Re: Running GADGET 2 on Vista

From: Jay Billings <jayjaybillings_at_gmail.com>
Date: Sun, 16 Aug 2009 20:45:14 -0400

Dimitry,

If you don't need HDF5, you can disable it in the Makefile.

Jay

On Sun, Aug 16, 2009 at 7:07 PM, Dimitry Ayzenberg
<dayzenbe_at_andrew.cmu.edu>wrote:

>
> So I got everything to work except hdf5. How do I link to it's libraries?
> Or how would I have the make just skip over it because I'm now getting an
> error that it can't find hdf5.h. I attempted to install it using
> ./configure but that failed, even after getting help from their help
> services. Just doesn't want to work on my computer. And I don't
> particularly need it. I have the linux version of it which is just the
> libraries and files. So either how do I link to it or how do I skip over
> it? Thanks,
>
> Dimitry
>
>
> On Wed, August 12, 2009 11:40, Dimitry Ayzenberg wrote:
> >
>
> > Well okay. I finished the configuration for lam mpi. Then I ran make like
> > the instructions say. Took forever, but then it stopped saying something
> > like access is denied for it to change a folder name. I figured it was
> > mostly done anyway so I then ran make install. After some time it hit the
> > same issue. I then tried to run make on gadget again. Some of the errors
> > went away and the only one that seems to be present is that mpio.h can't
> > be found. It says the issue exists in mpi.h so I looked in there. I
> > tried to have mpi.h include mpio.h by going straight to the file
> location,
> > but that didn't work. I now moved the lam folder to my C drive hopefully
> > so that there's no issue with permission. It was in my user folder
> before.
> > I
> > ran make clean and am now running make. Hopefully it'll complete this
> time.
> >
> >
> > -Dimitry
> >
> >
> >
> > On Wed, August 12, 2009 11:22, Sander Valcke wrote:
> >
> >>
> >
> >> As far as I can see there is no mpi package present in cygwin. I
> >> assumed that you had successfully installed lam mpi on cygwin? If not:
> >> install it (or mpich).
> >>
> >>
> >>
> >> It would help if you would be a bit more descriptive of your current
> >> progress and problems...
> >>
> >> Dimitry Ayzenberg wrote:
> >>
> >>
> >>> I've tried that. The problem is I can't find the mpich library in the
> >>> cygwin setup.
> >>>
> >>> Dimitry
> >>>
> >>>
> >>>
> >>>
> >>> On Wed, August 12, 2009 10:48, Arman Khalatyan wrote:
> >>>
> >>>
> >>>
> >>>> Mpich from Windows will not help you.
> >>>> Using cygwin setup install/add mpich library, and it will bring
> >>>> mpicc. cheers a.
> >>>>
> >>>>
> >>>> On Wed, Aug 12, 2009 at 3:22 PM, Sander Valcke
> >>>> <Sander.Valcke_at_ugent.be>wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>> Find the SYSTYPE part of the makefile, add your own type e.g.:
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> SYSTYPE="Dimitri"
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> ifeq ($(SYSTYPE),"Dimitri") CC = mpicc OPTIMIZE = -O3
> >>>>> -Wall
> >>>>> #OPTIMIZE = -g -Wall
> >>>>> GSL_INCL = -I/usr/include/gsl
> >>>>> GSL_LIBS = -L/usr/lib -Wl,"-R/usr/lib"
> >>>>> FFTW_INCL= -I/usr/include
> >>>>> FFTW_LIBS= -L/usr/lib
> >>>>> MPICHLIB = HDF5INCL = HDF5LIB = endif
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> try to compile, if packages or include files are missing some of
> >>>>> the above flags need to be adjusted (depending on where gsl and
> >>>>> fftw include files and libraries were installed). Personally I
> >>>>> don't have to specify anything for mpi, my lam mpicc seems to know
> >>>>> where to find its stuff.
> >>>>>
> >>>>> Sander
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Dimitry Ayzenberg wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>> Okay so now I need the change my makefile, but I'm not sure
> >>>>>> where to change it for mpi. Or for that matter in what format it
> >>>>>> should be in.
> >>>>>>
> >>>>>> -Dimitry
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On Tue, August 11, 2009 14:01, Jay Billings wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>> Configuration with Cygwin can take a really long time, just
> >>>>>>> hang in there.
> >>>>>>>
> >>>>>>> After that, you should be able to link to it. You will need
> >>>>>>> to edit your Makefile and change the mpi include directory
> >>>>>>> before you recompile.
> >>>>>>>
> >>>>>>> Jay
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On 8/11/09, Dimitry Ayzenberg <dayzenbe_at_andrew.cmu.edu>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>> I have mpich2 installed. Found a version for windows that
> >>>>>>>> just installs like any other windows program. Not sure how
> >>>>>>>> to link it though.
> >>>>>>>>
> >>>>>>>> And I'm trying LAM but the configuration for it is taking
> >>>>>>>> really long. Over an hour now.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Dimitry
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Tue, August 11, 2009 13:29, Jay Billings wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> Looks like you didn't compile and link the MPI library.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Jay
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Tue, Aug 11, 2009 at 10:17 AM, Dimitry Ayzenberg
> >>>>>>>>> <dayzenbe_at_andrew.cmu.edu
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> wrote:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> Okay so I added fftw and gsl but I still get errors.
> >>>>>>>>>> The
> >>>>>>>>>> first error I get is that mpicc is an unknown command.
> >>>>>>>>>> So
> >>>>>>>>>> I
> >>>>>>>>>> went into the makefile and changed the C compiler listed
> >>>>>>>>>> to gcc since that is what cygwin has. After that the
> >>>>>>>>>> mpicc error goes away but I get other ones that are
> >>>>>>>>>> confusing to me. This is what the output is when I do
> >>>>>>>>>> the make command:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> gcc -03 -Wall -DPERIODIC -DUNEQUALSOFTENINGS
> >>>>>>>>>> -DPEANOHILBERT
> >>>>>>>>>> -DWALLCLOCK
> >>>>>>>>>> DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> >>>>>>>>>> -I/usr/commmon/pdsoft/include
> >>>>>>>>>> -o main.o main.c
> >>>>>>>>>> main.c:5:17: mpi.h: No such file or directory
> >>>>>>>>>> In file included from main.c:8:
> >>>>>>>>>> proto.h:10:18: hdf5.h: No such file or directory
> >>>>>>>>>> In file included from main.c:8:
> >>>>>>>>>> proto.h:193: error: parse error before "handle"
> >>>>>>>>>> main.c: In function 'main':
> >>>>>>>>>> main.c:26: warning: implicit declaration of function
> >>>>>>>>>> 'MPI_Init'
> >>>>>>>>>> main.c:27: warning: implicit declaration of function
> >>>>>>>>>> 'MPI_Comm_rank'
> >>>>>>>>>> main.c:27: error: 'MPI_COMM_WORLD' undeclared (first use
> >>>>>>>>>> in this function) main.c:27: error: (Each undeclared
> >>>>>>>>>> identifier is reported only once main.c:27: error: for
> >>>>>>>>>> each function it appears in.) main.c:28: warning:
> >>>>>>>>>> implicit declaration of function 'MPI_Comm_size'
> >>>>>>>>>> main.c:73: warning:
> >>>>>>>>>> implicit declaration of function 'MPI_Finalize' make: ***
> >>>>>>>>>> [main.o] Error 1
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> And I don't really understand what does errors actually
> >>>>>>>>>> mean or how I can fix them. I'm used to c++ and java
> >>>>>>>>>> programming, where the errors are more straightforward.
> >>>>>>>>>> Thanks for the help.
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Tue, August 11, 2009 06:11, Arman Khalatyan wrote:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>> coming up with errors that I don't understand. Are
> >>>>>>>>>>> there
> >>>>>>>>>>>
> >>>>>>>>>>>> specific libraries I need to add to cygwin or is
> >>>>>>>>>>>> there a certain way I would need
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>> More detail would help.
> >>>>>>>>>>> What kind of errors?
> >>>>>>>>>>> You should install fftw(if you need cosmological runs)
> >>>>>>>>>>> and gls on cygwin. a.
> >>>>>>>>>>>
> >>>>>>>>>>> ------------------------------------------
> >>>>>>>>>>> Dr Arman Khalatyan,
> >>>>>>>>>>> Observatoire Astronomique de Marseille-Provence
> >>>>>>>>>>> Laboratoire d'Astrophysique de Marseille
> >>>>>>>>>>> -----------------------------------------
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>> --
> >>>>>>>>>> Dimitry Ayzenberg
> >>>>>>>>>> Carnegie Mellon University
> >>>>>>>>>> Physics - Class of 2012
> >>>>>>>>>> Cell:(732)-425-4534
> >>>>>>>>>> Email: dayzenbe_at_andrew.cmu.edu
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> -------------------------------------------------------
> >>>>>>>>>> --
> >>>>>>>>>> --
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> If you wish to unsubscribe from this mailing, send mail
> >>>>>>>>>> to minimalist_at_MPA-Garching.MPG.de with a subject of:
> >>>>>>>>>> unsubscribe gadget-list A web-archive of this mailing
> >>>>>>>>>> list is available here:
> >>>>>>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>> Dimitry Ayzenberg
> >>>>>>>> Carnegie Mellon University
> >>>>>>>> Physics - Class of 2012
> >>>>>>>> Cell:(732)-425-4534
> >>>>>>>> Email: dayzenbe_at_andrew.cmu.edu
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> -----------------------------------------------------------
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> If you wish to unsubscribe from this mailing, send mail to
> >>>>>>>> minimalist_at_MPA-Garching.MPG.de with a subject of:
> >>>>>>>> unsubscribe gadget-list A web-archive of this mailing list
> >>>>>>>> is available here:
> >>>>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>> -----------------------------------------------------------
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> If you wish to unsubscribe from this mailing, send mail to
> >>>>>>> minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe
> >>>>>>> gadget-list A web-archive of this mailing list is available
> >>>>>>> here:
> >>>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>> --
> >>>>> --------------------------------------------------
> >>>>> | Sander Valcke |
> >>>>> | Sterrenkundig Observatorium, Universiteit Gent |
> >>>>> | Krijgslaan 281 S9, B-9000 Gent, Belgium |
> >>>>> | phone +32-9-264-4796 | fax +32-9-264-4989 |
> >>>>> | https://sourceforge.net/projects/hyplot/ |
> >>>>> --------------------------------------------------
> >>>>> FORTUNE'S FUN FACTS TO KNOW AND TELL: #1
> >>>>> A guinea pig is not from Guinea but a rodent from South America.
> >>>>> A firefly is not a fly, but a beetle.
> >>>>> A giant panda bear is really a member of the racoon family.
> >>>>> A black panther is really a leopard that has a solid black coat
> >>>>> rather then a spotted one. Peanuts are not really nuts. The
> >>>>> majority of nuts grow on trees while peauts grow underground.
> >>>>> They
> >>>>> are classified as a legume -- part of the pea family. A cucumber
> >>>>> is not a vegetable but a fruit.
> >>>>> --------------------------------------------------
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> -----------------------------------------------------------
> >>>>> If you wish to unsubscribe from this mailing, send mail to
> >>>>> minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe
> >>>>> gadget-list A web-archive of this mailing list is available here:
> >>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>> ------------------------------------------
> >>>> Dr Arman Khalatyan,
> >>>> Observatoire Astronomique de Marseille-Provence
> >>>> Laboratoire d'Astrophysique de Marseille
> >>>> -----------------------------------------
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>
> >> --
> >> --------------------------------------------------
> >> | Sander Valcke |
> >> | Sterrenkundig Observatorium, Universiteit Gent |
> >> | Krijgslaan 281 S9, B-9000 Gent, Belgium |
> >> | phone +32-9-264-4796 | fax +32-9-264-4989 |
> >> | https://sourceforge.net/projects/hyplot/ |
> >> --------------------------------------------------
> >> FORTUNE'S FUN FACTS TO KNOW AND TELL: #1
> >> A guinea pig is not from Guinea but a rodent from South America.
> >> A firefly is not a fly, but a beetle.
> >> A giant panda bear is really a member of the racoon family.
> >> A black panther is really a leopard that has a solid black coat
> >> rather then a spotted one. Peanuts are not really nuts. The majority of
> >> nuts grow on trees while peauts grow underground. They are classified
> >> as a legume -- part of the pea family. A cucumber is not a vegetable but
> >> a fruit. --------------------------------------------------
> >>
> >>
> >>
> >>
> >>
> >> -----------------------------------------------------------
> >>
> >>
> >>
> >> If you wish to unsubscribe from this mailing, send mail to
> >> minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe
> >> gadget-list A web-archive of this mailing list is available here:
> >> http://www.mpa-garching.mpg.de/gadget/gadget-list
> >>
> >>
> >>
> >>
> >
> >
> > --
> > Dimitry Ayzenberg
> > Carnegie Mellon University
> > Physics - Class of 2012
> > Cell:(732)-425-4534
> > Email: dayzenbe_at_andrew.cmu.edu
> >
> >
> >
> >
> >
> > -----------------------------------------------------------
> >
> >
> > If you wish to unsubscribe from this mailing, send mail to
> > minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe
> gadget-list
> > A web-archive of this mailing list is available here:
> > http://www.mpa-garching.mpg.de/gadget/gadget-list
> >
> >
> >
>
>
> --
> Dimitry Ayzenberg
> Carnegie Mellon University
> Physics - Class of 2012
> Cell:(732)-425-4534
> Email: dayzenbe_at_andrew.cmu.edu
>
>
>
>
> -----------------------------------------------------------
>
> If you wish to unsubscribe from this mailing, send mail to
> minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe gadget-list
> A web-archive of this mailing list is available here:
> http://www.mpa-garching.mpg.de/gadget/gadget-list
>
Received on 2009-08-17 02:45:15

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