Re: pyngl-talk Digest, Vol 88, Issue 1

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On Mar 7, 2012, at 11:31 AM, pyngl-talk-request@ucar.edu wrote:

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> Today's Topics:
>
> 1. trouble installing pyngl in home directory of hopper
> (Charlie Koven)
> 2. Re: trouble installing pyngl in home directory of hopper
> (Mary Haley)
> 3. Re: trouble installing pyngl in home directory of hopper
> (Michael Rezny)
> 4. Re: trouble installing pyngl in home directory of hopper
> (Charlie Koven)
> 5. trouble installing PyNIO in home directory of hopper
> (Charlie Koven)
> 6. Re: trouble installing PyNIO in home directory of hopper
> (Mary Haley)
> 7. Re: trouble installing PyNIO in home directory of hopper
> (Charlie Koven)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 6 Mar 2012 11:40:35 -0800
> From: Charlie Koven <ckoven@gmail.com>
> Subject: trouble installing pyngl in home directory of
> hopper
> To: pyngl-talk@ucar.edu
> Message-ID: <302B5758-70F2-4A04-BF0F-E2EC16282C80@gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi,
>
> I am trying to install PyNGL from source into my home directory on hopper at nersc, in which I set up a virtualenv environment so that I can add my own libraries.
> I tried to use the following environment variables:
>
> export F2CLIBS="pgf90"
> export F2CLIBS_PREFIX="/opt/pgi/11.9.0/linux86-64/11.9/bin"
> export FC="pgf90"
> export F90="pgf90"
> export CXX="pgf90"
>
>
> when I try to load the library I get this error:
>
>
> In [1]: import Ngl
> ---------------------------------------------------------------------------
> ImportError Traceback (most recent call last)
> /global/u2/c/cdkoven/python_stuff/PyNGL-1.4.0/<ipython-input-1-ec4bb7966c2f> in <module>()
> ----> 1 import Ngl
>
> /global/u2/c/cdkoven/python_stuff/PyNGL-1.4.0/Ngl.py in <module>()
> 37
> 38 # PyNGL analysis functions
>
> ---> 39 import fplib
> 40
> 41 import sys
>
> ImportError: /global/homes/c/cdkoven/ENV/lib/python2.7/site-packages/PyNGL/fplib.so: undefined symbol: _gfortran_concat_string
>
>
> Any ideas for a fix?
> Thanks,
> Charlie Koven
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 6 Mar 2012 15:59:51 -0700
> From: Mary Haley <haley@ucar.edu>
> Subject: Re: trouble installing pyngl in home directory
> of hopper
> To: Charlie Koven <ckoven@gmail.com>
> Cc: pyngl-talk@ucar.edu
> Message-ID: <FE387724-1144-4D9E-B895-BF5240B5F578@ucar.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Charlie,
>
> It looks like maybe the F2CLIBS_PREFIX is not set correctly. It should be set to the location of the "libgfortran.so" file, and not the location of the "gfortran" binary.
>
> To help locate the file, try typing:
>
> locate libgfortran.so
>
> It might be something like:
>
> /opt/pgi/11.9.0/linux86-64/11.9/lib
>
> You would then set:
>
> export F2CLIBS_PREFIX=/opt/pgi/11.9.0/linux86-64/11.9/bin
>
> Make sure you remove the "build" directory that was created from the last build,
> and then type "python setup.py install" again.
>
> (Note that I removed the double quotes.)
>
> If this doesn't work, then can you send the compilation output from the python setup.py install command?
>
> Thanks,
>
> --Mary
>
> On Mar 6, 2012, at 12:40 PM, Charlie Koven wrote:
>
>> Hi,
>>
>> I am trying to install PyNGL from source into my home directory on hopper at nersc, in which I set up a virtualenv environment so that I can add my own libraries.
>> I tried to use the following environment variables:
>>
>> export F2CLIBS="pgf90"
>> export F2CLIBS_PREFIX="/opt/pgi/11.9.0/linux86-64/11.9/bin"
>> export FC="pgf90"
>> export F90="pgf90"
>> export CXX="pgf90"
>>
>>
>> when I try to load the library I get this error:
>>
>>
>> In [1]: import Ngl
>> ---------------------------------------------------------------------------
>> ImportError Traceback (most recent call last)
>> /global/u2/c/cdkoven/python_stuff/PyNGL-1.4.0/<ipython-input-1-ec4bb7966c2f> in <module>()
>> ----> 1 import Ngl
>>
>> /global/u2/c/cdkoven/python_stuff/PyNGL-1.4.0/Ngl.py in <module>()
>> 37
>> 38 # PyNGL analysis functions
>>
>> ---> 39 import fplib
>> 40
>> 41 import sys
>>
>> ImportError: /global/homes/c/cdkoven/ENV/lib/python2.7/site-packages/PyNGL/fplib.so: undefined symbol: _gfortran_concat_string
>>
>>
>> Any ideas for a fix?
>> Thanks,
>> Charlie Koven
>>
>>
>> _______________________________________________
>> pyngl-talk mailing list
>> List instructions, subscriber options, unsubscribe:
>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 7 Mar 2012 10:04:54 +1100
> From: Michael Rezny <michael.rezny@monash.edu>
> Subject: Re: trouble installing pyngl in home directory
> of hopper
> To: Mary Haley <haley@ucar.edu>
> Cc: pyngl-talk@ucar.edu
> Message-ID: <804C2BC9-9EBB-4D3D-86D0-285BA959307C@monash.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Mary,
> small typo?
>> You would then set:
>>
>> export F2CLIBS_PREFIX=/opt/pgi/11.9.0/linux86-64/11.9/bin
>
> export F2CLIBS_PREFIX=/opt/pgi/11.9.0/linux86-64/11.9/lib
>
> regards
> Mike
>
> On 07/03/2012, at 9:59 AM, Mary Haley wrote:
>
>> Hi Charlie,
>>
>> It looks like maybe the F2CLIBS_PREFIX is not set correctly. It should be set to the location of the "libgfortran.so" file, and not the location of the "gfortran" binary.
>>
>> To help locate the file, try typing:
>>
>> locate libgfortran.so
>>
>> It might be something like:
>>
>> /opt/pgi/11.9.0/linux86-64/11.9/lib
>>
>> You would then set:
>>
>> export F2CLIBS_PREFIX=/opt/pgi/11.9.0/linux86-64/11.9/bin
>>
>> Make sure you remove the "build" directory that was created from the last build,
>> and then type "python setup.py install" again.
>>
>> (Note that I removed the double quotes.)
>>
>> If this doesn't work, then can you send the compilation output from the python setup.py install command?
>>
>> Thanks,
>>
>> --Mary
>>
>> On Mar 6, 2012, at 12:40 PM, Charlie Koven wrote:
>>
>>> Hi,
>>>
>>> I am trying to install PyNGL from source into my home directory on hopper at nersc, in which I set up a virtualenv environment so that I can add my own libraries.
>>> I tried to use the following environment variables:
>>>
>>> export F2CLIBS="pgf90"
>>> export F2CLIBS_PREFIX="/opt/pgi/11.9.0/linux86-64/11.9/bin"
>>> export FC="pgf90"
>>> export F90="pgf90"
>>> export CXX="pgf90"
>>>
>>>
>>> when I try to load the library I get this error:
>>>
>>>
>>> In [1]: import Ngl
>>> ---------------------------------------------------------------------------
>>> ImportError Traceback (most recent call last)
>>> /global/u2/c/cdkoven/python_stuff/PyNGL-1.4.0/<ipython-input-1-ec4bb7966c2f> in <module>()
>>> ----> 1 import Ngl
>>>
>>> /global/u2/c/cdkoven/python_stuff/PyNGL-1.4.0/Ngl.py in <module>()
>>> 37
>>> 38 # PyNGL analysis functions
>>>
>>> ---> 39 import fplib
>>> 40
>>> 41 import sys
>>>
>>> ImportError: /global/homes/c/cdkoven/ENV/lib/python2.7/site-packages/PyNGL/fplib.so: undefined symbol: _gfortran_concat_string
>>>
>>>
>>> Any ideas for a fix?
>>> Thanks,
>>> Charlie Koven
>>>
>>>
>>> _______________________________________________
>>> pyngl-talk mailing list
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>>
>> _______________________________________________
>> pyngl-talk mailing list
>> List instructions, subscriber options, unsubscribe:
>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 6 Mar 2012 15:29:52 -0800
> From: Charlie Koven <ckoven@gmail.com>
> Subject: Re: trouble installing pyngl in home directory
> of hopper
> To: pyngl-talk@ucar.edu
> Message-ID: <79EFC9A0-C853-4342-B4F8-65DB6F96822A@gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Mary,
>
> Thanks. got it to work. there was no libgfortran.so for the default pgi compiler, so I just switched everything to use the gcc compilers using the "module load gcc" command. I then set the env variables as:
>
> export F2CLIBS=gfortran
> export F2CLIBS_PREFIX=/opt/gcc/4.6.1/snos/lib/
> export FC=gcc
> export F90=gfortran
> export CXX=gcc
> export NCARG_ROOT=/usr/common/usg/ncar/6.0.0
>
>
> Yours,
> Charlie
>
>
> On Mar 6, 2012, at 2:59 PM, Mary Haley wrote:
>
>> Hi Charlie,
>>
>> It looks like maybe the F2CLIBS_PREFIX is not set correctly. It should be set to the location of the "libgfortran.so" file, and not the location of the "gfortran" binary.
>>
>> To help locate the file, try typing:
>>
>> locate libgfortran.so
>>
>> It might be something like:
>>
>> /opt/pgi/11.9.0/linux86-64/11.9/lib
>>
>> You would then set:
>>
>> export F2CLIBS_PREFIX=/opt/pgi/11.9.0/linux86-64/11.9/bin
>>
>> Make sure you remove the "build" directory that was created from the last build,
>> and then type "python setup.py install" again.
>>
>> (Note that I removed the double quotes.)
>>
>> If this doesn't work, then can you send the compilation output from the python setup.py install command?
>>
>> Thanks,
>>
>> --Mary
>>
>> On Mar 6, 2012, at 12:40 PM, Charlie Koven wrote:
>>
>>> Hi,
>>>
>>> I am trying to install PyNGL from source into my home directory on hopper at nersc, in which I set up a virtualenv environment so that I can add my own libraries.
>>> I tried to use the following environment variables:
>>>
>>> export F2CLIBS="pgf90"
>>> export F2CLIBS_PREFIX="/opt/pgi/11.9.0/linux86-64/11.9/bin"
>>> export FC="pgf90"
>>> export F90="pgf90"
>>> export CXX="pgf90"
>>>
>>>
>>> when I try to load the library I get this error:
>>>
>>>
>>> In [1]: import Ngl
>>> ---------------------------------------------------------------------------
>>> ImportError Traceback (most recent call last)
>>> /global/u2/c/cdkoven/python_stuff/PyNGL-1.4.0/<ipython-input-1-ec4bb7966c2f> in <module>()
>>> ----> 1 import Ngl
>>>
>>> /global/u2/c/cdkoven/python_stuff/PyNGL-1.4.0/Ngl.py in <module>()
>>> 37
>>> 38 # PyNGL analysis functions
>>>
>>> ---> 39 import fplib
>>> 40
>>> 41 import sys
>>>
>>> ImportError: /global/homes/c/cdkoven/ENV/lib/python2.7/site-packages/PyNGL/fplib.so: undefined symbol: _gfortran_concat_string
>>>
>>>
>>> Any ideas for a fix?
>>> Thanks,
>>> Charlie Koven
>>>
>>>
>>> _______________________________________________
>>> pyngl-talk mailing list
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 6 Mar 2012 16:07:01 -0800
> From: Charlie Koven <ckoven@gmail.com>
> Subject: trouble installing PyNIO in home directory of
> hopper
> To: pyngl-talk@ucar.edu
> Message-ID: <8F932855-D60E-4DC3-8759-3E9F5074456E@gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi,
>
> now that I've gotten PyNGL to install successfully in my home directory on hopper, I thought I should try to get PyNIO working.
>
> i set the module environment to use gcc by:
>
> module unload pgi
> module load gcc
>
> and the env variables I am using are:
>
> export F2CLIBS=gfortran
> export F2CLIBS_PREFIX=/opt/gcc/4.6.1/snos/lib/
> export HAS_OPENDAP=0
> export NETCDF_PREFIX=/opt/cray/netcdf/4.1.1.0/netcdf-gnu
>
>
> the library seems to build ok but when I try to load a CLM history file, I get the following error:
>
>
> IPython 0.12 -- An enhanced Interactive Python.
> ? -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help -> Python's own help system.
> object? -> Details about 'object', use 'object??' for extra details.
>
> In [1]: import Nio
>
> In [2]: file_in = Nio.open_file('cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc')
> Error: in routine alloca() there is a
> stack overflow: thread 0, max 8180KB, used 0KB, request 8B
>
>
> It does seem to be able to load smaller files, however. Any idea what is causing this?
>
> Thanks,
> Charlie
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 7 Mar 2012 07:57:00 -0700
> From: Mary Haley <haley@ucar.edu>
> Subject: Re: trouble installing PyNIO in home directory
> of hopper
> To: Charlie Koven <ckoven@gmail.com>
> Cc: pyngl-talk@ucar.edu
> Message-ID: <7303D57E-2CFF-4C33-96CD-D07D74B2CCD2@ucar.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Charlie,
>
> Thanks for the typo correction in the previous email. :-)
>
> With the problem below, are you able to open this file from straight python (not IPython)? How big is the file, and how big are the ones you are able to open successfully?
>
> What version of PyNIO are you using?
>
> Finally, would you be able to provide the cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc file so we can try opening it here?
>
> ftp ftp.cgd.ucar.edu
> anonymous
> <use your email address for the password>
> cd incoming
> put cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc
> quit
>
> Thanks,
>
> --Mary
>
> On Mar 6, 2012, at 5:07 PM, Charlie Koven wrote:
>
>> Hi,
>>
>> now that I've gotten PyNGL to install successfully in my home directory on hopper, I thought I should try to get PyNIO working.
>>
>> i set the module environment to use gcc by:
>>
>> module unload pgi
>> module load gcc
>>
>> and the env variables I am using are:
>>
>> export F2CLIBS=gfortran
>> export F2CLIBS_PREFIX=/opt/gcc/4.6.1/snos/lib/
>> export HAS_OPENDAP=0
>> export NETCDF_PREFIX=/opt/cray/netcdf/4.1.1.0/netcdf-gnu
>>
>>
>> the library seems to build ok but when I try to load a CLM history file, I get the following error:
>>
>>
>> IPython 0.12 -- An enhanced Interactive Python.
>> ? -> Introduction and overview of IPython's features.
>> %quickref -> Quick reference.
>> help -> Python's own help system.
>> object? -> Details about 'object', use 'object??' for extra details.
>>
>> In [1]: import Nio
>>
>> In [2]: file_in = Nio.open_file('cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc')
>> Error: in routine alloca() there is a
>> stack overflow: thread 0, max 8180KB, used 0KB, request 8B
>>
>>
>> It does seem to be able to load smaller files, however. Any idea what is causing this?
>>
>> Thanks,
>> Charlie
>>
>>
>> _______________________________________________
>> pyngl-talk mailing list
>> List instructions, subscriber options, unsubscribe:
>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 7 Mar 2012 09:30:54 -0800
> From: Charlie Koven <ckoven@gmail.com>
> Subject: Re: trouble installing PyNIO in home directory
> of hopper
> To: Mary Haley <haley@ucar.edu>
> Cc: pyngl-talk@ucar.edu
> Message-ID: <D9CA1F07-F709-4E54-BEF3-FD7EF4B462DA@gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Mary,
>
> On Mar 7, 2012, at 6:57 AM, Mary Haley wrote:
>
>> Hi Charlie,
>>
>> Thanks for the typo correction in the previous email. :-)
>
> That was Michael with the typo correction, not me :) -- thanks Michael
>
>>
>> With the problem below, are you able to open this file from straight python (not IPython)? How big is the file, and how big are the ones you are able to open successfully?
>>
>
> Yes, same problem.
>
> the only two files I tried it on are a CLM history file and a CLM restart file. for some reason the restart file loads but the history file doesn't. the restart file is actually bigger, 1.2G vs. 75M for the history file. I don't think there is any issue with the file though--I can open both files on the Nio install I have working on my workstation.
>
>> What version of PyNIO are you using?
>
>>>> Nio.__version__
> '1.4.1'
>
>>
>> Finally, would you be able to provide the cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc file so we can try opening it here?
>>
>
> Sure. I just uploaded the file.
>
> Thanks,
>
> Charlie
>
>
>
>
>> ftp ftp.cgd.ucar.edu
>> anonymous
>> <use your email address for the password>
>> cd incoming
>> put cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc
>> quit
>>
>> Thanks,
>>
>> --Mary
>>
>> On Mar 6, 2012, at 5:07 PM, Charlie Koven wrote:
>>
>>> Hi,
>>>
>>> now that I've gotten PyNGL to install successfully in my home directory on hopper, I thought I should try to get PyNIO working.
>>>
>>> i set the module environment to use gcc by:
>>>
>>> module unload pgi
>>> module load gcc
>>>
>>> and the env variables I am using are:
>>>
>>> export F2CLIBS=gfortran
>>> export F2CLIBS_PREFIX=/opt/gcc/4.6.1/snos/lib/
>>> export HAS_OPENDAP=0
>>> export NETCDF_PREFIX=/opt/cray/netcdf/4.1.1.0/netcdf-gnu
>>>
>>>
>>> the library seems to build ok but when I try to load a CLM history file, I get the following error:
>>>
>>>
>>> IPython 0.12 -- An enhanced Interactive Python.
>>> ? -> Introduction and overview of IPython's features.
>>> %quickref -> Quick reference.
>>> help -> Python's own help system.
>>> object? -> Details about 'object', use 'object??' for extra details.
>>>
>>> In [1]: import Nio
>>>
>>> In [2]: file_in = Nio.open_file('cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc')
>>> Error: in routine alloca() there is a
>>> stack overflow: thread 0, max 8180KB, used 0KB, request 8B
>>>
>>>
>>> It does seem to be able to load smaller files, however. Any idea what is causing this?
>>>
>>> Thanks,
>>> Charlie
>>>
>>>
>>> _______________________________________________
>>> pyngl-talk mailing list
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>>
>
>
>
> ------------------------------
>
> _______________________________________________
> pyngl-talk mailing list
> pyngl-talk@ucar.edu
> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>
>
> End of pyngl-talk Digest, Vol 88, Issue 1
> *****************************************
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Received on Sat Mar 10 15:18:10 2012