Compile pnetcdf library at a new Linux cluster at NERSC

[Yu-Heng Tseng]

Yes. Only part of MPI-2 is implemented in the compiler.
Both MPI_Type_dup and MPI_Request_get_status 
are not supported in the Linux cluster at NERSC (jacquard).
Is it possible to test the library without both functionalities?

---------------------------------------------------
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: William Gropp <gropp at mcs.anl.gov>
Date: Friday, December 9, 2005 5:02 am
Subject: Re: Compile pnetcdf library at a new Linux cluster at NERSC

> 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 
> 
>