Re: Running GADGET 2 on Vista

From: Dimitry Ayzenberg <dayzenbe_at_andrew.cmu.edu>
Date: Mon, 17 Aug 2009 10:41:27 -0400

Okay now I'm getting an error saying that
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../1686-pc-cygwin/bin/ld:
cannot find -lsrfftw_mpi
collect2: ld returned 1 exit status
make: *** [Gadget2] Error 1

I don't know what's causing that. Both mpi and fftw are installed.


On Sun, August 16, 2009 20:45, Jay Billings wrote:
> 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
>>
>>
>


-- 
Dimitry Ayzenberg
Carnegie Mellon University
Physics - Class of 2012
Cell:(732)-425-4534
Email: dayzenbe_at_andrew.cmu.edu
Received on 2009-08-17 16:41:30

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