Closed GeorgeVandenberghe-NOAA closed 2 years ago
I finally have corners in the EXCH.f working. Corner exchange code looks like this
!! corner points. After the exchanges above, corner points are replicated in ! neighbour halos so we can get them from the neighbors rather than ! calculating more corner neighbor numbers ! A(ista-1,jsta-1) is in the ileft a(iend,jsta-1) location ! A(ista-1,jend+1) is in the ileft a(iend,jend+1) location ! A(iend+1,jsta-1) is in the iright a(ista,jsta-1) location ! A(iend+1,jend+1) is in the iright a(ista,jend+1) location ibl=max(ista-1,1) ibu=min(im,iend+1) jbu=min(jm,jend+1) jbl=max(jsta-1,1)
call mpi_sendrecv(a(iend,jbl ),1, MPI_REAL,iright,1 , &
& a(ibl ,jbl ),1, MPI_REAL,ileft ,1, &
& MPI_COMM_COMP,status,ierr)
call mpi_sendrecv(a(iend,jbu ),1, MPI_REAL,iright,1 , &
& a(ibl ,jbu ),1, MPI_REAL,ileft ,1, &
& MPI_COMM_COMP,status,ierr)
call mpi_sendrecv(a(ista,jbl ),1, MPI_REAL,ileft ,1, &
& a(ibu ,jbl ),1, MPI_REAL,iright,1, &
& MPI_COMM_COMP,status,ierr)
call mpi_sendrecv(a(ista,jbu ),1, MPI_REAL,ileft ,1 , &
& a(ibu ,jbu ),1, MPI_REAL,iright,1, &
& MPI_COMM_COMP,status,ierr)
It does work. I need to strip out a lot of debug code before publishing I tested it by exchanging with an array of coordinates and ensuring coordinates matched I and J for all I, J from ista-1 to iend+1 and jsta-1 to jend+1 with the constraints these had to be in the bounds 1:im,1:jm A second possible test would to be to broadcast one full domain 2D array and then also scatter and exchange it and compare the exchanged results with the broadcast subcomain. These should be exact.
Great! Please let me know where to grab your files. wcoss production switched yesterday. I have my files backup and transfer to mars, but I don't have yours. I need your MPI_FIRST.f, CTLBLK.f, and EXCH.f, anything else you have modified? Did you also change the COLLECT?
COLLECT is untested because I haven't gotten it called yet. I will send a tarball with the most recent versions. EXCH.f has a LOT of extra code right now to check the transfers.
I also haven't found anything calling EXCH2
it's on MARS /gpfs/dell2/pmp/gwv/post.0813.exch.tar
On Fri, Aug 13, 2021 at 2:05 PM JesseMeng-NOAA @.***> wrote:
Great! Please let me know where to grab your files. wcoss production switched yesterday. I have my files backup and transfer to mars, but I don't have yours. I need your MPI_FIRST.f, CTLBLK.f, and EXCH.f. Anything else you have modified? Did you also change the COLLECT?
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George's new fix works! The tests reproduced bitwise identical results including SLP for numx=1,2,4. Thanks, George!
Well that's a good way to end a Friday.
Sometimes we win one😐
On Fri, Aug 13, 2021 at 4:51 PM JesseMeng-NOAA @.***> wrote:
George's new fix works! The tests reproduced bitwise identical results including SLP for numx=1,2,4. Thanks, George!
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Totally agreed! Thank you!
Huiya
Sent from my iPhone
On Aug 13, 2021, at 5:28 PM, GeorgeVandenberghe-NOAA @.***> wrote:
Well that's a good way to end a Friday.
Sometimes we win one😐
On Fri, Aug 13, 2021 at 4:51 PM JesseMeng-NOAA @.***> wrote:
George's new fix works! The tests reproduced bitwise identical results including SLP for numx=1,2,4. Thanks, George!
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The branch post_2d_decomp was just synced with upstream/develop.
@GeorgeVandenberghe-NOAA great news from last Friday. Will you commit your latest EXCH.f to The branch post_2d_decomp @JesseMeng-NOAA did you commit your updated SLP subroutines?
The branch post_2d_decomp was just synced with upstream/develop.
thank you for doing the update
Easy to get the git syntax wrong. What are the command lines for doing this commit.
Also I need to remove some of the debug code and comment out the rest. I plan to change my plan for coordinate debug and use real rather than integer coordinate arrays for debugging so debug code can be placed outside of exch. I didn't do this before because of precision concerns embedding the coordinates in a single real location. I don't plan to do this until the next issue with exch if that happens.
On Mon, Aug 16, 2021 at 10:18 AM HuiyaChuang-NOAA @.***> wrote:
@GeorgeVandenberghe-NOAA https://github.com/GeorgeVandenberghe-NOAA great news from last Friday. Will you commit your latest EXCH.f to The branch post_2d_decomp @JesseMeng-NOAA https://github.com/JesseMeng-NOAA did you commit your updated SLP subroutines?
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I tested George's code with Wen's latest merge for numx=4 and got bitwise identical results. I will comment out most of George's print statements in EXCH and commit the changes today.
There is a lot of extra code to to do coordinate exchange testing. Next time I have a scatter,gather, or exchange issue I will use real coordinates and do the debugging in the caller. However for now all of the code that does exchanges on INTEGERs need to be commented out.
I am extremely tired, my son is home from school for a few days
(That's great!!) and I may just take some time off this week.
On Mon, Aug 16, 2021 at 11:43 AM Jesse Meng @.***> wrote:
I tested George's code with Wen's latest merge for numx=4 and got bitwise identical results. I will comment out most of George's print statements in EXCH and commit the changes today.
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After push to Wen's repo I received a message of Run failed: Build and Test. Github claimed an error in "use ifcore" in EXCH.f, Fatal Error: Cannot open module file ‘ifcore.mod’ for reading at (1): No such file or directory
But it works fine on wcoss, compiles and runs without errors. Does any one know the reason and solution?
ifcore is an intel specific module used to generate runtime stack traces without terminating the program. Get rid of the ifcore use and the subsequent traceback call tracebackqq (which seems to have already been removed). Tracebackqq generates a traceback indicating the call chain above. I used it to determine who was calling exch.
Since it's intel specific it can't be used in generalized released code
Note EXCH is still exchanging coordinate arrays in a test EVERY call. My first thought was to get rid of it but on second thought, if we do more decomposition changes I'd like to go through this code and check for exact coordinate matches every time, just for now. If we do this it's important to grep for FAIL in stderr because I didn't make these errors fatal.
On Mon, Aug 16, 2021 at 12:45 PM Jesse Meng @.***> wrote:
After push to Wen's repo I received a message of Run failed: Build and Test. Github claimed an error in "use ifcore" in EXCH.f, Fatal Error: Cannot open module file ‘ifcore.mod’ for reading at (1): No such file or directory
But it works fine on wcoss, compiles and runs without errors. Does any one know the reason and solution?
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It's good now after removing ifcore. Thanks you George! I will continue modifying all im loops to ista:iend style. Agree to keep those debugging code until we are fully tested with 2d decomposition for the complete variable list.
It's good now after removing ifcore. Thanks you George! I will continue modifying all im loops to ista:iend style. Agree to keep those debugging code until we are fully tested with 2d decomposition for the complete variable list.
Great!
@JesseMeng-NOAA @GeorgeVandenberghe-NOAA @WenMeng-NOAA @BoCui-NOAA This is to follow up on why exch and exch_f are identical in EXCH.f As I explained exch_f was for input array that were dimensioned (im,jm). However, now that Bo has updated UPP to dimension (im, jsta_2l,jend_2u), let's remove exch_f section.
I know. Thanks
@JesseMeng-NOAA Great!
I think you mentioned you've updated MDL2P.f
In your current regression test, do you have pressure level output? If not, could you add them
and run regression tests again?
Wen's test case only has hybrid level. I will try pressure level.
@JesseMeng-NOAA you can see https://github.com/WenMeng-NOAA/EMC_post/blob/post_2d_decomp/parm/postcntrl_gfs_f00.xml about adding isobaric level variables. Also, Can you report timing when running with different tasks at Thursday's tagup?
@GeorgeVandenberghe-NOAA @JesseMeng-NOAA @WenMeng-NOAA @BoCui-NOAA Summary for today's 2D decomposition tag up:
Action items:
I need a way to get COLLECT_LOC called. In the testcase supplied by Jesse it isn't so I can't verify it works although. of course I would NEVER make a misteak
On Fri, Aug 13, 2021 at 3:17 PM George Vandenberghe - NOAA Affiliate < @.***> wrote:
COLLECT is untested because I haven't gotten it called yet. I will send a tarball with the most recent versions. EXCH.f has a LOT of extra code right now to check the transfers.
I also haven't found anything calling EXCH2
it's on MARS /gpfs/dell2/pmp/gwv/post.0813.exch.tar
On Fri, Aug 13, 2021 at 2:05 PM JesseMeng-NOAA @.***> wrote:
Great! Please let me know where to grab your files. wcoss production switched yesterday. I have my files backup and transfer to mars, but I don't have yours. I need your MPI_FIRST.f, CTLBLK.f, and EXCH.f. Anything else you have modified? Did you also change the COLLECT?
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George W Vandenberghe
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5830 University Research Ct., Rm. 2141
College Park, MD 20740
@.***
301-683-3769(work) 3017751547(cell)
The testcase Wen generated uses netcdfpara input handled by INITPOST_GFS_NETCDF_PARA.f in which call collect_loc is commented out. Wen, what do you think?
@GeorgeVandenberghe-NOAA @JesseMeng-NOAA @BoCui-NOAA @WenMeng-NOAA
actually I asked Bo to comment that section out until we're ready to test collect_loc.
Jesse please uncomment the section to help George test out his version of collect_loc
The branch post_2d_decomp was synced with upstream/develop. The conflicts were solved.
Does this mean that a clone of develop has some support for 2D decomposition?
On the COLLECT_LOC testing issue I can test it with a call to gather the coordinate array, inverting my scatter test. If this works it's going to work for other arrays.
grib2_module.f uses a different array to gather with possibly different shape on the remote ranks. The shape of the gathered object is the same, a full domain array. It's just bookkeeping but new and additional because of the different remote side shape.
On Thu, Sep 2, 2021 at 1:22 PM WenMeng-NOAA @.***> wrote:
The branch post_2d_decomp was synced with upstream/develop. The conflicts were solved.
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@GeorgeVandenberghe-NOAA No, my updates are syncing the latest changes of branch develop at authoritative UPP repso. in the 2d decomposition developing branch.
@GeorgeVandenberghe-NOAA @JesseMeng-NOAA @WenMeng-NOAA @BoCui-NOAA Summary for today's 2D decomposition tag up:
- George updated EXCH.f and it worked in his test
- Jesse tested George's new EXCH.f in his regression test that outputs model level variables and SLP as SLP computation calls SLP
- Jesse verified that his tests reproduced all above output with numx=1,2,4
- Jesse added isobaric height to his tests and tests still reproduced with different values of numx
- Jesse reported that timings are similar with different numbers of numx
- George indicated he added several debug statements in exch.f which will add overhead. He suggested to keep them in until 2D decomposition work is completed. Once these debug statements are removed, we should see improvements in timing.
- Huiya indicated only one UPP subroutine _calls EXCH2 which is SLP_NMM.f_ which consists of SLP computation for E grid
- Huiya indicated all INITPOST* calls collect to gather latitude and longitude
INITPOST_GFS.f: call collect_loc(gdlat,dummy)
Action items:
- Huiya will email HWRF lead and DTC to indicate our intention to retire SLP_NMM.f after 2D decomposition branch is merged to devop
Huiya emailed Zhang and Kate from DTC indicating our plan to retire SLP_NMM,f as it only is used for HWRF operationally and HWRF will be replaced by HAFS. Additionally, HWRF maintains its own branch.
@JesseMeng-NOAA @BoCui-NOAA @WenMeng-NOAA @GeorgeVandenberghe-NOAA Per discussion from tag up on this project yesterday, we will plan on retiring SLP_NMM.f and EXCH2.f in this branch.
@JesseMeng-NOAA Jesse, please remove the following list of UPP subroutines from 2D decomposition branch:
Thank you.
@HuiyaChuang-NOAA I could remove the INITPOST_SIGIO.f and INITPOST_GFS_NEMS.f in UPP develop branch before 2D decomposition branch merging.
Are these still used for older applications that use GFS NEMSIO and even older SIGIO files? Or did the developers fork their own versions long ago as the NAM people did?
On Fri, Sep 17, 2021 at 2:22 PM WenMeng-NOAA @.***> wrote:
@HuiyaChuang-NOAA https://github.com/HuiyaChuang-NOAA I could remove the INITPOST_SIGIO.f and INITPOST_GFS_NEMS.f in UPP develop branch before 2D decomposition branch merging.
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These are legacy read interfaces which are not used in operational applications any more. We still keep the interface for NAM.
These are legacy read interfaces which are not used in operational applications any more. We still keep the interface for NAM.
@WenMeng-NOAA thank you. that would be great. @GeorgeVandenberghe-NOAA you're right that these two subroutines are read interfaces for old GFS sigio and serial nems io output. However, we're still keeping INITPOST_GFS_NEMS_MPIIO.f which was what's used operationally to parallel read nemsio output.
Somehow I cannot get rid of INITPOST_GFS_NEMS. Does not compile without it. I have commented out the call from WRFPOST and doublechecked that no other subroutines call INITPOST_GFS_NEMS. Just let it sit there for now until we know the reason.
@JesseMeng-NOAA I ran across this issue when doing a bit or Grib1 cleanup of RQSTFLDS.f. I have been able to remove INITPOST_GFS_NEMS.f and build successfully with some additional changes to WRFPOST.f and thought I would pass this information along. I made changes made in WRFPOST.f to use the 'nemsio_module_mpi' instead of 'nemsio_module' since otherwise there was an error with building related to INITPOST_GFS_NEMS.f being removed from the CMakeLists. You can see the changes via https://github.com/hertneky/UPP/tree/th_grib1_cleanup
Note: this is work that is part of issue #344
@hertneky Thanks for your help. However, I tried the same thing you did for WRFPOST but still have the link errors as
/gpfs/dell2/usrx/local/nceplibs/dev/hpc-stack/libs/hpc-stack/ips-18.0.1.163/impi-18.0.1/nemsio/2.5.2/lib/libnemsio.a(nemsio_read.f90.o): In function nemsio_read_mp_nemsio_readrecgrb8_': /usrx/local/nceplibs/dev/hpc-stack/src/hpc-stack/pkg/nemsio-v2.5.2/src/nemsio_read.f90:979: undefined reference to
getgbm_'
/gpfs/dell2/usrx/local/nceplibs/dev/hpc-stack/libs/hpc-stack/ips-18.0.1.163/impi-18.0.1/nemsio/2.5.2/lib/libnemsio.a(nemsio_read.f90.o): In function nemsio_read_mp_nemsio_readrecvgrb8_': /usrx/local/nceplibs/dev/hpc-stack/src/hpc-stack/pkg/nemsio-v2.5.2/src/nemsio_read.f90:1032: undefined reference to
getgbm_'
/gpfs/dell2/usrx/local/nceplibs/dev/hpc-stack/libs/hpc-stack/ips-18.0.1.163/impi-18.0.1/nemsio/2.5.2/lib/libnemsio.a(nemsio_read.f90.o): In function nemsio_read_mp_nemsio_readrecgrb4w34_': /usrx/local/nceplibs/dev/hpc-stack/src/hpc-stack/pkg/nemsio-v2.5.2/src/nemsio_read.f90:870: undefined reference to
getgbm_'
/gpfs/dell2/usrx/local/nceplibs/dev/hpc-stack/libs/hpc-stack/ips-18.0.1.163/impi-18.0.1/nemsio/2.5.2/lib/libnemsio.a(nemsio_read.f90.o): In function nemsio_read_mp_nemsio_readrecvgrb4w34_': /usrx/local/nceplibs/dev/hpc-stack/src/hpc-stack/pkg/nemsio-v2.5.2/src/nemsio_read.f90:924: undefined reference to
getgbm_'
I am testing on wcoss dell phase 3. What machine and what version of libnemsio.a do you use?
@JesseMeng-NOAA I ran across this issue when doing a bit or Grib1 cleanup of RQSTFLDS.f. I have been able to remove INITPOST_GFS_NEMS.f and build successfully with some additional changes to WRFPOST.f and thought I would pass this information along. I made changes made in WRFPOST.f to use the 'nemsio_module_mpi' instead of 'nemsio_module' since otherwise there was an error with building related to INITPOST_GFS_NEMS.f being removed from the CMakeLists. You can see the changes via https://github.com/hertneky/UPP/tree/th_grib1_cleanup
Note: this is work that is part of issue #344
@JesseMeng-NOAA and @HuiyaChuang-NOAA I would suggest removing legacy INITPOST_SIGIO.f and INITPOST_GFS_NEMS.f in Tracy's PR which would be merged in develop branch before 2D decomposition PR. Please let me know your thoughts.
Sounds good.
@JesseMeng-NOAA and @HuiyaChuang-NOAA I would suggest removing legacy INITPOST_SIGIO.f and INITPOST_GFS_NEMS.f in Tracy's PR which would be merged in develop branch before 2D decomposition PR. Please let me know your thoughts.
@JesseMeng-NOAA I was testing on NCARs Cheyenne initially. The nemsio library used was version 2.5.2. I will test on Hera as well.
Sounds good.
@JesseMeng-NOAA and @HuiyaChuang-NOAA I would suggest removing legacy INITPOST_SIGIO.f and INITPOST_GFS_NEMS.f in Tracy's PR which would be merged in develop branch before 2D decomposition PR. Please let me know your thoughts.
@JesseMeng-NOAA Could you back up the changes for removing these two routines in branch post_2d_decomp ? Thanks!
Sounds good.
@JesseMeng-NOAA and @HuiyaChuang-NOAA I would suggest removing legacy INITPOST_SIGIO.f and INITPOST_GFS_NEMS.f in Tracy's PR which would be merged in develop branch before 2D decomposition PR. Please let me know your thoughts.
@JesseMeng-NOAA Could you back up the changes for removing these two routines in branch post_2d_decomp ? Thanks!
INITPOST_GFS_SIGIO.f was removed. I am keeping INITPOST_GFS_NEMS.f, but commented out all calls, until we have a solution to compile without it.
Turns out the post doesn't have a generalized namelist read. The closest analog is itag. I could add a line in itag but then versions that don't yet support 2D would break. I could try to read it in itag and branch around a failure. Or I could put it in the environment or another file and if the file weren't there, assume default numx=1. Considering options.
Wen's 2d Post currently passes all of the use case regression tests on Jet where I first checked including the ones where we are not considering 2D enhancement
I have modified the numx setting in the 2D post to be done in WRFPOST.f with the value of numx read from a line in itag (numx=4) for example. This would be the first line in itag and if absent, the value DEFAULTS to 1 so current itags can still be used and cause the code to fall back to a 1D decomposition.
It requires disabling the hardwire in MPI_FIRST.f, adding it to CTLBLK.mod and setting it with a read or default value in WRFPOST.f
This all passes regression tests on Jet (which basically test the fallback to 1D in the old itags)
On Fri, Sep 17, 2021 at 3:15 PM Jesse Meng @.***> wrote:
Will do
Dr. Jesse Meng IMSG at NOAA/NWS/NCEP/EMC 5830 University Research Ct. Room 2037 College Park, MD 20740 email: @.***
On Fri, Sep 17, 2021 at 2:12 PM HuiyaChuang-NOAA @.***> wrote:
@JesseMeng-NOAA https://github.com/JesseMeng-NOAA Jesse, please remove the following list of UPP subroutines from 2D decomposition branch:
- SLP_NMM.f
- EXCH2.f
- INITPOST_SIGIO.f
- INITPOST_GFS_NEMS.f
Thank you.
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George W Vandenberghe
IMSG at NOAA/NWS/NCEP/EMC
5830 University Research Ct., Rm. 2141
College Park, MD 20740
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Great! Please let me know where to grab your files. Thanks!
/gpfs/dell3/ptmp/gwv/post.runtime2d.tar
To actually use it place numx=$something in the FIRST line of itag. WRFPOST.f checks for this and backspaces itag to the first line if it isn't present so the rest of the itag input is unaffected
On Thu, Sep 30, 2021 at 11:47 AM Jesse Meng @.***> wrote:
Great! Please let me know where to grab your files. Thanks!
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George W Vandenberghe
IMSG at NOAA/NWS/NCEP/EMC
5830 University Research Ct., Rm. 2141
College Park, MD 20740
@.***
301-683-3769(work) 3017751547(cell)
Thanks George! It works great! numx is read from itag, with default =1 if not present in itag. Both cases generate identical results in my 2d test.
Turns out the post doesn't have a generalized namelist read. The closest analog is itag. I could add a line in itag but then versions that don't yet support 2D would break. I could try to read it in itag and branch around a failure. Or I could put it in the environment or another file and if the file weren't there, assume default numx=1. Considering options.
Wen's 2d Post currently passes all of the use case regression tests on Jet where I first checked including the ones where we are not considering 2D enhancement
@GeorgeVandenberghe-NOAA @JesseMeng-NOAA Sorry I meant to reply earlier but was attending DTC SAB meetings. UPP does read in a namelist "nampgb" namelist/nampgb/kpo,po,kth,th,kpv,pv,fileNameAER,d3d_on,gocart_on,popascal & ,hyb_sigp,rdaod,aqfcmaq_on I think this would be an ideal place to add numx. I like George's idea of setting numx=1 as default. If you look at WRFPOST.f, you can see UPP is setting default too for all namelist variables.
@HuiyaChuang-NOAA @WenMeng-NOAA @GeorgeVandenberghe-NOAA @JesseMeng-NOAA - I also meant to comment. DTC's @kayeekayee is working on some development to translate all info in the itag to a formal fortran namelist (Issue #115) and has the work largely done and tested with current develop branch. Woudl this be of interest to review and push this feature enhancement to help aid the 2d decomp work?
EMC_post is currently decmposed on latitude (J) only. This is adequate for several more years but since post is generally being refactored, now is a good time to make the jump to 2D. A second goal is to make the 2D decomposition either flexible, or just have it mimic the ufs-weather-model decomposition so developers working on both codes can exploit commonality. This will be a modestly difficult project with most effort, figuring out the plumbing of the code (in progress). This issue is being created for management and project leader tracking and per EMC management directives and also best practices, results should be tracked through this Github issue or slack, NOT email.
There are many OTHER scaling issues in the post that are not affected by the decomposition. Most of the issues are orthogonal to the decomposition though and can be worked independently. The most salient is input I/O of model state fields in the standalone post.
By 03/01/2021:
The offline post testing procedure provided by Jesse can be found at here
The inline post testing procedure provided by Bo can be found at here
Jesse's FV3 branch can be found at here