@GLIBC_2.34'
/usr/bin/ld: /home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib/libhdf5.so: undefined reference to `lstat64@GLIBC_2.33'
/usr/bin/ld: /home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib/libhdf5.so: undefined reference to `dlsym@GLIBC_2.34'
/usr/bin/ld: /home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib/libhdf5.so: undefined reference to `dlopen@GLIBC_2.34'

collect2: error: ld returned 1 exit status
make[2]: *** [Common/common-rules.mk:212: Common/test_evecs.real.x] Error 1
make[2]: Leaving directory '/home/vinod/programs/BerkeleyGW-3.0.1'
make[1]: *** [Makefile:8: pre] Error 2
make[1]: Leaving directory '/home/vinod/programs/BerkeleyGW-3.0.1'
make: *** [Makefile:115: all] Error 2

The modified arch.mk file is printed below.

# arch.mk for BerkeleyGW codes
#
# Suitable for Ubuntu 10.10 in parallel.
# Install packages: liblapack-dev, fftw-dev, gfortran, g++, mpi-default-dev
# Build BLACS according to http://www.open-mpi.org/faq/?category=mpi-apps#blacs
# Build ScaLAPACK according to http://www.open-mpi.org/faq/?category=mpi-apps#scalapack,
#
# Jamal I. Mustafa
# July 2014, UC Berkeley

COMPFLAG  = -DGNU
PARAFLAG  = -DMPI -DOMP
MATHFLAG  = -DUSESCALAPACK -DHDF5 -DUSEFFTW3

# Only uncomment DEBUGFLAG if you need to develop/debug BerkeleyGW.
# The output will be much more verbose, and the code will slow down by ~20%.
#DEBUGFLAG = -DDEBUG

#########################################################################
#   NOTE: This arch.mk is used by a buildslave. The compiler flags are  #
#   optimized to debug the code and not for code performance.           #
#########################################################################

#HDF5LIB      = -L/home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib -lhdf5_hl -lhdf5 -lz
HDF5LIB      = -L/home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/lib -lhdf5_hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz

HDF5INCLUDE  = /home/vinod/programs/hdf5-1.14.1/hdf/HDF_Group/HDF5/1.14.1/include

#need to export MPIEXEC=/usr/bin/mpirun if this is not default in `which mpiexec`
TESTSCRIPT = make check-parallel

[Mauro Del Ben]

Hi Vinod,

This is not something we can really solve, the error says that the HDF5 libraries you are linking in are missing dependencies. You have 3 options:

- Reach out to the system administrator (open a ticket at the computer center you're working) and ask assistance to rebuild and link HDF5 

- Build your own HDF5 library https://www.hdfgroup.org/solutions/hdf5/

- Don't use HDF5, comment out in arch.mk  -DHDF5 HDF5LIB and HDF5INCLUDE flags 

Best

-M