Re: error when doing make

From: <guidomunoz_at_on.br>
Date: Wed, 12 Aug 2015 15:11:42 -0300

Hello,

Yes that was the problem, I could compile after using the same version
of openmpi that gadget was using from the cluster.

How ever another problem arose:
****************************************************************************
[gmunoz_at_clustercoge galaxy]$ ./Gadget2 -np 32 galaxy.param
./Gadget2: error while loading shared libraries: libgsl.so.0: cannot
open shared object file: No such file or directory

However I put the right paths to GSL in the Gadget Makefile:

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 =

gmunoz_at_clustercoge galaxy]$ locate libgsl.so.0
/mnt/share/data35/gmunoz/bagpack/gsl-1.16/.libs/libgsl.so.0
/mnt/share/data35/gmunoz/bagpack/gsl-1.16/.libs/libgsl.so.0.17.0
/mnt/share/data35/gmunoz/libraries/lib/libgsl.so.0
/mnt/share/data35/gmunoz/libraries/lib/libgsl.so.0.10.0
/mnt/share/data35/gmunoz/libraries/lib/libgsl.so.0.17.0


I don't know what causes that.



Citando Antonio Bibiano <antbbn_at_gmail.com>:

> 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 Muņoz
>
>
>
>
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Guido Granda Muņoz
Received on 2015-08-12 20:12:02

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