[MITgcm-support] Build with netcdf
Roopashree Shrivastava
rss1901 at gmail.com
Mon Jul 30 09:00:58 EDT 2012
Dear Martin,
i am using export NETCDF_ROOT=/home/roopa/netcdf-3.6.1 only. in fact at
the command prompt the command echo $NETCDF_ROOT points correctly to the
above location. where is the file ./genmake_warnings i cud not locate it.
any other suggestions??
thanks
Roopa
On Fri, Jul 27, 2012 at 9:08 PM, <mitgcm-support-request at mitgcm.org> wrote:
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> Today's Topics:
>
> 1. Re: nPx vs. nPy (Martin Losch)
> 2. Re: Build with netcdf (Martin Losch)
> 3. Re: nPx vs. nPy (taimaz.bahadory)
> 4. Re: Build with netcdf (Abhisek Chakraborty)
> 5. Re: nPx vs. nPy (Gus Correa)
> 6. Re: nPx vs. nPy (taimaz.bahadory)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 27 Jul 2012 13:31:14 +0200
> From: Martin Losch <Martin.Losch at awi.de>
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] nPx vs. nPy
> Message-ID: <B2A357CB-404C-4D16-B795-45F1005FF292 at awi.de>
> Content-Type: text/plain; CHARSET=US-ASCII
>
> There you have the answer to your question (one of the cases with a useful
> diagnosis):
> On Jul 27, 2012, at 12:33 AM, taimaz.bahadory wrote:
>
> > Here is what is said inside one of the ten STDERR files generated:
> >
> > (PID.TID 0004.0001) *** ERROR *** S/R ZONAL_FILT_INIT: Multi-tiles (
> nSx*nPx= 10 )
> > (PID.TID 0004.0001) *** ERROR *** in Zonal (X) dir. not implemented in
> Zonal-Filter code
>
> Turn off the zonal filter package and it'll work. I hope you don't need
> this package.
>
> General remark: some compilers can do a little bit of vectorization. In
> that case the x-loops should be as long as possible, so dividing in
> y-direction first is usually the best idea anyway.
>
> Martin
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 27 Jul 2012 13:43:28 +0200
> From: Martin Losch <Martin.Losch at awi.de>
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] Build with netcdf
> Message-ID: <80FEF9D1-49E2-4BC8-BBEE-8C73202E9670 at awi.de>
> Content-Type: text/plain; CHARSET=US-ASCII
>
> I am not sure but try
> export NETCDF_ROOT=/home/roopa/netcdf- 3.6.1
> in your .bashrc, otherwise genmake2 may not inherit it from the calling
> shell?
> genmake2 is looking for files in $NETCDF_ROOT/include and $NETCDF_ROOT/lib
> if in doubht check genmake_warnings for more details.
>
> Martin
>
> On Jul 27, 2012, at 11:31 AM, Roopashree Shrivastava wrote:
>
> > Dear all,
> > Good afternoon. I have a query with building MITGCM with netcdf
> enabled. The details of netcdf installation are as follows
> >
> > FC=gfortran
> > CC=gcc
> > CXX=g++
> > PATH /home/roopa/netcdf- 3.6.1
> >
> > I am building MITGCM also with gfortran. The OPTFILE used is
> linux_amd64_gfortran. In that i have defined the path of netcdf to the
> above installation. however the genmake2 step still shows an error with
> building the netcdf enabled binary. The OPTFILE is attached here for
> reference
> >
> > The specific error is "Can we create netcdf enabled binaries no"
> > check the lib path in the netcdf installation
> >
> > Also in .bashrc I have defined NETCDF_ROOT=/home/roopa/netcdf- 3.6.1
> >
> > then what should NETCDF_HOME and NETCDF_LIB be set to??. According to me
> if NETCDF_ROOT is defined then NETCDF_HOME and NETCDF_LIB are not needed.
> >
> > Thanks to all
> > <linux_amd64_gfortran>_______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 27 Jul 2012 10:37:28 -0230
> From: "taimaz.bahadory" <taimaz.bahadory at mun.ca>
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] nPx vs. nPy
> Message-ID:
> <
> CACtVHujVriBVyvP21cFu4_gpBXthLXfdSYeXyZsWkgTjPQpxrA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Yes it worked!
> Thanks a lot for your help
>
>
>
> On Fri, Jul 27, 2012 at 9:01 AM, Martin Losch <Martin.Losch at awi.de> wrote:
>
> > There you have the answer to your question (one of the cases with a
> useful
> > diagnosis):
> > On Jul 27, 2012, at 12:33 AM, taimaz.bahadory wrote:
> >
> > > Here is what is said inside one of the ten STDERR files generated:
> > >
> > > (PID.TID 0004.0001) *** ERROR *** S/R ZONAL_FILT_INIT: Multi-tiles (
> > nSx*nPx= 10 )
> > > (PID.TID 0004.0001) *** ERROR *** in Zonal (X) dir. not implemented in
> > Zonal-Filter code
> >
> > Turn off the zonal filter package and it'll work. I hope you don't need
> > this package.
> >
> > General remark: some compilers can do a little bit of vectorization. In
> > that case the x-loops should be as long as possible, so dividing in
> > y-direction first is usually the best idea anyway.
> >
> > Martin
> >
> >
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
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>
> ------------------------------
>
> Message: 4
> Date: Fri, 27 Jul 2012 20:26:06 +0530
> From: Abhisek Chakraborty <abhisek.sac at gmail.com>
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] Build with netcdf
> Message-ID:
> <
> CAHQ0S7guhbqCdA7b7SThO3+NEVCecoZ-OG8nN_MvJx52d9+OEg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> If you still have problem, simply modify (in your OPTFILE)
>
> CC=gcc -I/home/roopa/netcdf- 3.6.1/include -L/home/roopa/netcdf- 3.6.1/lib
> -lnetcdf
> FC=gfortran -I/home/roopa/netcdf- 3.6.1/include -L/home/roopa/netcdf-
> 3.6.1/lib -lnetcdf
> F90C=gfortran -I/home/roopa/netcdf- 3.6.1/include -L/home/roopa/netcdf-
> 3.6.1/lib -lnetcdf
>
> I think this will work for you.
>
> Abhisek
>
> On Fri, Jul 27, 2012 at 5:13 PM, Martin Losch <Martin.Losch at awi.de> wrote:
>
> > I am not sure but try
> > export NETCDF_ROOT=/home/roopa/netcdf- 3.6.1
> > in your .bashrc, otherwise genmake2 may not inherit it from the calling
> > shell?
> > genmake2 is looking for files in $NETCDF_ROOT/include and
> $NETCDF_ROOT/lib
> > if in doubht check genmake_warnings for more details.
> >
> > Martin
> >
> > On Jul 27, 2012, at 11:31 AM, Roopashree Shrivastava wrote:
> >
> > > Dear all,
> > > Good afternoon. I have a query with building MITGCM with netcdf
> > enabled. The details of netcdf installation are as follows
> > >
> > > FC=gfortran
> > > CC=gcc
> > > CXX=g++
> > > PATH /home/roopa/netcdf- 3.6.1
> > >
> > > I am building MITGCM also with gfortran. The OPTFILE used is
> > linux_amd64_gfortran. In that i have defined the path of netcdf to the
> > above installation. however the genmake2 step still shows an error with
> > building the netcdf enabled binary. The OPTFILE is attached here for
> > reference
> > >
> > > The specific error is "Can we create netcdf enabled binaries no"
> > > check the lib path in the netcdf installation
> > >
> > > Also in .bashrc I have defined NETCDF_ROOT=/home/roopa/netcdf- 3.6.1
> > >
> > > then what should NETCDF_HOME and NETCDF_LIB be set to??. According to
> me
> > if NETCDF_ROOT is defined then NETCDF_HOME and NETCDF_LIB are not needed.
> > >
> > > Thanks to all
> > > <linux_amd64_gfortran>_______________________________________________
> > > MITgcm-support mailing list
> > > MITgcm-support at mitgcm.org
> > > http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
> >
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
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>
> ------------------------------
>
> Message: 5
> Date: Fri, 27 Jul 2012 11:26:53 -0400
> From: Gus Correa <gus at ldeo.columbia.edu>
> To: MITgcm Support <mitgcm-support at mitgcm.org>
> Subject: Re: [MITgcm-support] nPx vs. nPy
> Message-ID: <5012B33D.8000909 at ldeo.columbia.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Taimaz
>
> Another detail is that you need to recompile the code
> whenever you change the number of processors and subgrid sizes
> in SIZE.h, as most memory is allocated statically.
> Well, at least it used to be this way.
> Did you recompile?
>
> Gus Correa
>
> On 07/26/2012 05:38 PM, taimaz.bahadory wrote:
> > My total grid is 130x100, which matches a Nx=13x1x10 and Ny=100x1x1.
> > As I said, when I play with y-direction (i.e. changing nPy to from 1 to
> > 10 and sNy from 100 to 10, while nPx is 1 and sNx is 130), everything
> > works fine. The problem arises when I try to increase the nPx to
> > something else than 1, also I'm careful of the total product to match
> > the total grid size mentioned in data file.
> >
> >
> >
> > On Thu, Jul 26, 2012 at 6:21 PM, Gus Correa <gus at ldeo.columbia.edu
> > <mailto:gus at ldeo.columbia.edu>> wrote:
> >
> > Hi Taimaz
> >
> > Nx, Ny, Nr are the number of points in your [full] domain,
> > which should match the domain size in your initial condtion files,
> > etc, so they should be fixed for each experiment you run.
> > If there is no match the run fails.
> >
> > Given Nx, you need to find out the the values
> > nPx, and sNx such that their product is Nx
> > [assuming nSx is 1, i.e. you're not using threads/OpenMP].
> > Likewise for nPy, sNy, etc.
> >
> > Note that in SIZE.h is defined as
> > Nx = sNx*nSx*nPx,
> > and Ny = sNy*nSy*nPy.
> > Hence, it is you need to choose the
> > right factors to get the expected products Nx and Ny.
> >
> > I hope this helps,
> > Gus Correa
> >
> >
> > On 07/26/2012 03:56 PM, taimaz.bahadory wrote:
> >
> > Attached
> >
> >
> > On Thu, Jul 26, 2012 at 5:17 PM, Chris Horvat
> > <horvat at fas.harvard.edu <mailto:horvat at fas.harvard.edu>
> > <mailto:horvat at fas.harvard.edu
> > <mailto:horvat at fas.harvard.edu>__>> wrote:
> >
> > Taimaz,
> >
> > Could you include your SIZE.h file so we can see what the
> > other set
> > parameters are?
> >
> > Chris Horvat
> >
> >
> > On Thu, Jul 26, 2012 at 3:45 PM, taimaz.bahadory
> > <taimaz.bahadory at mun.ca <mailto:taimaz.bahadory at mun.ca>
> > <mailto:taimaz.bahadory at mun.ca
> > <mailto:taimaz.bahadory at mun.ca>__>> wrote:
> >
> > Hi;
> >
> > I have configures a code to run my topography file using
> > parallel system (mpi). Everything works fine when I set
> > nPy=10
> > (or anything), but the errors come out when I try to
> > break the
> > x-direction to different sections, i.e. increasing nPx
> to
> > something more than 1.
> > summary:
> >
> > * nPx = 1; nPy = 10 => works fine
> > * nPx = 10; nPy = 1 => fails
> >
> >
> > Is there any limitation on the x-axis?
> >
> > _________________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
> > <mailto:MITgcm-support at mitgcm.__org
> > <mailto:MITgcm-support at mitgcm.org>>
> >
> > http://mitgcm.org/mailman/__listinfo/mitgcm-support
> > <http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >
> >
> >
> > _________________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
> > <mailto:MITgcm-support at mitgcm.__org
> > <mailto:MITgcm-support at mitgcm.org>>
> >
> > http://mitgcm.org/mailman/__listinfo/mitgcm-support
> > <http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >
> >
> >
> >
> > _________________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
> > http://mitgcm.org/mailman/__listinfo/mitgcm-support
> > <http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >
> >
> >
> > _________________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
> > http://mitgcm.org/mailman/__listinfo/mitgcm-support
> > <http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >
> >
> >
> >
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 27 Jul 2012 13:08:25 -0230
> From: "taimaz.bahadory" <taimaz.bahadory at mun.ca>
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] nPx vs. nPy
> Message-ID:
> <
> CACtVHujG1SRCaDgcQy27sayFiN_3NtXPGNxagctUs7YG_ki3MQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Yes I always recompile the code when changing packages and sizes in /code
> directory.
> I can run the code now using 100 processors.
> Thanks
>
>
> On Fri, Jul 27, 2012 at 12:56 PM, Gus Correa <gus at ldeo.columbia.edu>
> wrote:
>
> > Hi Taimaz
> >
> > Another detail is that you need to recompile the code
> > whenever you change the number of processors and subgrid sizes
> > in SIZE.h, as most memory is allocated statically.
> > Well, at least it used to be this way.
> > Did you recompile?
> >
> > Gus Correa
> >
> >
> > On 07/26/2012 05:38 PM, taimaz.bahadory wrote:
> >
> >> My total grid is 130x100, which matches a Nx=13x1x10 and Ny=100x1x1.
> >> As I said, when I play with y-direction (i.e. changing nPy to from 1 to
> >> 10 and sNy from 100 to 10, while nPx is 1 and sNx is 130), everything
> >> works fine. The problem arises when I try to increase the nPx to
> >> something else than 1, also I'm careful of the total product to match
> >> the total grid size mentioned in data file.
> >>
> >>
> >>
> >> On Thu, Jul 26, 2012 at 6:21 PM, Gus Correa <gus at ldeo.columbia.edu
> >> <mailto:gus at ldeo.columbia.edu>**> wrote:
> >>
> >> Hi Taimaz
> >>
> >> Nx, Ny, Nr are the number of points in your [full] domain,
> >> which should match the domain size in your initial condtion files,
> >> etc, so they should be fixed for each experiment you run.
> >> If there is no match the run fails.
> >>
> >> Given Nx, you need to find out the the values
> >> nPx, and sNx such that their product is Nx
> >> [assuming nSx is 1, i.e. you're not using threads/OpenMP].
> >> Likewise for nPy, sNy, etc.
> >>
> >> Note that in SIZE.h is defined as
> >> Nx = sNx*nSx*nPx,
> >> and Ny = sNy*nSy*nPy.
> >> Hence, it is you need to choose the
> >> right factors to get the expected products Nx and Ny.
> >>
> >> I hope this helps,
> >> Gus Correa
> >>
> >>
> >> On 07/26/2012 03:56 PM, taimaz.bahadory wrote:
> >>
> >> Attached
> >>
> >>
> >> On Thu, Jul 26, 2012 at 5:17 PM, Chris Horvat
> >> <horvat at fas.harvard.edu <mailto:horvat at fas.harvard.edu**>
> >> <mailto:horvat at fas.harvard.edu
> >>
> >> <mailto:horvat at fas.harvard.edu**>__>> wrote:
> >>
> >> Taimaz,
> >>
> >> Could you include your SIZE.h file so we can see what the
> >> other set
> >> parameters are?
> >>
> >> Chris Horvat
> >>
> >>
> >> On Thu, Jul 26, 2012 at 3:45 PM, taimaz.bahadory
> >> <taimaz.bahadory at mun.ca <mailto:taimaz.bahadory at mun.ca**>
> >> <mailto:taimaz.bahadory at mun.ca
> >>
> >> <mailto:taimaz.bahadory at mun.ca**>__>> wrote:
> >>
> >> Hi;
> >>
> >> I have configures a code to run my topography file
> using
> >> parallel system (mpi). Everything works fine when I set
> >> nPy=10
> >> (or anything), but the errors come out when I try to
> >> break the
> >> x-direction to different sections, i.e. increasing nPx
> to
> >> something more than 1.
> >> summary:
> >>
> >> * nPx = 1; nPy = 10 => works fine
> >> * nPx = 10; nPy = 1 => fails
> >>
> >>
> >> Is there any limitation on the x-axis?
> >>
> >> ______________________________**___________________
> >>
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.**org<
> MITgcm-support at mitgcm.org>
> >> >
> >> <mailto:MITgcm-support at mitgcm.**__org
> >> <mailto:MITgcm-support at mitgcm.**org <MITgcm-support at mitgcm.org
> >>>
> >>
> >> http://mitgcm.org/mailman/__**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/__listinfo/mitgcm-support>
> >> <http://mitgcm.org/mailman/**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >> >
> >>
> >>
> >>
> >> ______________________________**___________________
> >>
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.**org<
> MITgcm-support at mitgcm.org>
> >> >
> >> <mailto:MITgcm-support at mitgcm.**__org
> >> <mailto:MITgcm-support at mitgcm.**org <MITgcm-support at mitgcm.org
> >>>
> >>
> >> http://mitgcm.org/mailman/__**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/__listinfo/mitgcm-support>
> >> <http://mitgcm.org/mailman/**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >> >
> >>
> >>
> >>
> >>
> >> ______________________________**___________________
> >>
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.**org<
> MITgcm-support at mitgcm.org>
> >> >
> >> http://mitgcm.org/mailman/__**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/__listinfo/mitgcm-support>
> >> <http://mitgcm.org/mailman/**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >> >
> >>
> >>
> >>
> >> ______________________________**___________________
> >>
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.**org<
> MITgcm-support at mitgcm.org>
> >> >
> >> http://mitgcm.org/mailman/__**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/__listinfo/mitgcm-support>
> >>
> >> <http://mitgcm.org/mailman/**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >> >
> >>
> >>
> >>
> >>
> >> ______________________________**_________________
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org
> >> http://mitgcm.org/mailman/**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >>
> >
> >
> > ______________________________**_________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/**listinfo/mitgcm-support<
> http://mitgcm.org/mailman/listinfo/mitgcm-support>
> >
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> MITgcm-support at mitgcm.org
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