RE: Help to run gadget2 in macbook

From: Prem Dhungel <premrd_at_hotmail.com>
Date: Wed, 12 Jan 2011 20:31:06 +0530

Hi,

I am still stuck up ..... !

I went gadget2 user's guide thoroughly.
Installed mpi and gsl successfully.
Configured fftw with necessary flags.
But while I do "make", finally I got the following error :

Undefined symbols:
  "_lam_mpi_float", referenced from:
      _lam_mpi_float$non_lazy_ptr in libsfftw_mpi.a(transpose_mpi.o)
  "_lam_mpi_int", referenced from:
      _lam_mpi_int$non_lazy_ptr in test_transpose_mpi.o
  "_lam_mpi_comm_world", referenced from:
      _lam_mpi_comm_world$non_lazy_ptr in test_transpose_mpi.o
      _lam_mpi_comm_world$non_lazy_ptr in libsfftw_mpi.a(fftwnd_mpi.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [test_transpose_mpi] Error 1
make: *** [all-recursive] Error 1

Sorry to trouble again and again.

Thanks.
Prem

Date: Wed, 22 Dec 2010 15:10:00 +0100
From: Sander.Valcke_at_UGent.be
To: gadget-list_at_MPA-Garching.MPG.DE
Subject: Re: [gadget-list] Help to run gadget2 in macbook






  


Hi Prem,



as you can see the error is with the linking against the fftw library.
I'm going to assume here that you haven't thouroughly followed the
specifics given in the gadget users guide ; ) You'll have to check
which fftw version you installed: the single precision or the double
precision. If double: enable -DDOUBLEPRECISION_FFTW in the Makefile. If
your fftw library was created without the 's' or 'd' prefix: enable
-DNOTYPEPREFIX_FFTW.



You can check which library you have by looking at the name of the fftw
libraries, i.e. libdfftw.a (possibly .dylib on your system) for double
precision, libsfftw.a for single precision or libfftw.a for the library
without type prefix. All of this is actually detailed very well in the
gadget users guide.



hth,



Sander



Prem Dhungel wrote:

  Hi
Sander,

  

I successfully completed "configure, make and sudo make install" for
each of the following:

fftw-2.1.5

lam-7.0.6 for MPI

gsl

  

Also commented out the HDF5. But for the Gadget2, I still have the
following error:

  

  

  prems-macbook:~ prem$ cd gadget2

  prems-macbook:gadget2 prem$ make

  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 -lgsl -lgslcblas -lm
-lsrfftw_mpi -lsfftw_mpi -lsrfftw -lsfftw -o Gadget2

  ld: library not found for
-lsrfftw_mpi

  collect2: ld returned 1 exit
status

  make: *** [Gadget2] Error 1

  

Thanks.

Prem

  

  Date: Mon, 20 Dec 2010 09:06:42 +0100

From: Sander.Valcke_at_UGent.be

To: gadget-list_at_MPA-Garching.MPG.DE

Subject: Re: [gadget-list] Help to run gadget2 in macbook

  

  
  
Hi Prem,

  

you'll have to solve the compilation errors in order to be able to run
Gadget 2. In this case it seems that you have to install the gsl
libraries, and you might want to switch off HDF5 support (comment out
-DHAVE_HDF5) in the Makefile. If you look in the first pages of the
user manual, all the required steps are listed there in detail (you
also have to install fftw 2.x).

  

cheers,

  

Sander

  

Prem Dhungel wrote:
  
    Hi
Florian!

    

When I tried to "make" within gadjet2 directory, the error messages are
like this:

    

    prems-macbook:~ prem$ cd gadget2

    prems-macbook:gadget2 prem$
make

    mpicc -O3 -Wall
-DPERIODIC
-DUNEQUALSOFTENINGS -DPEANOHILBERT -DWALLCLOCK -DPMGRID=128
-DSYNCHRONIZATION -DHAVE_HDF5 -I/usr/common/pdsoft/include -c -o
main.o main.c

    In file included from
main.c:7:

    allvars.h:20:25: error:
gsl/gsl_rng.h: No such file or directory

    In file included from
main.c:7:

    allvars.h:157: error: syntax
error before '*' token

    allvars.h:157: warning: type
defaults to 'int' in declaration of 'random_generator'

    allvars.h:157: warning: data
definition has no type or storage class

    In file included from
main.c:8:

    proto.h:10:18: error: hdf5.h:
No such file or directory

    In file included from
main.c:8:

    proto.h:193: error: syntax
error before 'handle'

    make: *** [main.o] Error 1

    

Thank you.

Prem

    From: florian.buerzle_at_uni-konstanz.de

Date: Sun, 19 Dec 2010 16:48:54 +0100

To: gadget-list_at_MPA-Garching.MPG.DE

Subject: Re: [gadget-list] Help to run gadget2 in macbook

    

    

    

Hi Prem!
    

Am 19.12.2010 um 08:56 schrieb Prem Dhungel <premrd_at_hotmail.com>:

    

    
    
      Hi every one,

      

I need to do the simulation for galaxy formation using Gadget2.

But before doing the large full-fledged simulation, I want to do small
ones in my MacBook and be familiar with gadget.

      

I downloaded and installed/configured the necessary components:

gadget 2.0.6

gcc 4.0

HDF5 1.6.10 (mac-intel-x86_64-static version)

fftw-2.1.5

lam-7.0.6 for MPI

      

All these are in the directory \Users /prem

      

When I type the command "mpirun -np 2 ./Gadget2 myparameterfile.param"
in Terminal, the following error message comes:

      

Failed to find or execute the following executable:

Host: prems-macbook.local

Executable: ./Gadget2

Cannot continue.

      

      

It seems that it very simple silly mistake, but I am not able to figure
it out as I'm not so used to in Terminal.

Can anybody help please?

      

      
    
    

    
    I installed Gadget on a Macbook, too, but I don't think your
problem is Macbook specific. It seems that the executable is not
found...Have you actually generated the executale by typing "make"? If
yes, is it in the current directory or somewhere else? Does it have a
name different than Gadget2?
    

    
    If these hints do not help, please describe your workflow in
Terminal in more detail.
    

    
    Cheers
    Florian
    

    
      Thank you.

Prem

      
    
    
      

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| Sander Valcke                                  |
| Sterrenkundig Observatorium, Universiteit Gent |
| Krijgslaan 281 S9, B-9000 Gent, Belgium        |
| phone +32-9-264-4796  |  fax +32-9-264-4989    |
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Disclaimer:
By sending an email to ANY of my addresses you are agreeing that:
   1. I am by definition, "the intended recipient"
   2. All information in the email is mine to do with as I see fit and
      make such financial profit, political mileage, or good joke as
      it lends itself to.
   3. I may take the contents as representing the views of your company.
   4. This overrides any disclaimer or statement of confidentiality
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Received on 2011-01-12 16:01:08

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