Compile pnetcdf library at a new Linux cluster at NERSC

[William Gropp]

At 02:44 AM 12/9/2005, Yu-Heng Tseng wrote:
>Hi,
>
>I couldn't compile the library using "pathf90/pathcc" compiler. It
>gives me the following error during "gmake". It seems "MPI_Type_dup"
>is not defined. A bug in the compiler or the library?

Both MPI_Type_dup and MPI_Request_get_status are part of MPI-2.  What 
version of MPI does your system support?
It sounds like we should add tests for these routines to the configure step.

Bill


>mpicc -o ncmpigen -g -O2 -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64
>main.o load.o ncgentab.o escapes.o getfill.o init.o genlib.o -
>L../../../src/lib -lpnetcdf
>../../../src/lib/libpnetcdf.a(mpinetcdf.o)(.text+0x1041d): In function
>`ncmpi_request_get_status':
>/scratch/scratchdirs/yhtseng/cam_PIO/CAMMODELS/parallel-netcdf-
>1.0.1/src/lib/mpinetcdf.c:8218: undefined reference to
>`MPI_Request_get_status'
>../../../src/lib/libpnetcdf.a(mpinetcdf.o)(.text+0x10cf4): In function
>`ncmpi_iget_var1':
>/scratch/scratchdirs/yhtseng/cam_PIO/CAMMODELS/parallel-netcdf-
>1.0.1/src/lib/mpinetcdf.c:8528: undefined reference to `MPI_Type_dup'
>
>---------------------------------------------------
>Yu-Heng Tseng
>
>Computational Research Division
>Lawrence Berkeley National Laboratory
>One Cyclotron Rd, MS: 50F-1650
>Berkeley, CA94720
>YHTseng at lbl.gov
>510.495.2904
>
>----- Original Message -----
>From: Jim Edwards <jedwards at ucar.edu>
>Date: Tuesday, December 6, 2005 0:40 am
>Subject: Re: Compile pnetcdf library in IBM SP at NCAR
>
> > There is a pnetcdf version installed in the /contrib file system
> > on the NCAR
> > IBM machines.  I have already reported this problem with configure
> > to the
> > parallel netcdf developers.   They have provided a patched release to
> > address the problem.
> >
> > Jim Edwards
> > IBM applications support
> > NCAR
> >
> > On 12/6/05, Yu-Heng Tseng <YHTseng at lbl.gov> wrote:
> > >
> > > Hi,
> > >
> > > I couldn't compile the library in NCAR's IBM SP.
> > > It works fine in NERSC's IBM SP machine.
> > > I am not sure if this is compiler's or the library's problem.
> > > When I tried to "./configure" the
> > > it stops at the following line
> > >
> > > checking for Fortran-equivalent to netCDF "byte"... byte
> > > checking for Fortran-equivalent to netCDF "short"... integer*2
> > > checking for Fortran "integer*"... no
> > > configure: error: F77 does not support "integer*"
> > >
> > > The "integer*" is actually "integer8" in a successful check.
> > >
> > > Anyone has clues to solve the problem? The c compiler at NCAR
> > > seems different from that at NERSC.
> > > NCAR uses  VisualAge C++ Professional / C for AIX Compiler,
> > Version 6
> > >
> > > Thanks a lot for your help!
> > >
> > > Yu-heng
> > > ---------------------------------------------------
> > > Yu-Heng Tseng
> > >
> > > Computational Research Division
> > > Lawrence Berkeley National Laboratory
> > > One Cyclotron Rd, MS: 50F-1650
> > > Berkeley, CA94720
> > > YHTseng at lbl.gov
> > > 510.495.2904
> > >
> > >
> >

William Gropp
http://www.mcs.anl.gov/~gropp