Re: error when doing make

From: Nathan Goldbaum <nathan12343_at_gmail.com>
Date: Wed, 12 Aug 2015 13:14:29 -0500

You need to add /mnt/share/data35/gmunoz/libraries/lib to your
LD_LIBRARY_PATH.

On Wed, Aug 12, 2015 at 1:11 PM, <guidomunoz_at_on.br> wrote:

>
> 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 Muñoz
>>
>>
>>
>>
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>>
>
>
> Guido Granda Muñoz
>
>
>
>
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Received on 2015-08-12 20:14:52

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