[Ncep.list.fv3-announce] fv3gfs release beta test
Jun Wang - NOAA Affiliate
jun.wang at noaa.gov
Thu May 11 13:00:27 UTC 2017
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
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>> fv3-announce
>>>>>
>>>>>
>>>>
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>>>> 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>
>
>
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