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
Received on 2009-08-17 01:07:07