Re: error when doing make

From: <guidomunoz_at_on.br>
Date: Wed, 12 Aug 2015 16:24:44 -0300

That solved the problem. Thank you.



Citando Nathan Goldbaum <nathan12343_at_gmail.com>:

> 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 Muņoz
>>>
>>>
>>>
>>>
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>>>
>>>
>>
>>
>> Guido Granda Muņoz
>>
>>
>>
>>
>> -----------------------------------------------------------
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>>
>



Guido Granda Muņoz
Received on 2015-08-12 21:25:38

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