[Met_help] [rt.rap.ucar.edu #75787] History for Running MET Series_analysis on Jet

Mon Apr 18 12:17:19 MDT 2016

----------------------------------------------------------------
  Initial Request
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Howdy!

I am attempting to use the MET 5.1 installation on Jet and I am getting a
run time error that the libnetcdf can't be found:

/lfs2/projects/dtc-hurr/MET/MET_releases/met-5.1/bin/series_analysis: error
while loading shared libraries: libnetcdf_c++.so.4: cannot open shared
object file: No such file or directory

If I run an ldd on the executable, I get the following:
linux-vdso.so.1 =>  (0x00007fff4efc0000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00007f5a96366000)
libz.so.1 => /lib64/libz.so.1 (0x00007f5a9614f000)
libm.so.6 => /lib64/libm.so.6 (0x00007f5a95ecb000)
libnetcdf_c++.so.4 => not found
libnetcdf.so.7 => /apps/netcdf/4.2.1.1-intel/lib/libnetcdf.so.7
(0x00007f5a95ada000)
libgsl.so.0 => /usr/lib64/libgsl.so.0 (0x00007f5a956e3000)
libgslcblas.so.0 => /usr/lib64/libgslcblas.so.0 (0x00007f5a954ac000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f5a951a5000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f5a94f8f000)
libc.so.6 => /lib64/libc.so.6 (0x00007f5a94bfb000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f5a949f6000)
libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00007f5a947a6000)
libhdf5_hl.so.7 => /apps/hdf5/1.8.9-intel/lib/libhdf5_hl.so.7
(0x00007f5a94571000)
libhdf5.so.7 => /apps/hdf5/1.8.9-intel/lib/libhdf5.so.7 (0x00007f5a93fe7000)
librt.so.1 => /lib64/librt.so.1 (0x00007f5a93ddf000)
libsz.so.2 => /apps/szip/2.1/lib/libsz.so.2 (0x00007f5a93bcc000)
libimf.so =>
/apps/intel/12.1/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libimf.so
(0x00007f5a93800000)
libsvml.so =>
/apps/intel/12.1/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libsvml.so
(0x00007f5a93086000)
libintlc.so.5 =>
/apps/intel/12.1/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libintlc.so.5
(0x00007f5a92f37000)
/lib64/ld-linux-x86-64.so.2 (0x00007f5a965a4000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5a92d19000)

Any suggestions on moving past this quickly?

I know that on Jet, you have to do "module load netcdf4" to get v4 of
netcdf, but that doesn't set your NETCDF env var, it sets NETCDF4. It's a
pain! Not sure if that's related here on my side or with the installation
of MET.

Thanks,
Christina

----------------------------------------------------------------
  Complete Ticket History
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Subject: Running MET Series_analysis on Jet
From: Randy Bullock
Time: Wed Apr 06 11:21:15 2016

Hi Christina -

Sounds like a run-time error, not a compile-time error.  The run-time
loader is complaining that it can't find the netcdf shared object
libraries.  There are two ways to tell the run-time loader where to
look
for libraries: one uses the compiler command line, the other uses
environment variables.

I don't work on Jet, but I'm told that there are two families of
compilers
used there: the gnu family and the intel family.

If MET was compiled with the gnu compilers, then try adding the full
path
to the netcdf shared object files to your LD_RUN_PATH enviroment
variable.
(The LD_RUN_PATH environment variable is a list of directories, much
like
the PATH variable, that tells the run-time loader where to look for
any
libraries it needs.)  If you're not sure where the netcdf libraries
are
located in your filesystem, try asking one of your sys/admin support
people.

If you're using the intel compilers, then have a look at the man page
for
the intel version of ld, and see what the variable analagous to
LD_RUN_PATH
is.

Hope this helps.

Randy

On Wed, Apr 6, 2016 at 11:01 AM, christina.holt at noaa.gov via RT <
met_help at ucar.edu> wrote:

>
> Wed Apr 06 11:01:57 2016: Request 75787 was acted upon.
> Transaction: Ticket created by christina.holt at noaa.gov
>        Queue: met_help
>      Subject: Running MET Series_analysis on Jet
>        Owner: Nobody
>   Requestors: christina.holt at noaa.gov
>       Status: new
>  Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=75787 >
>
>
> Howdy!
>
> I am attempting to use the MET 5.1 installation on Jet and I am
getting a
> run time error that the libnetcdf can't be found:
>
> /lfs2/projects/dtc-hurr/MET/MET_releases/met-
5.1/bin/series_analysis: error
> while loading shared libraries: libnetcdf_c++.so.4: cannot open
shared
> object file: No such file or directory
>
> If I run an ldd on the executable, I get the following:
> linux-vdso.so.1 =>  (0x00007fff4efc0000)
> libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00007f5a96366000)
> libz.so.1 => /lib64/libz.so.1 (0x00007f5a9614f000)
> libm.so.6 => /lib64/libm.so.6 (0x00007f5a95ecb000)
> libnetcdf_c++.so.4 => not found
> libnetcdf.so.7 => /apps/netcdf/4.2.1.1-intel/lib/libnetcdf.so.7
> (0x00007f5a95ada000)
> libgsl.so.0 => /usr/lib64/libgsl.so.0 (0x00007f5a956e3000)
> libgslcblas.so.0 => /usr/lib64/libgslcblas.so.0 (0x00007f5a954ac000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f5a951a5000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f5a94f8f000)
> libc.so.6 => /lib64/libc.so.6 (0x00007f5a94bfb000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00007f5a949f6000)
> libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00007f5a947a6000)
> libhdf5_hl.so.7 => /apps/hdf5/1.8.9-intel/lib/libhdf5_hl.so.7
> (0x00007f5a94571000)
> libhdf5.so.7 => /apps/hdf5/1.8.9-intel/lib/libhdf5.so.7
> (0x00007f5a93fe7000)
> librt.so.1 => /lib64/librt.so.1 (0x00007f5a93ddf000)
> libsz.so.2 => /apps/szip/2.1/lib/libsz.so.2 (0x00007f5a93bcc000)
> libimf.so =>
>
/apps/intel/12.1/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libimf.so
> (0x00007f5a93800000)
> libsvml.so =>
>
>
/apps/intel/12.1/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libsvml.so
> (0x00007f5a93086000)
> libintlc.so.5 =>
>
>
/apps/intel/12.1/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libintlc.so.5
> (0x00007f5a92f37000)
> /lib64/ld-linux-x86-64.so.2 (0x00007f5a965a4000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5a92d19000)
>
> Any suggestions on moving past this quickly?
>
> I know that on Jet, you have to do "module load netcdf4" to get v4
of
> netcdf, but that doesn't set your NETCDF env var, it sets NETCDF4.
It's a
> pain! Not sure if that's related here on my side or with the
installation
> of MET.
>
> Thanks,
> Christina
>
>

------------------------------------------------
Subject: Running MET Series_analysis on Jet
From: christina.holt at noaa.gov
Time: Wed Apr 06 11:57:07 2016

Randy,

My script was plagued by an unfortunate combination copy/paste and a
line
break. I made it through the problem. Thanks for your help!

Christina

On Wed, Apr 6, 2016 at 11:21 AM, Randy Bullock via RT
<met_help at ucar.edu>
wrote:

> Hi Christina -
>
> Sounds like a run-time error, not a compile-time error.  The run-
time
> loader is complaining that it can't find the netcdf shared object
> libraries.  There are two ways to tell the run-time loader where to
look
> for libraries: one uses the compiler command line, the other uses
> environment variables.
>
> I don't work on Jet, but I'm told that there are two families of
compilers
> used there: the gnu family and the intel family.
>
> If MET was compiled with the gnu compilers, then try adding the full
path
> to the netcdf shared object files to your LD_RUN_PATH enviroment
variable.
> (The LD_RUN_PATH environment variable is a list of directories, much
like
> the PATH variable, that tells the run-time loader where to look for
any
> libraries it needs.)  If you're not sure where the netcdf libraries
are
> located in your filesystem, try asking one of your sys/admin support
> people.
>
> If you're using the intel compilers, then have a look at the man
page for
> the intel version of ld, and see what the variable analagous to
LD_RUN_PATH
> is.
>
> Hope this helps.
>
> Randy
>
>
> On Wed, Apr 6, 2016 at 11:01 AM, christina.holt at noaa.gov via RT <
> met_help at ucar.edu> wrote:
>
> >
> > Wed Apr 06 11:01:57 2016: Request 75787 was acted upon.
> > Transaction: Ticket created by christina.holt at noaa.gov
> >        Queue: met_help
> >      Subject: Running MET Series_analysis on Jet
> >        Owner: Nobody
> >   Requestors: christina.holt at noaa.gov
> >       Status: new
> >  Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=75787 >
> >
> >
> > Howdy!
> >
> > I am attempting to use the MET 5.1 installation on Jet and I am
getting a
> > run time error that the libnetcdf can't be found:
> >
> > /lfs2/projects/dtc-hurr/MET/MET_releases/met-
5.1/bin/series_analysis:
> error
> > while loading shared libraries: libnetcdf_c++.so.4: cannot open
shared
> > object file: No such file or directory
> >
> > If I run an ldd on the executable, I get the following:
> > linux-vdso.so.1 =>  (0x00007fff4efc0000)
> > libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00007f5a96366000)
> > libz.so.1 => /lib64/libz.so.1 (0x00007f5a9614f000)
> > libm.so.6 => /lib64/libm.so.6 (0x00007f5a95ecb000)
> > libnetcdf_c++.so.4 => not found
> > libnetcdf.so.7 => /apps/netcdf/4.2.1.1-intel/lib/libnetcdf.so.7
> > (0x00007f5a95ada000)
> > libgsl.so.0 => /usr/lib64/libgsl.so.0 (0x00007f5a956e3000)
> > libgslcblas.so.0 => /usr/lib64/libgslcblas.so.0
(0x00007f5a954ac000)
> > libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f5a951a5000)
> > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f5a94f8f000)
> > libc.so.6 => /lib64/libc.so.6 (0x00007f5a94bfb000)
> > libdl.so.2 => /lib64/libdl.so.2 (0x00007f5a949f6000)
> > libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00007f5a947a6000)
> > libhdf5_hl.so.7 => /apps/hdf5/1.8.9-intel/lib/libhdf5_hl.so.7
> > (0x00007f5a94571000)
> > libhdf5.so.7 => /apps/hdf5/1.8.9-intel/lib/libhdf5.so.7
> > (0x00007f5a93fe7000)
> > librt.so.1 => /lib64/librt.so.1 (0x00007f5a93ddf000)
> > libsz.so.2 => /apps/szip/2.1/lib/libsz.so.2 (0x00007f5a93bcc000)
> > libimf.so =>
> >
>
/apps/intel/12.1/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libimf.so
> > (0x00007f5a93800000)
> > libsvml.so =>
> >
> >
>
/apps/intel/12.1/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libsvml.so
> > (0x00007f5a93086000)
> > libintlc.so.5 =>
> >
> >
>
/apps/intel/12.1/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libintlc.so.5
> > (0x00007f5a92f37000)
> > /lib64/ld-linux-x86-64.so.2 (0x00007f5a965a4000)
> > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5a92d19000)
> >
> > Any suggestions on moving past this quickly?
> >
> > I know that on Jet, you have to do "module load netcdf4" to get v4
of
> > netcdf, but that doesn't set your NETCDF env var, it sets NETCDF4.
It's a
> > pain! Not sure if that's related here on my side or with the
installation
> > of MET.
> >
> > Thanks,
> > Christina
> >
> >
>
>

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