Compile pnetcdf library at a new Linux cluster at NERSC

[Rob Ross]

Hi,

It looks like that mpicc is putting the MPI library too far forward in 
the link line, so objects that libpnetcdf.a needs aren't getting resolved?

Rob

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?
> 
> 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
>>>
>>>
>