Re: error when doing make

From: Antonio Bibiano <antbbn_at_gmail.com>
Date: Wed, 12 Aug 2015 09:31:24 +0200

Hi,
Looks like a problem with your fftw installation, maybe the openmpi version
it was compiled against it's not the same you are using to compile gadget,
Can you check that?

Antonio Bibiano


Hello guys,

I had a problem when I tried to compile Gadget 2 on a cluster. My Makefile
is the following :

***************************************************************
#--------------------------------------- Basic operation mode of code
OPT += -DPERIODIC
#OPT += -DUNEQUALSOFTENINGS


#--------------------------------------- Things that are always recommended
OPT += -DPEANOHILBERT
OPT += -DWALLCLOCK


#--------------------------------------- TreePM Options
OPT += -DPMGRID=128
#OPT += -DPLACEHIGHRESREGION=3
#OPT += -DENLARGEREGION=1.2
#OPT += -DASMTH=1.25
#OPT += -DRCUT=4.5


#--------------------------------------- Single/Double Precision
OPT += -DDOUBLEPRECISION
OPT += -DDOUBLEPRECISION_FFTW


#--------------------------------------- Time integration options
OPT += -DSYNCHRONIZATION
#OPT += -DFLEXSTEPS
#OPT += -DPSEUDOSYMMETRIC
#OPT += -DNOSTOP_WHEN_BELOW_MINTIMESTEP
#OPT += -DNOPMSTEPADJUSTMENT


#--------------------------------------- Output
#OPT += -DHAVE_HDF5
#OPT += -DOUTPUTPOTENTIAL
#OPT += -DOUTPUTACCELERATION
#OPT += -DOUTPUTCHANGEOFENTROPY
#OPT += -DOUTPUTTIMESTEP


#--------------------------------------- Things for special behaviour
#OPT += -DNOGRAVITY
#OPT += -DNOTREERND
#OPT += -DNOTYPEPREFIX_FFTW
#OPT += -DLONG_X=60
#OPT += -DLONG_Y=5
#OPT += -DLONG_Z=0.2
#OPT += -DTWODIMS
#OPT += -DSPH_BND_PARTICLES
#OPT += -DNOVISCOSITYLIMITER
#OPT += -DCOMPUTE_POTENTIAL_ENERGY
#OPT += -DLONGIDS
#OPT += -DISOTHERM_EQS
#OPT += -DADAPTIVE_GRAVSOFT_FORGAS
#OPT += -DSELECTIVE_NO_GRAVITY=2+4+8+16

#--------------------------------------- Testing and Debugging options
#OPT += -DFORCETEST=0.1


#--------------------------------------- Glass making
#OPT += -DMAKEGLASS=262144


#----------------------------------------------------------------------
# Here, select compile environment for the target machine. This may need
# adjustment, depending on your local system. Follow the examples to add
# additional target platforms, and to get things properly compiled.
#----------------------------------------------------------------------

#--------------------------------------- Select some defaults

CC = mpicc # sets the C-compiler
OPTIMIZE = -O2 -Wall -g # sets optimization and warning flags
MPICHLIB = -lmpich


#--------------------------------------- Select target computer

SYSTYPE="ON"
#SYSTYPE="Mako"
#SYSTYPE="Regatta"
#SYSTYPE="RZG_LinuxCluster"
#SYSTYPE="RZG_LinuxCluster-gcc"
#SYSTYPE="OpteronMPA"
#SYSTYPE="OPA-Cluster32"
#SYSTYPE="OPA-Cluster64"


#--------------------------------------- Adjust settings for target computer

ifeq ($(SYSTYPE),"ON")
CC = mpicc
OPTIMIZE = -O3 -Wall
GSL_INCL = -I/mnt/share/data35/gmunoz/libraries/include
GSL_LIBS = -L/mnt/share/data35/gmunoz/libraries/lib
FFTW_INCL= -I/mnt/share/data35/gmunoz/libraries/include
FFTW_LIBS= -L/mnt/share/data35/gmunoz/libraries/lib
MPICHLIB = -L/mnt/share/data35/gmunoz/libraries/lib
HDF5INCL =
HDF5LIB =
endif
*********************************************************************

The error I got is:

mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o
init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o
density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o
forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o
longrange.o -g -L/mnt/share/data35/gmunoz/libraries/lib
-L/mnt/share/data35/gmunoz/libraries/lib -lgsl -lgslcblas -lm
-L/mnt/share/data35/gmunoz/libraries/lib -ldrfftw_mpi -ldfftw_mpi -ldrfftw
-ldfftw -o Gadget2
/mnt/share/data35/gmunoz/libraries/lib/libdfftw_mpi.a(transpose_mpi.o): In
function `transpose_start_exchange_step':
transpose_mpi.c:(.text+0x3f9): undefined reference to `ompi_request_null'
transpose_mpi.c:(.text+0x401): undefined reference to `ompi_request_null'
/mnt/share/data35/gmunoz/libraries/lib/libdfftw_mpi.a(transpose_mpi.o): In
function `transpose_mpi_create_plan':
transpose_mpi.c:(.text+0x1005): undefined reference to `ompi_mpi_double'
/mnt/share/data35/gmunoz/libraries/lib/libdfftw_mpi.a(transpose_mpi.o): In
function `transpose_mpi':
transpose_mpi.c:(.text+0x16f0): undefined reference to `ompi_request_null'
transpose_mpi.c:(.text+0x16f8): undefined reference to `ompi_request_null'
/mnt/share/data35/gmunoz/libraries/lib/libdfftw_mpi.a(fftwnd_mpi.o): In
function `fftw_mpi_die':
fftwnd_mpi.c:(.text+0x2d5): undefined reference to `ompi_mpi_comm_world'
fftwnd_mpi.c:(.text+0x307): undefined reference to `ompi_mpi_comm_world'
collect2: ld returned 1 exit status
make: *** [Gadget2] Error 1


Could you help, please?

Thank you in advance.

Guido Granda Muñoz




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Received on 2015-08-12 09:31:26

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