Re: Running GADGET 2 on Vista

From: Dimitry Ayzenberg <dayzenbe_at_andrew.cmu.edu>
Date: Wed, 12 Aug 2009 11:40:12 -0400

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
Received on 2009-08-12 17:40:15

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