[Met_help] [rt.rap.ucar.edu #81499] History for NetCDF-C library installation for MET6.0
Julie Prestopnik via RT
met_help at ucar.edu
Tue Aug 8 12:29:52 MDT 2017
----------------------------------------------------------------
Initial Request
----------------------------------------------------------------
Hello,
I am trying to install MET6.0 but I am getting an error when I try to
install the NetCDF-C libaray. I tried to follow the instructions from the
tutorial, but I already had all of the other libraries installed since I
have been using MET5.2. This is the error:
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-I../include -I../oc2 -I/home/s4m/met-6.0_bugfix//external_libs/include
-MT libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
-c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo './'`nc4file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I../oc2
-I/home/s4m/met-6.0_bugfix//external_libs/include -MT
libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo -c
nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
nc4file.c: In function 'nc4_open_file':
nc4file.c:2316: error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared (first use in
this function)
nc4file.c:2316: error: (Each undeclared identifier is reported only once
nc4file.c:2316: error: for each function it appears in.)
nc4file.c:2316: error: 'H5LT_FILE_IMAGE_DONT_RELEASE' undeclared (first use
in this function)
make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
make[1]: Leaving directory `/home/Shannon.Rees/netcdf-c-4.4.1.1/libsrc4'
I have attached the full log files for the compile and make. If I use
"--disable_netcdf4" it installs without error, but then the NetCDF-CXX
library cannot be installed. I am also concerned that this is using the
gcc compiler, but I use intel to install MET. Will this be a problem?
Thanks,
Shannon
--
Shannon Rees
Meteorologist
Engility
Geophysical Fluid Dynamics Lab
Princeton University Forrestal Campus
201 Forrestal Rd Princeton, NJ
609-452-5384
----------------------------------------------------------------
Complete Ticket History
----------------------------------------------------------------
Subject: NetCDF-C library installation for MET6.0
From: Julie Prestopnik
Time: Mon Aug 07 13:53:31 2017
Hi Shannon.
Yes, when compiling MET and all of the dependent libraries, the same
family
of compilers needs to be used. Mixing compiler families will likely
result
in errors.
There are definitely differences in some of the dependent libraries
between
METv5.2 and METv6.0. For METv5.2 we had users compiling NetCDF
version
4.1.1 or later, use the *--disable-netcdf-4* command line argument.
However, now we do not want to do that as you noted, because we are
now
using NetCDF4 and because NetCDF-CXX cannot be installed. Also, HDF5
is
now a required library. You may need to set LDFLAGS and CPPFLAGS when
installing HDF5.
Here are my installation instructions for HDF5 from my install on
"cheyenne":
Download the HDF5 package:
wget
https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-
1.8.18/src/hdf5-1.8.18.tar.gz
tar -zxf hdf5-1.8.18.tar.gz
cd hdf5-1.8.18
./configure --prefix=$iprefix --with-zlib=$libdir LDFLAGS=-L$libdir
CPPFLAGS=-I$incdir
make
make install
where the following vars are set:
export
libdir=/glade/p/ral/jnt/MET/MET_releases/cheyenne/external_libs/lib
export
incdir=/glade/p/ral/jnt/MET/MET_releases/cheyenne/external_libs/include
export
iprefix=/glade/p/ral/jnt/MET/MET_releases/cheyenne/external_libs/
I'll go ahead an list my install instructions for NetCDF-C and NetCDF-
CXX
below:
Download the NetCDF C package:
wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.4.1.1.zip
unzip netcdf-4.4.1.1
cd netcdf-4.4.1.1
export FC=''
export F90=''
./configure --prefix=$iprefix LDFLAGS=-L$libdir CPPFLAGS=-I$incdir
make; make install
Download the NetCDF CXX package:
wget
https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-cxx4-
4.3.0.tar.gz
tar -zxf netcdf-cxx4-4.3.0.tar.gz
cd netcdf-cxx4-4.3.0
./configure --prefix=$iprefix LDFLAGS=-L$libdir CPPFLAGS=-I$incdir
make; make install
Please give those a try and let us know how it goes.
Also, depending on what machine you are running on, you may have
access to
METv6.0 already. Please see this page for a list of existing MET
Builds:
http://www.dtcenter.org/met/users/downloads/existing_met_builds.php
I hope this helps. Please let us know if you have any other questions
or
problems.
Thanks,
Julie
On Mon, Aug 7, 2017 at 9:15 AM, Shannon Rees - NOAA Affiliate via RT <
met_help at ucar.edu> wrote:
>
> Mon Aug 07 09:15:34 2017: Request 81499 was acted upon.
> Transaction: Ticket created by shannon.rees at noaa.gov
> Queue: met_help
> Subject: NetCDF-C library installation for MET6.0
> Owner: Nobody
> Requestors: shannon.rees at noaa.gov
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=81499 >
>
>
> Hello,
>
> I am trying to install MET6.0 but I am getting an error when I try
to
> install the NetCDF-C libaray. I tried to follow the instructions
from the
> tutorial, but I already had all of the other libraries installed
since I
> have been using MET5.2. This is the error:
>
> /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I..
> -I../include -I../oc2 -I/home/s4m/met-
6.0_bugfix//external_libs/include
> -MT libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
'./'`nc4file.c
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> -I/home/s4m/met-6.0_bugfix//external_libs/include -MT
> libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo
-c
> nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> nc4file.c: In function 'nc4_open_file':
> nc4file.c:2316: error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared (first
use in
> this function)
> nc4file.c:2316: error: (Each undeclared identifier is reported only
once
> nc4file.c:2316: error: for each function it appears in.)
> nc4file.c:2316: error: 'H5LT_FILE_IMAGE_DONT_RELEASE' undeclared
(first use
> in this function)
> make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> make[1]: Leaving directory `/home/Shannon.Rees/netcdf-c-
4.4.1.1/libsrc4'
>
> I have attached the full log files for the compile and make. If I
use
> "--disable_netcdf4" it installs without error, but then the NetCDF-
CXX
> library cannot be installed. I am also concerned that this is using
the
> gcc compiler, but I use intel to install MET. Will this be a
problem?
>
> Thanks,
> Shannon
> --
> Shannon Rees
> Meteorologist
> Engility
> Geophysical Fluid Dynamics Lab
> Princeton University Forrestal Campus
> 201 Forrestal Rd Princeton, NJ
> 609-452-5384
>
>
------------------------------------------------
Subject: NetCDF-C library installation for MET6.0
From: Shannon Rees - NOAA Affiliate
Time: Tue Aug 08 12:22:01 2017
Hi Julie,
Thanks for your help! I was able to install MET6.0 successfully
following
these directions. I think the problem was that it was not linking
properly
to the HDF5 libraries already on this system so it was best to do a
fresh
HDF5 install.
Best,
Shannon
On Mon, Aug 7, 2017 at 3:53 PM, Julie Prestopnik via RT
<met_help at ucar.edu>
wrote:
> Hi Shannon.
>
> Yes, when compiling MET and all of the dependent libraries, the same
family
> of compilers needs to be used. Mixing compiler families will likely
result
> in errors.
>
> There are definitely differences in some of the dependent libraries
between
> METv5.2 and METv6.0. For METv5.2 we had users compiling NetCDF
version
> 4.1.1 or later, use the *--disable-netcdf-4* command line argument.
> However, now we do not want to do that as you noted, because we are
now
> using NetCDF4 and because NetCDF-CXX cannot be installed. Also,
HDF5 is
> now a required library. You may need to set LDFLAGS and CPPFLAGS
when
> installing HDF5.
>
> Here are my installation instructions for HDF5 from my install on
> "cheyenne":
>
> Download the HDF5 package:
> wget
> https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/
> hdf5-1.8.18/src/hdf5-1.8.18.tar.gz
> tar -zxf hdf5-1.8.18.tar.gz
> cd hdf5-1.8.18
> ./configure --prefix=$iprefix --with-zlib=$libdir LDFLAGS=-L$libdir
> CPPFLAGS=-I$incdir
> make
> make install
>
> where the following vars are set:
> export
libdir=/glade/p/ral/jnt/MET/MET_releases/cheyenne/external_libs/lib
> export
>
incdir=/glade/p/ral/jnt/MET/MET_releases/cheyenne/external_libs/include
> export
iprefix=/glade/p/ral/jnt/MET/MET_releases/cheyenne/external_libs/
>
> I'll go ahead an list my install instructions for NetCDF-C and
NetCDF-CXX
> below:
>
> Download the NetCDF C package:
> wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.4.1.1.zip
> unzip netcdf-4.4.1.1
> cd netcdf-4.4.1.1
> export FC=''
> export F90=''
> ./configure --prefix=$iprefix LDFLAGS=-L$libdir CPPFLAGS=-I$incdir
> make; make install
>
>
> Download the NetCDF CXX package:
> wget
> https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/
> netcdf-cxx4-4.3.0.tar.gz
> tar -zxf netcdf-cxx4-4.3.0.tar.gz
> cd netcdf-cxx4-4.3.0
> ./configure --prefix=$iprefix LDFLAGS=-L$libdir CPPFLAGS=-I$incdir
> make; make install
>
> Please give those a try and let us know how it goes.
>
> Also, depending on what machine you are running on, you may have
access to
> METv6.0 already. Please see this page for a list of existing MET
Builds:
> http://www.dtcenter.org/met/users/downloads/existing_met_builds.php
>
> I hope this helps. Please let us know if you have any other
questions or
> problems.
>
> Thanks,
> Julie
>
> On Mon, Aug 7, 2017 at 9:15 AM, Shannon Rees - NOAA Affiliate via RT
<
> met_help at ucar.edu> wrote:
>
> >
> > Mon Aug 07 09:15:34 2017: Request 81499 was acted upon.
> > Transaction: Ticket created by shannon.rees at noaa.gov
> > Queue: met_help
> > Subject: NetCDF-C library installation for MET6.0
> > Owner: Nobody
> > Requestors: shannon.rees at noaa.gov
> > Status: new
> > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=81499 >
> >
> >
> > Hello,
> >
> > I am trying to install MET6.0 but I am getting an error when I try
to
> > install the NetCDF-C libaray. I tried to follow the instructions
from
> the
> > tutorial, but I already had all of the other libraries installed
since I
> > have been using MET5.2. This is the error:
> >
> > /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I.
> -I..
> > -I../include -I../oc2 -I/home/s4m/met-6.0_bugfix//
> external_libs/include
> > -MT libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.
> Tpo
> > -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> './'`nc4file.c
> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> > -I/home/s4m/met-6.0_bugfix//external_libs/include -MT
> > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo -c
> > nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> > nc4file.c: In function 'nc4_open_file':
> > nc4file.c:2316: error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared
(first use
> in
> > this function)
> > nc4file.c:2316: error: (Each undeclared identifier is reported
only once
> > nc4file.c:2316: error: for each function it appears in.)
> > nc4file.c:2316: error: 'H5LT_FILE_IMAGE_DONT_RELEASE' undeclared
(first
> use
> > in this function)
> > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > make[1]: Leaving directory `/home/Shannon.Rees/netcdf-c-
4.4.1.1/libsrc4'
> >
> > I have attached the full log files for the compile and make. If I
use
> > "--disable_netcdf4" it installs without error, but then the
NetCDF-CXX
> > library cannot be installed. I am also concerned that this is
using the
> > gcc compiler, but I use intel to install MET. Will this be a
problem?
> >
> > Thanks,
> > Shannon
> > --
> > Shannon Rees
> > Meteorologist
> > Engility
> > Geophysical Fluid Dynamics Lab
> > Princeton University Forrestal Campus
> > 201 Forrestal Rd Princeton, NJ
> > 609-452-5384
> >
> >
>
>
--
Shannon Rees
Meteorologist
Engility
Geophysical Fluid Dynamics Lab
Princeton University Forrestal Campus
201 Forrestal Rd Princeton, NJ
609-452-5384
------------------------------------------------
Subject: NetCDF-C library installation for MET6.0
From: Julie Prestopnik
Time: Tue Aug 08 12:29:34 2017
Great, Shannon! Thanks for letting us know that you were able to
install
MET successfully. I'll go ahead and close this ticket.
Julie
On Tue, Aug 8, 2017 at 12:22 PM, Shannon Rees - NOAA Affiliate via RT
<
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=81499 >
>
> Hi Julie,
>
> Thanks for your help! I was able to install MET6.0 successfully
following
> these directions. I think the problem was that it was not linking
properly
> to the HDF5 libraries already on this system so it was best to do a
fresh
> HDF5 install.
>
> Best,
> Shannon
>
> On Mon, Aug 7, 2017 at 3:53 PM, Julie Prestopnik via RT
<met_help at ucar.edu
> >
> wrote:
>
> > Hi Shannon.
> >
> > Yes, when compiling MET and all of the dependent libraries, the
same
> family
> > of compilers needs to be used. Mixing compiler families will
likely
> result
> > in errors.
> >
> > There are definitely differences in some of the dependent
libraries
> between
> > METv5.2 and METv6.0. For METv5.2 we had users compiling NetCDF
version
> > 4.1.1 or later, use the *--disable-netcdf-4* command line
argument.
> > However, now we do not want to do that as you noted, because we
are now
> > using NetCDF4 and because NetCDF-CXX cannot be installed. Also,
HDF5 is
> > now a required library. You may need to set LDFLAGS and CPPFLAGS
when
> > installing HDF5.
> >
> > Here are my installation instructions for HDF5 from my install on
> > "cheyenne":
> >
> > Download the HDF5 package:
> > wget
> > https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/
> > hdf5-1.8.18/src/hdf5-1.8.18.tar.gz
> > tar -zxf hdf5-1.8.18.tar.gz
> > cd hdf5-1.8.18
> > ./configure --prefix=$iprefix --with-zlib=$libdir LDFLAGS=-
L$libdir
> > CPPFLAGS=-I$incdir
> > make
> > make install
> >
> > where the following vars are set:
> > export libdir=/glade/p/ral/jnt/MET/MET_releases/cheyenne/
> external_libs/lib
> > export
> >
incdir=/glade/p/ral/jnt/MET/MET_releases/cheyenne/external_libs/include
> > export
iprefix=/glade/p/ral/jnt/MET/MET_releases/cheyenne/external_libs/
> >
> > I'll go ahead an list my install instructions for NetCDF-C and
NetCDF-CXX
> > below:
> >
> > Download the NetCDF C package:
> > wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.4.1.1.zip
> > unzip netcdf-4.4.1.1
> > cd netcdf-4.4.1.1
> > export FC=''
> > export F90=''
> > ./configure --prefix=$iprefix LDFLAGS=-L$libdir CPPFLAGS=-I$incdir
> > make; make install
> >
> >
> > Download the NetCDF CXX package:
> > wget
> > https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/
> > netcdf-cxx4-4.3.0.tar.gz
> > tar -zxf netcdf-cxx4-4.3.0.tar.gz
> > cd netcdf-cxx4-4.3.0
> > ./configure --prefix=$iprefix LDFLAGS=-L$libdir CPPFLAGS=-I$incdir
> > make; make install
> >
> > Please give those a try and let us know how it goes.
> >
> > Also, depending on what machine you are running on, you may have
access
> to
> > METv6.0 already. Please see this page for a list of existing MET
Builds:
> >
http://www.dtcenter.org/met/users/downloads/existing_met_builds.php
> >
> > I hope this helps. Please let us know if you have any other
questions or
> > problems.
> >
> > Thanks,
> > Julie
> >
> > On Mon, Aug 7, 2017 at 9:15 AM, Shannon Rees - NOAA Affiliate via
RT <
> > met_help at ucar.edu> wrote:
> >
> > >
> > > Mon Aug 07 09:15:34 2017: Request 81499 was acted upon.
> > > Transaction: Ticket created by shannon.rees at noaa.gov
> > > Queue: met_help
> > > Subject: NetCDF-C library installation for MET6.0
> > > Owner: Nobody
> > > Requestors: shannon.rees at noaa.gov
> > > Status: new
> > > Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=81499
> >
> > >
> > >
> > > Hello,
> > >
> > > I am trying to install MET6.0 but I am getting an error when I
try to
> > > install the NetCDF-C libaray. I tried to follow the
instructions from
> > the
> > > tutorial, but I already had all of the other libraries installed
since
> I
> > > have been using MET5.2. This is the error:
> > >
> > > /bin/sh ../libtool --tag=CC --mode=compile gcc
-DHAVE_CONFIG_H -I.
> > -I..
> > > -I../include -I../oc2 -I/home/s4m/met-6.0_bugfix//
> > external_libs/include
> > > -MT libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.
> > Tpo
> > > -c -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo
> > './'`nc4file.c
> > > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../include
-I../oc2
> > > -I/home/s4m/met-6.0_bugfix//external_libs/include -MT
> > > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-
nc4file.Tpo
> -c
> > > nc4file.c -fPIC -DPIC -o .libs/libnetcdf4_la-nc4file.o
> > > nc4file.c: In function 'nc4_open_file':
> > > nc4file.c:2316: error: 'H5LT_FILE_IMAGE_DONT_COPY' undeclared
(first
> use
> > in
> > > this function)
> > > nc4file.c:2316: error: (Each undeclared identifier is reported
only
> once
> > > nc4file.c:2316: error: for each function it appears in.)
> > > nc4file.c:2316: error: 'H5LT_FILE_IMAGE_DONT_RELEASE' undeclared
(first
> > use
> > > in this function)
> > > make[1]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > > make[1]: Leaving directory `/home/Shannon.Rees/netcdf-c-
> 4.4.1.1/libsrc4'
> > >
> > > I have attached the full log files for the compile and make. If
I use
> > > "--disable_netcdf4" it installs without error, but then the
NetCDF-CXX
> > > library cannot be installed. I am also concerned that this is
using
> the
> > > gcc compiler, but I use intel to install MET. Will this be a
problem?
> > >
> > > Thanks,
> > > Shannon
> > > --
> > > Shannon Rees
> > > Meteorologist
> > > Engility
> > > Geophysical Fluid Dynamics Lab
> > > Princeton University Forrestal Campus
> > > 201 Forrestal Rd Princeton, NJ
> > > 609-452-5384
> > >
> > >
> >
> >
>
>
> --
> Shannon Rees
> Meteorologist
> Engility
> Geophysical Fluid Dynamics Lab
> Princeton University Forrestal Campus
> 201 Forrestal Rd Princeton, NJ
> 609-452-5384
>
>
------------------------------------------------
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