[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[netCDF #XCV-291469]: NetCDF 4.1.3 build on Mac OS X 10.7 (Lion)

Greetings!

There have been some changes with the netCDF configure script which included 
dropping the --with-zlib and --with-szlib flags (those flags actually broke the 
install on some systems, so they had to go). In order to tell the configure 
script to use szlib and zlib, you simply have to point it the directory where 
they live, except now you need to do so with the CPPFLAGS and LDFLAGS:

CPPFLAGS="-I/path/to/zlib/include -I/path/to/szlib/include" 
LDFLAGS=-"L/path/to/zlib/lib -L/path/to/szlib/lib" ./configure <options>

If configure can find the zlib and szlib libs in the paths you specify in 
CPPFLAGS and LDFLAGS, then it will use them.

We don't use a --enable-parallel flag - in order to build the parallel version 
of netCDF (and HDF), check out the following page:

http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install/parallel.html#parallel

Cheers!

Sean

> Thank you, Sean!
> 
> I just downloaded the daily snapshot and ran configure with:
> 
> ./configure --prefix=${NETCDF4} --enable-netcdf4 --enable-parallel 
> --with-zlib=${LIBZ}/lib --with-szlib=${SZIP}/lib
> 
> I received these new warnings:
> 
> configure: WARNING: unrecognized options: --enable-parallel, --with-zlib, 
> --with-szlib
> 
> If I specify CC=mpicc, FF=mpif77, FC=mpif90, etc., does configure 
> automatically know to build a parallel version?
> 
> 'configure --help' tells me this:
> 
> Optional Packages:
> --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
> 
> How will configure know to build with zlib and szip?
> 
> Craig
> 
> On Aug 12, 2011, at 10:56 AM, Unidata netCDF Support wrote:
> 
> > Greetings Craig,
> >
> > It looks like this bug in the tests has been fixed. I am not sure if the 
> > fix has been pushed to the nightly build yet or not, but as a work around, 
> > compile netCDF without either the --enable-large-file-tests or 
> > --enable-benchmarks flags.
> >
> > Please let me know how this goes! Cheers!
> >
> > Sean
> >
> >> Great -- thank you for keeping me updated on the situation, Sean!
> >>
> >> Craig
> >>
> >> On Aug 5, 2011, at 4:26 PM, Unidata netCDF Support wrote:
> >>
> >>> Thanks for the logs Craig. This appears to be a bug. The main developers 
> >>> of netCDF are looking into the problem, and I'll let you know when it 
> >>> gets fixed in the nightly build.
> >>>
> >>> Thanks!
> >>>
> >>> Sean
> >>>
> >>>> Hi Sean,
> >>>>
> >>>> Attached are the logs, compressed with 'gzip' to prevent contamination 
> >>>> by e-mail clients:
> >>>>
> >>>> config.log.gz
> >>>> make.log.gz
> >>>> check.log.gz
> >>>>
> >>>> Guess I could edit the source (tst_create_files.c), but there must be 
> >>>> some reason why the function signatures don't match.
> >>>>
> >>>> Thanks for your help!
> >>>> Craig
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On Jul 29, 2011, at 10:28 PM, Unidata netCDF Support wrote:
> >>>>
> >>>>> Hi Craig,
> >>>>>
> >>>>> Unfortunately, I've never passed step one with users in trying to fix 
> >>>>> this one. Step one is "please send me the logs from configure, make, 
> >>>>> and make check", but I get silence after that. So, I'll cross my 
> >>>>> fingers and ask, would you mind sending those logs?
> >>>>>
> >>>>> Sorry for the lack of magic, but with your help, we'll do our best!
> >>>>>
> >>>>> Sean
> >>>>>
> >>>>>> Hi Sean,
> >>>>>>
> >>>>>> That fix got me past those errors!
> >>>>>>
> >>>>>> However, now I am running into this mpicc build error:
> >>>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> >>>>>> gnumake[2]: `tst_large' is up to date.
> >>>>>> depbase=`echo tst_create_files.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
> >>>>>> mpicc -DHAVE_CONFIG_H -I. -I.. -I../fortran  -I../include -I../oc  
> >>>>>> -DNDEBUG -DpgiFortran  -w -O3 -xHost -ip -fp-model fast=2 -no-prec-div 
> >>>>>> -no-prec-sqrt -ftz -no-multibyte-chars -m64 -I/usr/local/phdf5/include 
> >>>>>> -I/usr/local/szip/include -MT tst_create_files.o -MD -MP -MF 
> >>>>>> $depbase.Tpo -c -o tst_create_files.o tst_create_files.c &&\
> >>>>>> mv -f $depbase.Tpo $depbase.Po
> >>>>>> tst_create_files.c(61): error #140: too many arguments in function call
> >>>>>> if (nc_def_var_chunking(ncid, varid, NULL, chunk_sizes, NULL)) ERR;
> >>>>>> ^
> >>>>>> gnumake[2]: *** [tst_create_files.o] Error 2
> >>>>>> gnumake[1]: *** [check-am] Error 2
> >>>>>> make: *** [check-recursive] Error 1
> >>>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> >>>>>>
> >>>>>> Any magic for this one?
> >>>>>>
> >>>>>> Craig
> >>>>>>
> >>>>>>
> >>>>>> On Jul 29, 2011, at 4:48 PM, Unidata netCDF Support wrote:
> >>>>>>
> >>>>>>> Greetings Craig!
> >>>>>>>
> >>>>>>> The issue has to do with a test related to libsz - a fix has recently 
> >>>>>>> be added, but is only avaliable in the nightly build at this point. 
> >>>>>>> Please try using the nightly build to see if this fixes the issue:
> >>>>>>>
> >>>>>>> ftp.unidata.ucar.edu/pub/netcdf/snapshot/netcdf-4-daily.tar.gz
> >>>>>>>
> >>>>>>> Cheers!
> >>>>>>>
> >>>>>>> Sean
> >>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> I am trying to build NetCDF 4.1.3 on Mac OS X 10.7 (Lion) with the 
> >>>>>>>> Intel 12.0.4.184 compilers using these settings:
> >>>>>>>>
> >>>>>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> >>>>>>>> setenv USR_LOCAL /usr/local
> >>>>>>>> setenv LIBZ /usr
> >>>>>>>> setenv HDF5 ${USR_LOCAL}/phdf5
> >>>>>>>>
> >>>>>>>> setenv INCS "-I${HDF5}/include"
> >>>>>>>> setenv LIBS "-L${HDF5}/lib -lhdf5 -L${LIBZ}/lib -lz"
> >>>>>>>>
> >>>>>>>> setenv NETCDF4 ${USR_LOCAL}/netcdf4
> >>>>>>>>
> >>>>>>>> setenv CPP "cpp -C -P -xassembler-with-cpp -traditional"
> >>>>>>>> setenv CC mpicc
> >>>>>>>> setenv CXX mpicxx
> >>>>>>>> setenv F77 mpif77
> >>>>>>>> setenv FF mpif77
> >>>>>>>> setenv FC mpif90
> >>>>>>>>
> >>>>>>>> setenv CPPFLAGS "-DNDEBUG -DpgiFortran"
> >>>>>>>> setenv CFLAGS "-w -O3 -xHost -ip -fp-model fast=2 -no-prec-div 
> >>>>>>>> -no-prec-sqrt -ftz -no-multibyte-chars -m64 ${INCS}"
> >>>>>>>> setenv CXXFLAGS "-w -O3 -xHost -ip -fp-model fast=2 -no-prec-div 
> >>>>>>>> -no-prec-sqrt -ftz -no-multibyte-chars -m64 ${INCS}"
> >>>>>>>> setenv FCLAGS "-w -O3 -xHost -ip -fp-model fast=2 -no-heap-arrays 
> >>>>>>>> -no-prec-div -no-prec-sqrt -ftz -align all -m64 ${INCS}"
> >>>>>>>> setenv FFLAGS "-w -O3 -xHost -ip -fp-model fast=2 -no-heap-arrays 
> >>>>>>>> -no-prec-div -no-prec-sqrt -ftz -align all -m64 ${INCS}"
> >>>>>>>> setenv LDFLAGS "-w -O3 -xHost -ip -fp-model fast=2 -no-heap-arrays 
> >>>>>>>> -no-prec-div -no-prec-sqrt -ftz -m64 ${LIBS}"
> >>>>>>>>
> >>>>>>>> ./configure --prefix=${NETCDF4} --enable-parallel 
> >>>>>>>> --with-zlib=/usr/lib --enable-large-file-tests --enable-benchmarks
> >>>>>>>>
> >>>>>>>> make |& tee make.log
> >>>>>>>> make check |& tee check.log
> >>>>>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> >>>>>>>>
> >>>>>>>> It builds fine and all the tests are successful, until it hits this 
> >>>>>>>> compiler glitch:
> >>>>>>>>
> >>>>>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> >>>>>>>> libtool: link: mpif90 -I../fortran -I../f90 -I../f90 -I../include 
> >>>>>>>> -I../oc -g -w -O3 -xHost -ip -fp-model fast=2 -no-heap-arrays 
> >>>>>>>> -no-prec-div -no-prec-sqrt -ftz -m64 -o f90tst_vars4 f90tst_vars4.o  
> >>>>>>>> -L/usr/local/phdf5/lib -L/usr/local/szip/lib -L/usr/lib 
> >>>>>>>> ../fortran/.libs/libnetcdff.a 
> >>>>>>>> /Users/cmattock/Downloads/netcdf-4.1.3/liblib/.libs/libnetcdf.a 
> >>>>>>>> /usr/local/phdf5/lib/libhdf5_hl.dylib -lcurl 
> >>>>>>>> /usr/local/phdf5/lib/libhdf5.dylib /usr/local/szip/lib/libsz.dylib 
> >>>>>>>> -lm -lz
> >>>>>>>> mpif90  -I../fortran -I../f90 -I../f90 -I../include -I../oc  -g -c 
> >>>>>>>> -o f90tst_vars2.o  f90tst_vars2.f90
> >>>>>>>> f90tst_vars2.f90(37): error #6418: This name has already been 
> >>>>>>>> assigned a data type.   [CACHE_SIZE]
> >>>>>>>> integer, parameter :: CACHE_SIZE = 8, CACHE_NELEMS = 571, 
> >>>>>>>> CACHE_PREEMPTION = 66
> >>>>>>>> ------------------------^
> >>>>>>>> f90tst_vars2.f90(37): error #6418: This name has already been 
> >>>>>>>> assigned a data type.   [CACHE_NELEMS]
> >>>>>>>> integer, parameter :: CACHE_SIZE = 8, CACHE_NELEMS = 571, 
> >>>>>>>> CACHE_PREEMPTION = 66
> >>>>>>>> ----------------------------------------^
> >>>>>>>> f90tst_vars2.f90(77): error #6284: There is no matching specific 
> >>>>>>>> function for this generic function reference.   [NF90_DEF_VAR]
> >>>>>>>> call check(nf90_def_var(ncid, VAR5_NAME, NF90_INT, dimids, varid5, 
> >>>>>>>> chunksizes = chunksizes, &
> >>>>>>>> -------------^
> >>>>>>>> f90tst_vars2.f90(85): error #6404: This name does not have a type, 
> >>>>>>>> and must have an explicit type.   [NF90_SET_VAR_CHUNK_CACHE]
> >>>>>>>> call check(nf90_set_var_chunk_cache(ncid, varid1, CACHE_SIZE, &
> >>>>>>>> -------------^
> >>>>>>>> compilation aborted for f90tst_vars2.f90 (code 1)
> >>>>>>>> gnumake[2]: *** [f90tst_vars2.o] Error 1
> >>>>>>>> gnumake[1]: *** [check-am] Error 2
> >>>>>>>> make: *** [check-recursive] Error 1
> >>>>>>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> >>>>>>>>
> >>>>>>>> Is this repetitive parameter information coming in through the "use 
> >>>>>>>> netcdf" import? What is the best way to fix this?
> >>>>>>>>
> >>>>>>>> Thank you!
> >>>>>>>> Craig
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Ticket Details
> >>>>>>> ===================
> >>>>>>> Ticket ID: XCV-291469
> >>>>>>> Department: Support netCDF
> >>>>>>> Priority: Normal
> >>>>>>> Status: Open
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>> Ticket Details
> >>>>> ===================
> >>>>> Ticket ID: XCV-291469
> >>>>> Department: Support netCDF
> >>>>> Priority: Normal
> >>>>> Status: Open
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>> Ticket Details
> >>> ===================
> >>> Ticket ID: XCV-291469
> >>> Department: Support netCDF
> >>> Priority: High
> >>> Status: Open
> >>>
> >>
> >>
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: XCV-291469
> > Department: Support netCDF
> > Priority: Urgent
> > Status: Open
> >
> 
> 


Ticket Details
===================
Ticket ID: XCV-291469
Department: Support netCDF
Priority: Urgent
Status: Open