Compiling VASP.4.6 on Operton with gfortran

[yxie]

Dear VASP users,

Due to the bad performance on mpich2, the computer center administrator of my university decided to change the system to openmpi. And now it only avialable with gfortran. I have read some post here for the solution of gfortran, but I met something not mentioned at all.

Everything goes fine during the compilation expect the well-known xml.F bug. But at the end, there is a error:

[yxie@brutus3 vasp.4.6]$ make
./preprocess <base.F | /usr/bin/cpp -P -C -traditional >base.f -DMPI -DHOST=\"Linux\" -Dkind8 -DNGZhalf -DCACHE_SIZE=2000 -DPGF90 -Davoidalloc -DRPROMU_DGEMV
mpif90 -ffree-form -march=opteron -mfpmath=sse -O2 -c base.f
./preprocess <mpi.F | /usr/bin/cpp -P -C -traditional >mpi.f -DMPI -DHOST=\"Linux\" -Dkind8 -DNGZhalf -DCACHE_SIZE=2000 -DPGF90 -Davoidalloc -DRPROMU_DGEMV
mpif90 -ffree-form -march=opteron -mfpmath=sse -O2 -c mpi.f
./preprocess <smart_allocate.F | /usr/bin/cpp -P -C -traditional >smart_allocate.f -DMPI -DHOST=\"Linux\" -Dkind8 -DNGZhalf -DCACHE_SIZE=2000 -DPGF90 -Davoidalloc -DRPROMU_DGEMV
mpif90 -ffree-form -march=opteron -mfpmath=sse -O2 -c smart_allocate.f
./preprocess <xml.F | /usr/bin/cpp -P -C -traditional >xml.f -DMPI -DHOST=\"Linux\" -Dkind8 -DNGZhalf -DCACHE_SIZE=2000 -DPGF90 -Davoidalloc -DRPROMU_DGEMV
mpif90 -ffree-form -march=opteron -mfpmath=sse -O2 -c xml.f
In file xml.f:487

WRITE(strcounter,'(I)') dim
1
Warning: Nonnegative width required in format string at (1)
In file xml.f:1083

WRITE(strcounter,"(I)") i
1
Warning: Nonnegative width required in format string at (1)
In file xml.f:1086

WRITE(strcounter,"(I)") nk
1
Warning: Nonnegative width required in format string at (1)
In file xml.f:1152

WRITE(strcounter,"(I)") isp
1
Warning: Nonnegative width required in format string at (1)
In file xml.f:1197

WRITE(strcounter,"(I)") ni
1
Warning: Nonnegative width required in format string at (1)
In file xml.f:1200

WRITE(strcounter,"(I)") isp
1
Warning: Nonnegative width required in format string at (1)
In file xml.f:1280

WRITE(strcounter,"(I)") i
1
Warning: Nonnegative width required in format string at (1)
In file xml.f:1283

WRITE(strcounter,"(I)") nk
1
Warning: Nonnegative width required in format string at (1)
In file xml.f:1286

WRITE(strcounter,"(I)") n
1
Warning: Nonnegative width required in format string at (1)
...
...
...
rm -f vasp
mpif90 -o vasp main.o base.o mpi.o smart_allocate.o xml.o constant.o jacobi.o main_mpi.o scala.o asa.o lattice.o poscar.o ini.o setex.o radial.o pseudo.o mgrid.o mkpoints.o wave.o wave_mpi.o symmetry.o symlib.o lattlib.o random.o nonl.o nonlr.o dfast.o choleski2.o mix.o charge.o xcgrad.o xcspin.o potex1.o potex2.o metagga.o constrmag.o pot.o cl_shift.o force.o dos.o elf.o tet.o hamil.o steep.o chain.o dyna.o relativistic.o LDApU.o sphpro.o paw.o us.o ebs.o wavpre.o wavpre_noio.o broyden.o dynbr.o rmm-diis.o reader.o writer.o tutor.o xml_writer.o brent.o stufak.o fileio.o opergrid.o stepver.o dipol.o xclib.o chgloc.o subrot.o optreal.o davidson.o edtest.o electron.o shm.o pardens.o paircorrection.o optics.o constr_cell_relax.o stm.o finite_diff.o elpol.o setlocalpp.o fftmpi.o fftmpi_map.o fft3dlib.o -L../vasp.4.lib -ldmy ../vasp.4.lib/lapack_double.o -L/cluster/home/matl/yxie/Linux_HAMMER64SSE2_2/lib -LLIBDIR -llapack -lcblas -lf77blas -latlas -L/cluster/apps/openmp/gnu/lib -lmpi
elpol.o: In function `__elpol__berry':
elpol.f:(.text+0x6cbc): undefined reference to `zgeco_'
elpol.f:(.text+0x6d06): undefined reference to `zgedi_'
collect2: ld returned 1 exit status
make: *** [vasp] Error 1
[yxie@brutus3 vasp.4.6]$ mpif90 -o vasp main.o base.o mpi.o smart_allocate.o xml.o constant.o jacobi.o main_mpi.o scala.o asa.o lattice.o poscar.o ini.o setex.o radial.o pseudo.o mgrid.o mkpoints.o wave.o wave_mpi.o symmetry.o symlib.o lattlib.o random.o nonl.o nonlr.o dfast.o choleski2.o mix.o charge.o xcgrad.o xcspin.o potex1.o potex2.o metagga.o constrmag.o pot.o cl_shift.o force.o dos.o elf.o tet.o hamil.o steep.o chain.o dyna.o relativistic.o LDApU.o sphpro.o paw.o us.o ebs.o wavpre.o wavpre_noio.o broyden.o dynbr.o rmm-diis.o reader.o writer.o tutor.o xml_writer.o brent.o stufak.o fileio.o opergrid.o stepver.o dipol.o xclib.o chgloc.o subrot.o optreal.o davidson.o edtest.o electron.o shm.o pardens.o paircorrection.o optics.o constr_cell_relax.o stm.o finite_diff.o elpol.o setlocalpp.o fftmpi.o fftmpi_map.o fft3dlib.o -L../vasp.4.lib -ldmy ../vasp.4.lib/lapack_double.o -L/cluster/home/matl/yxie/Linux_HAMMER64SSE2_2/lib -LLIBDIR -llapack -lcblas -lf77blas -latlas -L/cluster/apps/openmp/gnu/lib -lmpi
elpol.o: In function `__elpol__berry':
elpol.f:(.text+0x6cbc): undefined reference to `zgeco_'
elpol.f:(.text+0x6d06): undefined reference to `zgedi_'
collect2: ld returned 1 exit status
[yxie@brutus3 vasp.4.6]$ elpol.o: In function `__elpol__berry':
> elpol.f:(.text+0x6cbc): undefined reference to `zgeco_'
> elpol.f:(.text+0x6d06): undefined reference to `zgedi_'
> collect2: ld returned 1 exit status
> make: *** [vasp] Error 1
>

My makefile is as following:
FC=gfortran
# fortran linker
FCL=$(FC)

# avoidalloc avoid ALLOCATE if possible
# IFC work around some IFC bugs
# CACHE_SIZE 1000 for PII,PIII, 5000 for Athlon, 8000 P4
# RPROMU_DGEMV use DGEMV instead of DGEMM in RPRO (usually faster)
# RACCMU_DGEMV use DGEMV instead of DGEMM in RACC (faster on P4)
# **** definitely use -DRACCMU_DGEMV if you use the mkl library
#-----------------------------------------------------------------------

CPP = $(CPP_) -DHOST=\"Linux\" \
-Dkind8 -DNGXhalf -DCACHE_SIZE=2000 -DPGF90 -Davoidalloc \
-DRPROMU_DGEMV

#-----------------------------------------------------------------------
# general fortran flags (there must a trailing blank on this line)
# the -Mx,119,0x200000 is required if you use older pgf90 versions
# on a more recent LINUX installation
# the option will not do any harm on other 3.X pgf90 distributions
#-----------------------------------------------------------------------

FFLAGS = -ffree-form -march=opteron -mfpmath=sse

#-----------------------------------------------------------------------
# optimization,
# we have tested whether higher optimisation improves
# the performance, and found no improvements with -O3-5 or -fast
# (even on Athlon system, Athlon specific optimistation worsens performance)
#-----------------------------------------------------------------------

OFLAG = -O2

OFLAG_HIGH = $(OFLAG)
OBJ_HIGH =
OBJ_NOOPT =
DEBUG = -g -O0
INLINE = $(OFLAG)


#-----------------------------------------------------------------------
# the following lines specify the position of BLAS and LAPACK
# what you chose is very system dependent
# P4: VASP works fastest with Intels mkl performance library
# Athlon: Atlas based BLAS are presently the fastest
# P3: no clue
#-----------------------------------------------------------------------

# Atlas based libraries
ATLASHOME= $(HOME)/Linux_HAMMER64SSE2_2/lib
BLAS= -L$(ATLASHOME) -LLIBDIR -llapack -lcblas -lf77blas -latlas

# use specific libraries (default library path points to other libraries)
#BLAS= $(ATLASHOME)/libf77blas.a $(ATLASHOME)/libatlas.a

# use the mkl Intel libraries for p4 (www.intel.com)
#BLAS=-L/opt/intel/mkl/lib/32 -lmkl_p4 -lpthread

# LAPACK, simplest use vasp.4.lib/lapack_double
#LAPACK= ../vasp.4.lib/lapack_double.o

# use atlas optimized part of lapack
#LAPACK= ../vasp.4.lib/lapack_atlas.o -llapack -lcblas

# use the mkl Intel lapack
#LAPACK= -lmkl_lapack


#-----------------------------------------------------------------------

LIB = -L../vasp.4.lib -ldmy \
../vasp.4.lib/linpack_double.o $(LAPACK) \
$(BLAS)

# options for linking (none required)
LINK =

#-----------------------------------------------------------------------
# fft libraries:
# VASP.4.5 can use FFTW (http://www.fftw.org)
# since the FFTW is very slow for radices 2^n the fft3dlib is used
# in these cases
# if you use fftw3d you need to insert -lfftw in the LIB line as well
# please do not send us any querries reltated to FFTW (no support)
# if it fails, use fft3dlib
#-----------------------------------------------------------------------

FFT3D = fft3dfurth.o fft3dlib.o
#FFT3D = fftw3d+furth.o fft3dlib.o


#=======================================================================
# MPI section, uncomment the following lines
#
# one comment for users of mpich or lam:
# You must *not* compile mpi with g77/f77, because f77/g77
# appends *two* underscores to symbols that contain already an
# underscore (i.e. MPI_SEND becomes mpi_send__). The pgf90
# compiler however appends only one underscore.
# Precompiled mpi version will also not work !!!
#
# We found that mpich.1.2.1 and lam-6.5.X are stable
# mpich.1.2.1 was configured with
# ./configure -prefix=/usr/local/mpich_nodvdbg -fc="pgf77 -Mx,119,0x200000" \
# -f90="pgf90 -Mx,119,0x200000" \
# --without-romio --without-mpe -opt=-O \
#
# lam was configured with the line
# ./configure -prefix /usr/local/lam-6.5.X --with-cflags=-O -with-fc=pgf90 \
# --with-f77flags=-O --without-romio
#
# lam was generally faster and we found an average communication
# band with of roughly 160 MBit/s (full duplex)
#
# please note that you might be able to use a lam or mpich version
# compiled with f77/g77, but then you need to add the following
# options: -Msecond_underscore (compilation) and -g77libs (linking)
#
# !!! Please do not send me any queries on how to install MPI, I will
# certainly not answer them !!!!
#=======================================================================
#-----------------------------------------------------------------------
# fortran linker for mpi: if you use LAM and compiled it with the options
# suggested above, you can use the following lines
#-----------------------------------------------------------------------


FC=mpif90
FCL=$(FC)

#-----------------------------------------------------------------------
# additional options for CPP in parallel version (see also above):
# NGZhalf charge density reduced in Z direction
# wNGZhalf gamma point only reduced in Z direction
# scaLAPACK use scaLAPACK (usually slower on 100 Mbit Net)
#-----------------------------------------------------------------------

CPP = $(CPP_) -DMPI -DHOST=\"Linux\" \
-Dkind8 -DNGZhalf -DCACHE_SIZE=2000 -DPGF90 -Davoidalloc -DRPROMU_DGEMV

#-----------------------------------------------------------------------
# location of SCALAPACK
# if you do not use SCALAPACK simply uncomment the line SCA
#-----------------------------------------------------------------------

#BLACS=/usr/local/BLACS_lam
#SCA_= /usr/local/SCALAPACK_lam

#SCA= $(SCA_)/scalapack_LINUX.a $(SCA_)/pblas_LINUX.a $(SCA_)/tools_LINUX.a \
$(BLACS)/LIB/blacsF77init_MPI-LINUX-0.a $(BLACS)/LIB/blacs_MPI-LINUX-0.a $(BLACS)/LIB/blacsF77init_MPI-LINUX-0.a

#SCA=

#-----------------------------------------------------------------------
# libraries for mpi
#-----------------------------------------------------------------------

LIB = -L../vasp.4.lib -ldmy \
../vasp.4.lib/lapack_double.o $(LAPACK) \
$(SCA) $(BLAS) -L/cluster/apps/openmp/gnu/lib -lmpi

# FFT: only option fftmpi.o with fft3dlib of Juergen Furthmueller

FFT3D = fftmpi.o fftmpi_map.o fft3dlib.o

#-----------------------------------------------------------------------
# general rules and compile lines
#-----------------------------------------------------------------------
BASIC= symmetry.o symlib.o lattlib.o random.o

SOURCE= base.o mpi.o smart_allocate.o xml.o \
constant.o jacobi.o main_mpi.o scala.o \
asa.o lattice.o poscar.o ini.o setex.o radial.o \
pseudo.o mgrid.o mkpoints.o wave.o wave_mpi.o $(BASIC) \
nonl.o nonlr.o dfast.o choleski2.o \
mix.o charge.o xcgrad.o xcspin.o potex1.o potex2.o \
metagga.o constrmag.o pot.o cl_shift.o force.o dos.o elf.o \
tet.o hamil.o steep.o \
chain.o dyna.o relativistic.o LDApU.o sphpro.o paw.o us.o \
ebs.o wavpre.o wavpre_noio.o broyden.o \
dynbr.o rmm-diis.o reader.o writer.o tutor.o xml_writer.o \
brent.o stufak.o fileio.o opergrid.o stepver.o \
dipol.o xclib.o chgloc.o subrot.o optreal.o davidson.o \
edtest.o electron.o shm.o pardens.o paircorrection.o \
optics.o constr_cell_relax.o stm.o finite_diff.o \
elpol.o setlocalpp.o

INC=

vasp: $(SOURCE) $(FFT3D) $(INC) main.o
rm -f vasp
$(FCL) -o vasp $(LINK) main.o $(SOURCE) $(FFT3D) $(LIB)
makeparam: $(SOURCE) $(FFT3D) makeparam.o main.F $(INC)
$(FCL) -o makeparam $(LINK) makeparam.o $(SOURCE) $(FFT3D) $(LIB)
zgemmtest: zgemmtest.o base.o random.o $(INC)
$(FCL) -o zgemmtest $(LINK) zgemmtest.o random.o base.o $(LIB)
dgemmtest: dgemmtest.o base.o random.o $(INC)
$(FCL) -o dgemmtest $(LINK) dgemmtest.o random.o base.o $(LIB)
ffttest: base.o smart_allocate.o mpi.o mgrid.o random.o ffttest.o $(FFT3D) $(INC)
$(FCL) -o ffttest $(LINK) ffttest.o mpi.o mgrid.o random.o smart_allocate.o base.o $(FFT3D) $(LIB)
kpoints: $(SOURCE) $(FFT3D) makekpoints.o main.F $(INC)
$(FCL) -o kpoints $(LINK) makekpoints.o $(SOURCE) $(FFT3D) $(LIB)

clean:
-rm -f *.g *.f *.o *.L *.mod ; touch *.F

main.o: main$(SUFFIX)
$(FC) $(FFLAGS)$(DEBUG) $(INCS) -c main$(SUFFIX)
xcgrad.o: xcgrad$(SUFFIX)
$(FC) $(FFLAGS) $(INLINE) $(INCS) -c xcgrad$(SUFFIX)
xcspin.o: xcspin$(SUFFIX)
$(FC) $(FFLAGS) $(INLINE) $(INCS) -c xcspin$(SUFFIX)

makeparam.o: makeparam$(SUFFIX)
$(FC) $(FFLAGS)$(DEBUG) $(INCS) -c makeparam$(SUFFIX)

makeparam$(SUFFIX): makeparam.F main.F
#
# MIND: I do not have a full dependency list for the include
# and MODULES: here are only the minimal basic dependencies
# if one strucuture is changed then touch_dep must be called
# with the corresponding name of the structure
#
base.o: base.inc base.F
mgrid.o: mgrid.inc mgrid.F
constant.o: constant.inc constant.F
lattice.o: lattice.inc lattice.F
setex.o: setexm.inc setex.F
pseudo.o: pseudo.inc pseudo.F
poscar.o: poscar.inc poscar.F
mkpoints.o: mkpoints.inc mkpoints.F
wave.o: wave.inc wave.F
nonl.o: nonl.inc nonl.F
nonlr.o: nonlr.inc nonlr.F

$(OBJ_HIGH):
$(CPP)
$(FC) $(FFLAGS) $(OFLAG_HIGH) $(INCS) -c $*$(SUFFIX)
$(OBJ_NOOPT):
$(CPP)
$(FC) $(FFLAGS) $(INCS) -c $*$(SUFFIX)

fft3dlib_f77.o: fft3dlib_f77.F
$(CPP)
$(F77) $(FFLAGS_F77) -c $*$(SUFFIX)

.F.o:
$(CPP)
$(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX)
.F$(SUFFIX):
$(CPP)
$(SUFFIX).o:
$(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX)

[yxie@brutus3 vasp.4.6]$

Could you experts give me some advices?

With my best regards,

Yu
<span class='smallblacktext'>[ Edited ]</span>

[job]

Upgrade to a newer version of vasp, where this bug is fixed. And if you are using an older release of gfortran than 4.3, pester your sysadmin to upgrade gfortran as well.

[digghost]

function of zgeco_ and zgedi are include in the ../vasp4.6lib/linpack.double.f .You can copy the subroutine zgeco and zgedi to the file epol.f, so you can pass the link process. :!