Re: Running GADGET 2 on Vista

From: Sander Valcke <Sander.Valcke_at_UGent.be>
Date: Wed, 12 Aug 2009 17:22:14 +0200

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.
--------------------------------------------------
Received on 2009-08-12 17:17:00

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