[MITgcm-support] Build with netcdf

Martin Losch Martin.Losch at awi.de
Mon Jul 30 10:33:17 EDT 2012


Sorry, I was wrong, I meant genmake.log 
genmake.log records the compiler messages, e.g. the netcdf section could look like this (shows the program that's being compiled, etc.):

> running: check_netcdf_libs()
> ===  genmake_tnc.F  >>>
>       program fgennc
> #include "netcdf.inc"
> #include "mpif.h"
>       integer iret, ncid, xid
>       iret = nf_create('genmake_tnc.nc', NF_CLOBBER, ncid)
>       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
>       iret = nf_def_dim(ncid, 'X', 11, xid)
>       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
>       iret = nf_close(ncid)
>       IF (iret .NE. NF_NOERR) write(*,*) NF_STRERROR(iret)
>       end
> <<<  genmake_tnc.F  ===
> cat genmake_tnc.F |  cpp -traditional -P -DWORDLENGTH=4 -DALLOW_USE_MPI -DALWAYS_USE_MPI -DHAVE_SYSTEM -DHAVE_FDATE -DHAVE_ETIME -DHAVE_CLOC -DHAVE_SETRLSTK -DHAVE_SIGREG -DHAVE_STAT -I/uv/soft/netcdf/3.6.3-intel/include -I/opt/sgi/mpt/mpt-2.05/include
> ifort  -W0 -WB -convert big_endian -assume byterecl -fPIC -O3 -align -c genmake_tnc.f  \ 
>   &&  ifort  -W0 -WB -convert big_endian -assume byterecl -fPIC -O3 -align -o genmake_tnc.o -L/uv/soft/netcdf/3.6.3-intel/lib/ -lmpi
> genmake_tnc.o: In function `MAIN__':
> genmake_tnc.f:(.text+0x54): undefined reference to `nf_create_'
> genmake_tnc.f:(.text+0x8e): undefined reference to `nf_def_dim_'
> genmake_tnc.f:(.text+0xac): undefined reference to `nf_close_'
> genmake_tnc.f:(.text+0xdd): undefined reference to `nf_strerror_'
> genmake_tnc.f:(.text+0x150): undefined reference to `nf_strerror_'
> genmake_tnc.f:(.text+0x1bf): undefined reference to `nf_strerror_'
> 
> ==> try again with added '-lnetcdf'
> cat genmake_tnc.F |  cpp -traditional -P -DWORDLENGTH=4 -DALLOW_USE_MPI -DALWAYS_USE_MPI -DHAVE_SYSTEM -DHAVE_FDATE -DHAVE_ETIME -DHAVE_CLOC -DHAVE_SETRLSTK -DHAVE_SIGREG -DHAVE_STAT -I/uv/soft/netcdf/3.6.3-intel/include -I/opt/sgi/mpt/mpt-2.05/include 
> > genmake_tnc.f \ 
>  &&  ifort  -W0 -WB -convert big_endian -assume byterecl -fPIC -O3 -align -c genmake_tnc.f \ 
>  &&  ifort  -W0 -WB -convert big_endian -assume byterecl -fPIC -O3 -align -o genmake_tnc genmake_tnc.o -L/uv/soft/netcdf/3.6.3-intel/lib/ -lmpi -lnetcdf
> check_netcdf: successful
>  --> set HAVE_NETCDF='t'

This could give you a clue, what's going on, whether your environment is correctly passed to genmake2.

Martin

On Jul 30, 2012, at 3:00 PM, Roopashree Shrivastava wrote:

> 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:
> Send MITgcm-support mailing list submissions to
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> 
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> 
> When replying, please edit your Subject line so it is more specific
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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
> >
> -------------- next part --------------
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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
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
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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
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