[Ncep.list.fv3-announce] fv3gfs release beta test

Jun Wang - NOAA Affiliate jun.wang at noaa.gov
Fri May 12 02:47:16 UTC 2017 

Dear all,

Thank you for the feedback. The beta tag
https://svnemc.ncep.noaa.gov/projects/nems/apps/NEMSfv3gfs/tags/fv3gfs.v0beta
is updated with following updates:

1)use nccmp -d to compare data fields in two netcdf files (ignore global
attributes) in diff_baseline.sh
2)remove variable setting in theia remap module files
3)move the line to find mpirun command after module load
4)improved formatting of the readme.txt
5)remove semi-column before some export commands in runjob_theia.sh and
runjob_cray.sh


M       release/v0/exp/diff_baseline.sh
M       release/v0/exp/runjob_cray.sh
M       release/v0/exp/runjob_theia.sh
M       release/v0/modulefiles/fv3gfs/fre-nctools.theia
M       release/v0/readme.txt

Please let me know if you still get errors when running remap or comparing
remap results with baseline. Thanks.

Jun

On Thu, May 11, 2017 at 5:01 PM, Gerard Ketefian - NOAA Affiliate <
gerard.ketefian at noaa.gov> wrote:

> Hi Jun,
>
> Yes, after the missing "cp" fix, I (and Jim too) still had a problem with
> this line in runjob_theia.sh:
>
> module load module.fre-nctools
>
> This syntax (where you specify a file name after "module load") is not
> supported in our environment.  So what we did was first change the above
> line to:
>
> . ./module.fre-nctools
>
> to just source the module.fre-nctools file.  Also, we changed the contents
> of the file ${BASE_DIR}/fv3gfs.v0beta/release/v0/modulefiles/fv3gfs/fre-nctools.theia
> to:
>
>    module load impi/5.1.2.150
>    module load netcdf/4.3.0
>    module load hdf5/1.8.14
>    export HDF5_DIR=$HDF5
>    export NETCDF_DIR=$NETCDF
>    export LIBRARY_PATH=${LIBRARY_PATH}:${NETCDF}/lib:${HDF5}/lib
>
> (Btw, should LIBRARY_PATH be changed to LD_LIBRARY_PATH in the last line?)
>  With this, the remapping worked without any error messages.  When I
> compared the output with the baseline run, all the files were the same
> EXCEPT the three 1deg files from the remapping.  I don't know why those
> were differnt.  They weren't exactly the same but had almost the same
> sizes.
>
> It would be nice to be able to use the syntax
>
> module load module.fre-nctools
>
> in our environment as well.  When I do a "module help", I don't see this
> syntax as an option (where you're specifying a file name that contains
> several commands).  Is there a way to get this to work on theia?
>
> Thanks,
> Gerard
>
>
> On Thu, May 11, 2017 at 7:00 AM, Jun Wang - NOAA Affiliate <
> jun.wang at noaa.gov> wrote:
>
>> Gerard,
>>
>> With the fix last night, do you still have problem load the module
>> module.fre-nctools?
>>
>> Thanks for pointing out the forecast time specified in runjob_theia.sh, I
>> changed it to be consistent with the baseline.
>>
>> Another fix on the forecast executable is Jim Abeles are also committed
>> to the tag.
>>
>> I am planning to commit all the changes made to the temporary beta tag to
>> trunk later today for Sam to add jet extension, please send me any
>> fix/suggestion. Thanks to all who are doing testing.
>>
>>
>> Jun
>>
>> On Thu, May 11, 2017 at 5:03 AM, Gerard Ketefian - NOAA Affiliate <
>> gerard.ketefian at noaa.gov> wrote:
>>
>>> Hi all,
>>>
>>> With Ligia's hints and Jun's last fix, I was able to complete the run
>>> but not the remap.  I think the remap fails because some modules don't get
>>> loaded properly.
>>>
>>> To get the remap to also work, I replaced the following line in
>>> runjob_theia.sh
>>>
>>> module load module.fre-nctools
>>>
>>> with the following block (copied and modified from the file
>>> module.fre-nctools):
>>>
>>> module load impi/5.1.2.150
>>> module load netcdf/4.3.0
>>> module load hdf5/1.8.14
>>> export HDF5_DIR=$HDF5
>>> export NETCDF_DIR=$NETCDF
>>> export LIBRARY_PATH=${LIBRARY_PATH}:${NETCDF}/lib:${HDF5}/lib
>>>
>>> This change should allow the 1deg remapped netcdf files to be generated.
>>>
>>> When I do the comparison of the sample run's netcdf files with baseline,
>>> there is a about factor of 5 difference (the sample run files being
>>> larger).  This is because there are only 8 output times in the baseline
>>> files but 40 in the run output.
>>>
>>> Gerard
>>>
>>>
>>> On Wed, May 10, 2017 at 9:56 PM, Jun Wang - NOAA Affiliate <
>>> jun.wang at noaa.gov> wrote:
>>>
>>>> Ligia,
>>>>
>>>> Thanks for the feedback.  The suggestion on instruction is put in
>>>> readme.txt. It is found that "cp " is missing  in line 124 in
>>>> runjob_theia.sh. I committed the changes to the beta test tag:
>>>> https://svnemc.ncep.noaa.gov/projects/nems/apps/NEMSfv3gfs/t
>>>> ags/fv3gfs.v0beta
>>>>
>>>> Please check again. The results differences will need further
>>>> investigation. Thanks.
>>>>
>>>> Jun
>>>>
>>>> On Wed, May 10, 2017 at 10:28 PM, Ligia Bernardet - NOAA Affiliate <
>>>> ligia.bernardet at noaa.gov> wrote:
>>>>
>>>>> Folks,
>>>>>
>>>>> Here is some feedback
>>>>>
>>>>>
>>>>> *About the instructions*
>>>>>
>>>>>    1. Minor typo. The word "trunk" should be removed: Four executable
>>>>>    files will be created under fv3gfs.v0beta/*trunk*/NEMS/exe
>>>>>    2. runjob_theia.sh: Non-NCEPDEV people need to change directories
>>>>>    DATA and ROTDIR to an area they can write to
>>>>>    3. diff_baseline.sh:
>>>>>       1. It would be helpful to tell users to add arguments
>>>>>       to diff_baseline.sh to set resolution and machine.
>>>>>       2. Non-NCEPDEV people need to change directory dir1 to location
>>>>>       of their output
>>>>>
>>>>> *Outcome*
>>>>> It seems I was able to get through the forecast but failed in remap.
>>>>> Problem seems related to loading modules, I did not fully investigate yet.
>>>>> Output is in /scratch4/BMC/gmtb/Ligia.Berna
>>>>> rdet/fv3gfs.v0beta/release/v0/exp
>>>>>
>>>>> When running diff, NetCDF files differ from the baseline. I noticed
>>>>> the file sizes are different (mine are larger than the baseline).
>>>>>
>>>>> Ligia
>>>>>
>>>>> /scratch4/BMC/gmtb/Ligia.Bernardet/fv3gfs.v0beta/release/v0/
>>>>> exp/../modulefiles/fv3gfs/fre-nctools.theia module.fre-nctools
>>>>>
>>>>> /var/spool/torque/mom_priv/jobs/23566207.bqs3.SC: line 126:
>>>>> /scratch4/BMC/gmtb/Ligia.Bernardet/fv3gfs.v0beta/release/v0/
>>>>> exp/../modulefiles/fv3gfs/fre-nctools.theia: *Permission denied*
>>>>>
>>>>> + module load module.fre-nctools
>>>>>
>>>>> ++ /apps/lmod/lmod/libexec/lmod bash load module.fre-nctools
>>>>>
>>>>> Lmod has detected the following error: The following module(s) are
>>>>> unknown:
>>>>>
>>>>> "module.fre-nctools"
>>>>>
>>>>> On Wed, May 10, 2017 at 5:47 PM, James Rosinski - NOAA Affiliate <
>>>>> james.rosinski at noaa.gov> wrote:
>>>>>
>>>>>> Hi Jun;
>>>>>>
>>>>>> I am about to head home for the day, but here are my comments so far,
>>>>>> after following the instructions for theia:
>>>>>>
>>>>>> o The builds of models and remap codes completed successfully. One
>>>>>> suggestion might be to have the user specify 32 or 64-bit, and nh vs. hydro
>>>>>> in order to cut down compilation time by a factor of 4.
>>>>>>
>>>>>> o The batch job attempting to run the model failed. Relevant lines in
>>>>>> err_theia are:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> *+ cd /scratch4/NCEPDEV/stmp3/James.Rosinski/C96fv3gfs2016092900+
>>>>>> /bin/cp -p
>>>>>> /scratch3/BMC/gsd-hpcs/rosinski/fv3gfs.v0beta/release/v0/exp/../../../NEMS/exe/fv3_gfs_nh.prod.32bit.x
>>>>>> /scratch4/NCEPDEV/stmp3/James.Rosinski/C96fv3gfs2016092900/.+ -prepend-rank
>>>>>> -np 288 ./fv3_gfs_nh.prod.32bit.x+ ERR=127+ export ERR+ err=127*
>>>>>> Looks like somehow "mpirun" was not found (note there is nothing in
>>>>>> front of "-prepend-rank"). FYI I use csh for my login shell--not sure if
>>>>>> this is behind the error. I had no modules loaded when submitting the job.
>>>>>>
>>>>>> If  you'd like to examine the output you should have read access to
>>>>>> it here on theia:
>>>>>>
>>>>>> /scratch3/BMC/gsd-hpcs/rosinski/fv3gfs.v0beta/release/v0/exp
>>>>>>
>>>>>> More info tomorrow...
>>>>>>
>>>>>> Regards,
>>>>>> Jim Rosinski
>>>>>>
>>>>>>
>>>>>> On Wed, May 10, 2017 at 2:55 PM, Jun Wang - NOAA Affiliate <
>>>>>> jun.wang at noaa.gov> wrote:
>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I was noticed that some directory names in the readme.txt are not
>>>>>>> correct. I just updated the tag version, please let me know if you have any
>>>>>>> further questions. Thanks.
>>>>>>>
>>>>>>> Jun
>>>>>>>
>>>>>>> On Wed, May 10, 2017 at 4:39 PM, Jun Wang - NOAA Affiliate <
>>>>>>> jun.wang at noaa.gov> wrote:
>>>>>>>
>>>>>>>> Rusty,
>>>>>>>>
>>>>>>>> Thanks for quick feedback. Today we just had a VLAB meeting on how
>>>>>>>> to provide information for the public release. Vijay mentioned that EMC
>>>>>>>> will be setting up an FV3GFS community web page through VLAB, some basic
>>>>>>>> document will be provided there. A formal instruction on how to get release
>>>>>>>> code, and to compile and run experiment will be on that web page too. For
>>>>>>>> questions/feedback,  a forum will be set up for users to post questions and
>>>>>>>> to provide answers &feedback, the purpose is that all the developers will
>>>>>>>> see the questions/answers, it is suggested not to send questions/feedback
>>>>>>>> to any individual's personal email (If people receive questions from users,
>>>>>>>> we suggest that they post the questions along with their answers to the
>>>>>>>> forum). The readme.txt is a temporary solution to get the testing started,
>>>>>>>> it may be changed in the final release.
>>>>>>>>
>>>>>>>> Kate Howard (kate.howard at noaa.gov) is working on the VLAB fv3gfs
>>>>>>>> web page, she can add the gfdl fv3gfs support email on the web page too, if
>>>>>>>> you have any fv3 document for general developers, please send to her.
>>>>>>>>
>>>>>>>> Thanks.
>>>>>>>>
>>>>>>>>
>>>>>>>> Jun
>>>>>>>>
>>>>>>>> On Wed, May 10, 2017 at 4:02 PM, Rusty Benson - NOAA Federal <
>>>>>>>> rusty.benson at noaa.gov> wrote:
>>>>>>>>
>>>>>>>>> Hi Jun and Vijay,
>>>>>>>>>
>>>>>>>>> In the readme.txt Q&A, you mention where to get help.  Has there
>>>>>>>>> been any thought to putting together a single email for tracking all
>>>>>>>>> questions/requests that can be used as a basis for creating a knowledgebase
>>>>>>>>> via a wiki or other forum?  By segmenting FV3 and physics support, I think
>>>>>>>>> we are missing an opportunity for personnel to get exposure to and learn
>>>>>>>>> about system pieces for which they may not necessarily be responsible.
>>>>>>>>>
>>>>>>>>> If we do go the route of a single support email, we have an
>>>>>>>>> existing email for FV3 support which could be used as an alias member.
>>>>>>>>> Otherwise, we would want to publish the email inside of the readme.txt and
>>>>>>>>> not have individual team members being contacted directly
>>>>>>>>>
>>>>>>>>> <oar.gfdl.fvgfs_support at noaa.gov>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Rusty
>>>>>>>>> --
>>>>>>>>> Rusty Benson, PhD
>>>>>>>>> Modeling Systems Group
>>>>>>>>> NOAA Geophysical Fluid Dynamics Lab
>>>>>>>>> Princeton, NJ
>>>>>>>>>
>>>>>>>>> On Wed, May 10, 2017 at 2:08 PM, Jun Wang - NOAA Affiliate <
>>>>>>>>> jun.wang at noaa.gov> wrote:
>>>>>>>>>
>>>>>>>>>> Dear all,
>>>>>>>>>>
>>>>>>>>>> The following email is for people who are willing to do beta
>>>>>>>>>> testing for the fv3gfs May 15 release. Please ignore the email if you are
>>>>>>>>>> not going to run the test.
>>>>>>>>>>
>>>>>>>>>> The svn tag for beta testing is located at:
>>>>>>>>>>
>>>>>>>>>>  https://svnemc.ncep.noaa.gov/projects/nems/apps/NEMSfv3gfs/
>>>>>>>>>> tags/fv3gfs.v0beta
>>>>>>>>>>
>>>>>>>>>> The instruction file on how to get and compile the code and to
>>>>>>>>>> run an experiment is at:
>>>>>>>>>>
>>>>>>>>>> https://svnemc.ncep.noaa.gov/projects/nems/apps/NEMSfv3gfs/t
>>>>>>>>>> ags/fv3gfs.v0beta/release/v0/readme.txt
>>>>>>>>>>
>>>>>>>>>> Please follow the instructions to see if you can run an
>>>>>>>>>> experiment.
>>>>>>>>>>
>>>>>>>>>>  Thanks.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Jun
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Ncep.list.fv3-announce mailing list
>>>>>>>>>> Ncep.list.fv3-announce at lstsrv.ncep.noaa.gov
>>>>>>>>>> https://www.lstsrv.ncep.noaa.gov/mailman/listinfo/ncep.list.
>>>>>>>>>> fv3-announce
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Ncep.list.fv3-announce mailing list
>>>>>>> Ncep.list.fv3-announce at lstsrv.ncep.noaa.gov
>>>>>>> https://www.lstsrv.ncep.noaa.gov/mailman/listinfo/ncep.list.
>>>>>>> fv3-announce
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Ncep.list.fv3-announce mailing list
>>>>>> Ncep.list.fv3-announce at lstsrv.ncep.noaa.gov
>>>>>> https://www.lstsrv.ncep.noaa.gov/mailman/listinfo/ncep.list.
>>>>>> fv3-announce
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Gerard Ketefian
>>> Research Scientist
>>> NOAA/OAR/ESRL/GSD/EMB, R/GSD1
>>> 325 Broadway
>>> Boulder, CO 80305
>>> phone: 303-497-6209 <(303)%20497-6209>
>>>
>>>
>>
>
>
> --
> Gerard Ketefian
> Research Scientist
> NOAA/OAR/ESRL/GSD/EMB, R/GSD1
> 325 Broadway
> Boulder, CO 80305
> phone: 303-497-6209 <(303)%20497-6209>
>
>
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