Re: Help to run gadget2 in macbook

From: Sander Valcke <Sander.Valcke_at_ugent.be>
Date: Wed, 12 Jan 2011 16:36:20 +0100

Hi Prem,

could you post the compile command giving you this error?

On 01/12/2011 04:01 PM, Prem Dhungel wrote:
> 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 <mailto:Sander.Valcke_at_UGent.be>
> To: gadget-list_at_MPA-Garching.MPG.DE
> <mailto: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
> <mailto:florian.buerzle_at_uni-konstanz.de>
> Date: Sun, 19 Dec 2010 16:48:54 +0100
> To: gadget-list_at_MPA-Garching.MPG.DE
> <mailto: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 <mailto: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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> | Sterrenkundig Observatorium, Universiteit Gent |
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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 |
> |http://sourceforge.net/apps/wordpress/hyplot/ |
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> Disclaimer:
> By sending an email to ANY of my addresses you are agreeing that:
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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    |
| http://sourceforge.net/apps/wordpress/hyplot/  |
--------------------------------------------------
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
      that may be included in your message.
Received on 2011-01-12 16:46:23

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