Error running GLBt0.72

[Lucas Pettey]

Hello,

I am trying to run the GLBt0.72 from HYCOM-examples. I ran the script successfully, but I am encountering an error when I run HYCOM in my experiment directory. Any advice is appreciated. Thanks!

Here is the output:

[ec2-user expt_02.0]$ ./hycom

CORE2  NY ; WOA13 SSS relax; SSS relax balanced; EMP balanced; ICE LOAN

17T Sigma2*; WOA13 Jan init; KPP; SeaWiFS chl;

Z(7):1-7,Z(16):8,Z(2):10-16,Z(13):dp00/f/x=36/1.18/262;Z(3):400-600m;

sigma:84-14m; depth_GLBt0.72_15; 2.3.

iversn =        23

iexpt  =        20

idm    =       500

jdm    =       382

itest  =       328

jtest  =        38

kdm    =        41

nhybrd =        41

nsigma =         0

dp0k   =    1.0000 m

dp0k   =    1.8000 m

dp0k   =    3.2400 m

dp0k   =    4.6800 m

dp0k   =    4.9300 m

dp0k   =    5.8100 m

dp0k   =    6.8700 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =    8.0000 m

dp0k   =   10.0000 m

dp0k   =   16.4000 m

dp0k   =   35.9200 m

dp0k   =   42.3800 m

dp0k   =   50.0200 m

dp0k   =   59.0200 m

dp0k   =   69.6400 m

dp0k   =   82.1800 m

dp0k   =   96.9700 m

dp0k   =  114.4300 m

dp0k   =  135.0200 m

dp0k   =  159.3300 m

dp0k   =  188.0100 m

dp0k   =  221.8400 m

dp0k   =  261.7800 m

dp0k   =  400.0000 m

dp0k   =  600.0000 m

dp0k   =  600.0000 m

dp00i  =    1.0000 m

isotop =   83.0000 m

saln0  =   34.7253

 error in blkinr - input saln0  but should be oneta0

     timer statistics

    ------------------

     total    calls =        1   time =    0.00081   time/call =    0.00081428

 **************************************************

 (blkinr)

 **************************************************

STOP (xcstop)

[Alexandra Bozec]

Hi Lucas, 

Your blkdat.input seems to be the one provided by expt_01.1 Of the HYCOM-EXAMPLES and is using version 2.3.00 of HYCOM. We updated the sources last month to 2.3.01 and updated the examples to provide the blkdat suitable for these new sources. Please check out HYCOM-EXAMPLES/GLBt0.72/expt_01.2, it should correct your error. 

More infos can also be found in the wiki page of GLBt0.72:

https://github.com/HYCOM/HYCOM-examples/wiki/GLBt0.72

Alex

On Jan 15, 2020, at 9:37 PM, Lucas Pettey <lucas.pe...@gmail.com> wrote:



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[Lucas Pettey]

Hi Alex,

I'm running into a problem working through that wiki. I compiled NetCDF and the HYCOM-tools that use NetCDF with no reported errors. I'm trying go through the scripts in 'GLBt0.72/force' and I'm encountering an error when I run the 'core_airtemp.csh' (first one I tried):

READING /AFTITL/

At line 247 of file kp_core.f (unit = 5, file = 'stdin')

Fortran runtime error: Cannot match namelist object name #title

Error termination. Backtrace:

#0  0xffffa64318f7 in ???

#1  0xffffa6432813 in ???

#2  0xffffa64330df in ???

#3  0xffffa64e179b in ???

#4  0xffffa64ea0f7 in ???

#5  0xffffa64ea353 in ???

#6  0x40461b in ???

#7  0x407d7b in ???

#8  0xffffa61c0ba3 in ???

#9  0x401927 in ???

Anythoughts on what high be happening here?

Thanks!

Lucas

On Thursday, January 16, 2020 at 8:09:12 AM UTC-6, Alexandra Bozec wrote:

Hi Lucas, 

Your blkdat.input seems to be the one provided by expt_01.1 Of the HYCOM-EXAMPLES and is using version 2.3.00 of HYCOM. We updated the sources last month to 2.3.01 and updated the examples to provide the blkdat suitable for these new sources. Please check out HYCOM-EXAMPLES/GLBt0.72/expt_01.2, it should correct your error. 

More infos can also be found in the wiki page of GLBt0.72:

https://github.com/HYCOM/HYCOM-examples/wiki/GLBt0.72

Alex

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[Lucas Pettey]

Nevermind that error, I found out that replacing the "C" comment character with "#" caused some issues. I have a new now that the kp_core runs successfully:

error in profout - from NetCDF library

nf90_open

No such file or directory

Any thoughts?

[Alan Wallcraft]

Lucas,

The "profout" is a bug.  It should say "kp_core", but that does not matter much.

nf90_open is called several times, and on one of those times the filename to be opened does not exist.

Usually the filename to be opened is written to the .log file first.  Or you could just look to see which needed .nc file isn't where it should be.

Alan.

[Lucas Pettey]

Alan,

Thank you for your patience and help;p getting me running.

I got through all the scripts without any visible errors, but the experiment doesn't run. The end of my output is:

relax  =         F

trcrlx =         F

priver =         T

epmass =         T

At line 2242 of file blkdat.F90 (unit = 2099, file = './limits')

Fortran runtime error: End of file

The "limits" file is empty. There is a 020y011a.limits file that has 2 numbers in it. Any idea where I goofed up the scripts?

Thanks,

Lucas

[Alan Wallcraft]

Lucas,

The model script uses a limits file if there is one, or makes one with awk:

C
C --- local input files.
C
if (-e ${D}/../${E}y${Y01}${A}.limits) then
  /bin/cp ${D}/../${E}y${Y01}${A}.limits limits
else
#  use "LIMITI"  when starting a run after day zero.
#  use "LIMITS9" (say) for a 9-day run
  echo "LIMITS" | awk -f ${D}/../${E}.awk y01=${Y01} ab=${A} >! limits
endif
cat limits

So the above logic failed for some reason.  Without your .log file I can't be more specific.

Alan.

[Lucas Pettey]

Hello again,

I am following the wiki example and I get a 020.csh script after running the new_expt.csh script. There are no errors from what I can see.

When I run the 020.csh script, I get an error running the hycom executable whether I run with 1 or 16 processors:

xcspmd: patch.input for wrong nreg

My "nreg" is set to 3 in the data/patch.input file. 

I performed a "git diff" and the only thing I have changed in the scripts is the root directory except for the datasets/get_datasets.csh. Here I uncommented the CORE2_NYF, CF2v2_GOM and PH3_HYCOM lines so that those datasets would be downloaded and extracted. I ran every script in all the directories as described in the wiki. 

Any ideas has to what my reg should be and how this gets properly set by the input scripts?

Thanks,

Lucas

[Alan Wallcraft]

Lucas,

nreg=3 is for global tripole grids, and the error you get is from HYCOM compiled for regional domains (i.e. not for global tripole domains).

The compile time domain type is selected by the Make*.csh script:

# Optional CPP flags
# Global or regional
setenv OCN_GLB -DARCTIC ## global tripolar simulation
#setenv OCN_GLB ""

There is a Make.csh and a Make_global.csh but check that this is the only difference before running Make_global.csh.

Remove all existing make products first:

/bin/rm *.o *.mod *.log hycom

Alan.

[Lucas Pettey]

Hi Alan,

Thanks, I recompiled and got a little further. Now my error is:

hkdf4: range =    0.0200    0.0500

  ...finished opening thkdf4 field

          error in zaiopf -  can't open unit  11, for array I/O.

          cfile = restart_in.a

 mpi_file_open - mpierr =           42

 **************************************************

 (zaiopf)

 **************************************************

 XCHALT CALLED ON PROC =            5           1           2

 **************************************************

I tried changing the "restart" variable from - to + in "new_expt.csh", but I got the same error.

Thanks for all the help!

Lucas

[Lucas Pettey]

I did some digging through the script output and it appears that several files are missing:

C --- time-invarent wind stress offset

C

setenv OFS

setenv OFS _era40-nogaps

if ( _era40-nogaps !=  ) then

touch forcing.ofstrs.a

touch forcing.ofstrs.b

if ( -z forcing.ofstrs.a ) then

[1] 14900

endif

if ( -z forcing.ofstrs.b ) then

/bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/force/offset/ofstrs_era40-nogaps.a forcing.ofstrs.a

[2] 14901

endif

endif

/bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/force/offset/ofstrs_era40-nogaps.b forcing.ofstrs.b

C

/bin/cp: cannot stat ‘/home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/force/offset/ofstrs_era40-nogaps.a’: No such file or directory

/bin/cp: cannot stat ‘/home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/force/offset/ofstrs_era40-nogaps.b’: No such file or directory

[2]  - Exit 1                        /bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/force/offset/ofstrs_era40-nogaps.b forcing.ofstrs.b

[1]  + Exit 1                        /bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/force/offset/ofstrs_era40-nogaps.a forcing.ofstrs.a

[...]

bin/cp: cannot stat ‘/home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/020/relax_rmu.a’: No such file or directory

/bin/cp: cannot stat ‘/home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/020/relax_rmu.b’: No such file or directory

[2]  - Exit 1                        /bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/020/relax_rmu.b relax.rmu.b

[1]  + Exit 1                        /bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/020/relax_rmu.a relax.rmu.a

[...]

/bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/SSH/relax_montg_019.a relax.montg.a

touch relax.montg.b

if ( -z relax.montg.b ) then

/bin/cp: cannot stat ‘/home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/SSH/relax_montg_019.a’: No such file or directory

[2] 14935

[1]    Exit 1                        /bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/SSH/relax_montg_019.a relax.montg.a

/bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/SSH/relax_montg_019.b relax.montg.b

endif

endif

setenv XR sp

if ( sp !=  ) then

touch relax.sefold.a

/bin/cp: cannot stat ‘/home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/SSH/relax_montg_019.b’: No such file or directory

[2]  + Exit 1                        /bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/../datasets/relax/SSH/relax_montg_019.b relax.montg.b

[...]

C --- get restart from permenant storage

/bin/rm -f restart_in.a restart_in.b

/bin/rm -f restart_out.a restart_out.b

/bin/rm -f restart_out1.a restart_out1.b

[1] 14973

/bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/data//restart_001a.a restart_in.a

[2] 14974

/bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/data//restart_001a.b restart_in.b

endif

if ( -e ./cice ) then

/bin/cp: cannot stat ‘/home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/data//restart_001a.a’: No such file or directory

C

/bin/cp: cannot stat ‘/home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/data//restart_001a.b’: No such file or directory

[2]  - Exit 1                        /bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/data//restart_001a.b restart_in.b

[1]  + Exit 1                        /bin/cp /home/ec2-user/HYCOM-examples/GLBt0.72/expt_02.0/data//restart_001a.a restart_in.a

This looks to be why Hycom can't open the file. My question is now how do I get or generate these missing files?

Thanks,

Lucas

[Lucas Pettey]

I am attaching the log files from running the new_expt script and then the 020.csh script. Any help is appreciated. Thanks!

[Alexandra Bozec]

Hi Lucas, 

HYCOM stops because it does not find the restart_in.[ab]. It is looking for a restart because in the limits files that it has been given, there is no negative sign before the first number. I see from the my020.log that your are starting your run at year 1 (setenv Y01 001) but the new_expt.log shows that the run is set for running year 11 (see setenv Y01 011)  and so it created beforehand a file name 020y011.limits with a negative sign NOT 020y001.limits.

Try created a 020y001.limits file starting with a negative sign and run again. 

Alex

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Alexandra Bozec

[Lucas Pettey]

Hi Alex,

Thanks for the information, but your suggestion did not work. I tried copying my 020y011.limits file (limits are -3653.00000 3684.00000) to both 020y001.limits and 020y001a.limits. The former gave me the same error. Copying to 020y001a.limits gave me this error:

error in forfunh - actual forcing must start after wind day 1462

dtime1 =     1.00000

I tried changing the start and end to 001 in the new_expt.csh but that yields the same error with a limits file that contains values (-1.00000 32.00000). The only thing that got a run to go at all was to set both Y01 and YXX in the 020.csh script created by new_expt.csh to 011.

Now I get a new error in that NaN's are being generated. I have attached my log file. 

Is this just me? Do the scripts work straight from Git for other people? I haven't changed anything except home directories in the scripts and number of processors to 16.

Thanks again for all the help,

Lucas

On Friday, January 24, 2020 at 12:46:36 PM UTC-6, Alexandra Bozec wrote:

Hi Lucas, 

HYCOM stops because it does not find the restart_in.[ab]. It is looking for a restart because in the limits files that it has been given, there is no negative sign before the first number. I see from the my020.log that your are starting your run at year 1 (setenv Y01 001) but the new_expt.log shows that the run is set for running year 11 (see setenv Y01 011)  and so it created beforehand a file name 020y011.limits with a negative sign NOT 020y001.limits.

Try created a 020y001.limits file starting with a negative sign and run again. 

Alex

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[Alexandra Bozec]

Hi Lucas, 

sorry for the confusion on the last email, I should have been more clear ...

There are several calendars in HYCOM yrflag=0,1,2 and 4 are climatological years (repeating forcing years) and by construction the time-stamps in the forcing files for these calendars should be either 1904 (yrflag=0,1,2) or 1905 (yrflag=4).

When using yrflag=3, you use actual years for the time-stamp of the forcing. We usually use that calendar when we have an interannual forcing and start the simulation with the same date as the forcing. In the HYCOM-examples, we set-up an example that treat a climatological forcing (CORE2) as an actual year and this is what you are doing. So I would suggest to start your simulation at any date/year after 1905 as to not "confuse" HYCOM. 

So for examples, if you start in January 1911, you will need a first limits files name 020y011a.limits, with the "011" begin the year and "a" being the month (a for January, b for February etc ...).

For your recent crash, I think the problem comes from the fact that you do not have any relax.montg files and you have sshflg=2 in your blkdat.input. Try putting sshflg=0 and run. I will try and see why HYCOM did not stop when not finding the file ... 

Alex

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[Lucas Pettey]

We're getting closer Alex!

I couldn't find any relax.montg files anywhere on the ftp site, so I changed to sshflg=0. Now the issues is:

175350 i,j,k=  210  293  1 neg. dp (m) in loop 19       -17.     fatal 

I have attached the log file for the new run and I'll do some digging on my own. 

On Monday, January 27, 2020 at 2:06:58 PM UTC-6, Alexandra Bozec wrote:

Hi Lucas, 

sorry for the confusion on the last email, I should have been more clear ...

There are several calendars in HYCOM yrflag=0,1,2 and 4 are climatological years (repeating forcing years) and by construction the time-stamps in the forcing files for these calendars should be either 1904 (yrflag=0,1,2) or 1905 (yrflag=4).

When using yrflag=3, you use actual years for the time-stamp of the forcing. We usually use that calendar when we have an interannual forcing and start the simulation with the same date as the forcing. In the HYCOM-examples, we set-up an example that treat a climatological forcing (CORE2) as an actual year and this is what you are doing. So I would suggest to start your simulation at any date/year after 1905 as to not "confuse" HYCOM. 

So for examples, if you start in January 1911, you will need a first limits files name 020y011a.limits, with the "011" begin the year and "a" being the month (a for January, b for February etc ...).

For your recent crash, I think the problem comes from the fact that you do not have any relax.montg files and you have sshflg=2 in your blkdat.input. Try putting sshflg=0 and run. I will try and see why HYCOM did not stop when not finding the file ... 

Alex

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[Alexandra Bozec]

The mistake was on my part for sshflg, it should have always been 0 for this configuration; I've changed the blkdat.input of this experiment on GitHub. 

Now you have a problem with your relax  files. From the log files, the relax.temp is all 0. and the salinity does not look reasonable either... you should check out how they were created. An examples of files is available on the HYCOM server for comparison (or use): 

wget ftp://ftp.hycom.org/pub/GitHub/HYCOM-examples/GLBt0.72/datasets/relax_010.tar.gz

Alex

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Alexandra Bozec

[Yen Lung Chen]

Hi,

I am a newer and I try the  same example (GLBt0.72) using HYCOM-src_2.3.01 with omp.

An new experiment is setted based on the expt_01.2, and named as  expt_01.3.

I have a similar problem as Lucas mentioned above (error: neg. dp (m) <    -10.00).

Please see the attachment, many thanks.

Alexandra Bozec 在 2020年1月28日 星期二清晨6:26:43 [UTC+8] 的信中寫道：

[Alan Wallcraft]

I suggest trying the following:

a) Run with NOMP set to 1

If that does not work, generate src_2.3.01-17tsig2_relo_one and

b) Run with NOMP set to 0

If either a or b works, the problem is with OpenMP.  We don't use OpenMP for HYCOM much, but we do test that it works by checking for bit-for-bit reproducibility with different NOMP's.  So in this case (a or b working), let us know what compiler and config file you used to build HYCOM and I'll try to reproduced the issue.

If (b), in particular, fails then something else is wrong.  Is your 1.3 supposed to be identical to the example 1.2?

Alan.

[Gerardo Cisneros]

Alexandra,

I am trying to figure out how to run HYCOM 2.3 using the GLBt0.72 test case but, after reading all of the suggestions in this thread and applying them, I am still getting the "error in blkinr - input saln0  but should be oneta0" message mentioned in the thread's first post.  My ultimate interest is in running a large test case (hundreds to thousands of MPI ranks) with a view to analyzing hycom's MPI communications over the interconnect.

I built hycom using Intel 2021.7.1 compilers and Open MPI 4.1.5rc2 from NVIDIA's (formerly Mellanox's) HPC-X 2.14.0.

I tried attaching the output log but for some reason the "attach file" feature isn't available.

Saludos,

Gerardo
--
Dr. Gerardo Cisneros-Stoianowski
HPC Applications Performance Specialist
HPC-AI Advisory Council

[Alexandra Bozec]

Hi Gerardo, 

This error means that when HYCOM reads the blkdat.input, it expects a variable named oneta0 but has saln0 instead. This type of error is common when the blkdat.input does not correspond to the version of HYCOM you are using. A new version of HYCOM has been released since the HYCOM-examples package was set-up and it incorporates a new variable in the blkdat.input (i.e. oneta0).  I've changed it in GLBt0.72/expt_01.2/blkdat.input but forgot to change it in the other directories. I will do so soon. 

So in your case, add the line in bold to your blkdat.input and that should fix the problem:

83.0 'isotop' = shallowest depth for isopycnal layers (m), <0 from file

0.1 'oneta0' = minimum 1+eta, must be > 0.0

34.7253 'saln0 ' = initial salinity value (psu), only used for iniflg<2

Best, 

Alex

--

Alexandra Bozec

[Gerardo Cisneros]

Alex,

Thank you very much for the prompt reply.  The addition you suggested partially worked, but now the run stopped as follows:

. . .

hybrlx =    8.0000 time steps
hybiso =    0.0100 kg/m^3
hybmap =    3.0000  
 
error in blkinr - input hybmap but should be hybthn

I assume there is another parameter missing in blkdat.input.

Saludos,

Gerardo

[Gerardo Cisneros]

Alex,

I looked in blkdat.F90 and figured that adding

  1.0    'hybthn' = HYBGEN: ratio of layer thicknesses to select the thiner

would fix the error, which it did, with the run now advancing to:

...

lbflag =         0
tidflg =         F
 
error in blkinl - input tidflg but should be lbmont

Next I added the following line to blkdat.input:

  0      'lbmont' = baro nesting

and the run advanced further, to:

model starts at day  3653.0, goes to day  3684.0   (steps   175344 --   176832)

 now initializing forcing fields ...
...

CORE CNYFv2, std
linear interpolation in time to every  0.25000000 days
i/jdm =  500  382
wnd_ewd: day,span,range =   731.00000  0.250000  -2.3870726E+01   2.5478317E+01

error in forfunh - actual forcing must start after wind day 1462

This new message is one I'm not sure how to fix.

Saludos,

Gerardo

[Alexandra Bozec]

This means the calendar you are using (yrflag in blkdat.input) is not compatible with the atmospheric forcing you are using. 

What is your yrflag and how did you create your forcing, i.e. was it beforehand or when running the model? 

Alex

--

Alexandra Bozec

[Gerardo Cisneros]

Alex,

Thanks again.  I have yrflag set to 3, and I did not create any atmospheric forcing (I guess I missed how to do that while reading the wiki).

Saludos,

Gerardo

[Gerardo Cisneros]

Alex,

I followed the instructions in the "How to create forcing and relax files for GLBt0.72" section of the GLBt0.72 wiki, but I'm still getting

error in forfunh - actual forcing must start after wind day 1462

dtime1 =     731.000   

I also tried changing yrflag to 2, but it didn't help.  Not sure how to proceed at this point.

Saludos,

Gerardo

[Alexandra Bozec]

Gerardo, 

When creating the forcing beforehand, i.e. with the scripts in GLBt0.72/force, the yrflag should be 4 which is for a 365-day calendar (Climatological forcing). 

If you want to use the actual calendar (yrflag=3) then you have to make the files “on the fly” by having "setenv MAKE_FORCE 1 “ in EXPT.src. We have an example for that in GLBt0.72/expt_01.1/. 

The forcing will be created automatically by the submission script with the right time stamps, ready to be used by HYCOM. 

Note that the forcing is still the climatological COREv2 forcing but with a time-stamp suitable for the actual calendar (with leap year and such). 

In the GOMb0.08 wiki page, you will see examples using inter annual forcing (CFSR,CFSv2).

Alex

[Gerardo Cisneros]

Alex,

I changed yrflag to 4, reran the core_time_interp.csh script under GLBt072/force (which is the only script that appears to depend on yrflag) and tried again.  This time the program ended with a different error elsewhere:

Rivers CORE v2 rain+snow (m/s)
Time-invariant Antarctic runoff added (0.073 Sv, distributed along coastline)
https://data1.gfdl.noaa.gov/~nnz/mom4/COREv2/data_IAF/CORRECTED/calendar_years/
(See https://data1.gfdl.noaa.gov/nomads/forms/core/COREv2/code_v2.html for rema
i/jdm  500 382
 river precip: month, range =   1  0.00000000E+00   5.47079151E-05              
 ...finished opening river   field  
 now opening mean SSH & Montg. Pot. fields ...
 
error in rdmonth - hit end of input
iunit,ios =          915          -1

Saludos,

Gerardo

[Alexandra Bozec]

Gerardo, 

I've just checked the default blkdat.input on github and the sshflg is 2, i.e that it need a file named relax.montg.[ab] that corrects the variable montg1 (Montgomery potential at surface) in order to be the steric SSH. This relax.montg file can be created from a time-average mean of the montg1 of a simulation with sshflg=0. Seea GLBt0.72/archive/data2d_archm_montg.csh. 

For more explanation, see section 6 in GOMb0.08 wiki:

https://github.com/HYCOM/HYCOM-examples/wiki/GOMb0.08#6-generate-a-montgomery-potential-offset 

For now, set the sshflg=0 in your blkdat.input. 

Alex

--

Alexandra Bozec

[Gerardo Cisneros]

Alex,

That worked; thank you very much!  I got a complete run with normal termination in about 10 minutes, on 28 cores of a single node that has Cascade Lake Xeon CPUs, with a single line in the LIST file.  What I really need now is a higher-resolution experiment that can scale across several nodes and up to a couple thousand MPI ranks, for benchmarking and communications analysis purposes.  Any help with that will be appreciated.

Saludos,

Gerardo

[Alexandra Bozec]

Gerardo, 

We are in the process of adding a benchmark configuration to the HYCOM-examples on Github. It will be a few days before it is ready. This will be a global 1/12º HYCOM configuration with 4500x3298 and 41 layers. 

I'll keep you updated.

Alex

--

Alexandra Bozec

[Gerardo Cisneros]

Alex,

Thank you!  I look forward to hearing about the benchmark configuration!

Saludos,

Gerardo

[_ solgi]

Dear Alan and Alex

I am trying to run the model. I did all the steps according to the user guide and solved many errors with your help. I tried without force and tide first. But it does not have a proper output. Now when I try to run the model for 010.csh the archive data is not created. I tried a lot to solve this problem but it's confusing. Why does it detect the files but not create the archive? Can you help me solve this problem?

Best regards

Solgi

root@mostafa-G41D3C:/home/HYCOM/hycom/PEGh0.02/expt_01.0# csh 010.csh
set time = 1
set timestamp
C
C --- Experiment PEGh0.02 - 01.X series
C --- 41 layer sig2star HYCOM on 0.08 degree Gulf of Mexico region
C --- 01.X - No winds, 9 day run for template restart, from WOA13 climatology
C --- EX is experiment directory, required because batch systems often start scripts in home
C
setenv EX /home/HYCOM/hycom/PEGh0.02/expt_01.0
C
C --- Preamble, defined in EXPT.src
C
C --- OS is operating system of machine
C --- R is region name.
C --- V is source code version number.
C --- T is topography number.
C --- K is number of layers.
C --- E is expt number.
C --- P is primary path.
C --- D is permanent directory.
C --- SCR is the scratch directory prefix.
C --- S is scratch directory, must not be the permanent directory.
C --- DS is the datasets directory.
C --- MAKE_FORCE is logical for creating forcing at run time.
C --- N is the name of the atmospheric forcing for PRE-processing.
C
source /home/HYCOM/hycom/PEGh0.02/expt_01.0/EXPT.src
setenv OS `uname`
uname
setenv R PEGh0.02
setenv V 2.3.01
setenv T 07
setenv K 41
setenv E 010
setenv X 01.0
setenv P /home/HYCOM/hycom/PEGh0.02/expt_01.0
setenv D /home/HYCOM/hycom/PEGh0.02/expt_01.0
setenv S /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH
setenv DS /home/HYCOM/hycom/PEGh0.02
setenv N cfsr_peg
setenv W /home/HYCOM/hycom/DATA/CFSR_PEG
setenv MAKE_FORCE 0
setenv NOMP 0
setenv NMPI 7
setenv restart off
setenv ARCHIVE 1
setenv QSUBMIT csh
setenv mnsqa 0
setenv mnsqe 0
setenv statm 1
setenv plots 1
setenv transp 0
setenv data2d 0
setenv netcdf 1
C
C --- Set parallel configuration, see ../README/README.expt_parallel.
C --- NOMP = number of OpenMP threads, 0 for no OpenMP, 1 for inactive OpenMP
C --- NMPI = number of MPI tasks, 0 for no MPI
C
switch ( Linux )
setenv NOMP 1
setenv NMPI 96
breaksw
C
C --- get to the scratch directory
C
mkdir -p /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH
cd /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH
C
C --- For whole year runs.
C --- Y01 initial model year of this run.
C --- YXX is the last model year of this run, and the first of the next run.
C --- A and B are identical, typically blank.
C --- For part year runs.
C --- A is this part of the year, B is next part of the year.
C --- Y01 is the start model year of this run.
C --- YXX is the end model year of this run, usually Y01.
C --- For a few hour/day run
C --- A is the start day and hour, of form dDDDhHH.
C --- B is the end day and hour, of form dXXXhYY.
C --- Y01 is the start model year of this run.
C --- YXX is the end model year of this run, usually Y01.
C --- Note that these variables are set by the .awk generating script.
C
@ ymx = 1
C
setenv A
setenv B
setenv Y01 103
setenv YXX 103
setenv YOF `echo ${Y01} | awk '{printf("%04.0f", $1)}'`
awk {printf("%04.0f", $1)}
echo 103
C
echo Y01 = 103 YXX =  103 A = B =
Y01 = 103 YXX =  103 A = B =
C --- annual offset, if needed
C
setenv YOF
setenv YOF `echo ${Y01} | awk '{printf("%04.0f", $1)}'`
awk {printf("%04.0f", $1)}
echo 103

C
C --- local input files.
C

if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/010y103.limits ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/expt_01.0/010y103.limits limits
else
cat limits
-0  360
C
C
if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/ports.input_103 ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/expt_01.0/ports.input ports.input
endif
C
if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/tracer.input_103 ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/expt_01.0/tracer.input tracer.input
endif
C
if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/blkdat.input_103 ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/expt_01.0/blkdat.input blkdat.input
endif
C
if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/archs.input_103 ) then
if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/archs.input ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/expt_01.0/archs.input archs.input
endif
C
if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/profile.input_103 ) then
if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/profile.input ) then
touch profile.input
endif
if ( ! -z profile.input ) then
C

if ( -e ./cice ) then

if ( 96 != 0 ) then
setenv NPATCH `echo $NMPI | awk '{printf("%03d", $1)}'`
awk {printf("%03d", $1)}
echo 96
echo 096
096
/bin/rm -f patch.input
/bin/cp /home/HYCOM/hycom/PEGh0.02/topo/partit/depth_PEGh0.02_07.096s8 patch.input
C
/bin/rm -f archt.input
if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/archt.input_103 ) then
if ( -e /home/HYCOM/hycom/PEGh0.02/expt_01.0/archt.input ) then
touch archt.input
endif
if ( ! -z archt.input ) then
endif
C
C --- check that iexpt from blkdat.input agrees with E from this script.
C
setenv EB `grep "'iexpt ' =" blk* | awk '{printf("%03d", $1)}'`
grep 'iexpt ' = blkdat.input
awk {printf("%03d", $1)}
if ( 010 != 010 ) then
C
C --- pget, pput copy files between scratch and permanent storage.
C --- Can both be cp if the permanent filesystem is mounted locally.
C
switch ( Linux )
setenv pget /bin/cp
setenv pput /bin/cp
endsw
C
C --- input files from file server.
C
touch regional.depth.a regional.depth.b
if ( -z regional.depth.a ) then
if ( -z regional.depth.b ) then
C
touch regional.grid.a regional.grid.b
if ( -z regional.grid.a ) then
if ( -z regional.grid.b ) then

if ( -e ./cice ) then

C
C --- vapmix or spchum
C
setenv flxflg `grep flxflg ${D}/blkdat.input | awk '{print $1}'`
grep flxflg /home/HYCOM/hycom/PEGh0.02/expt_01.0/blkdat.input
awk {print $1}
if ( 0 != 5 ) then
setenv HUM vapmix
else
C
if ( 0 == 0 ) then
C
C --- Climatological atmospheric forcing.
C
setenv FN ncep
touch forcing.tauewd.a forcing.taunwd.a forcing.wndspd.a
touch forcing.radflx.a forcing.shwflx.a forcing.vapmix.a forcing.precip.a
touch forcing.airtmp.a forcing.seatmp.a forcing.surtmp.a
touch forcing.mslprs.a
touch forcing.wndewd.a forcing.wndnwd.a
touch forcing.tauewd.b forcing.taunwd.b forcing.wndspd.b
touch forcing.radflx.b forcing.shwflx.b forcing.vapmix.b forcing.precip.b
touch forcing.airtmp.b forcing.seatmp.b forcing.surtmp.b
touch forcing.mslprs.b
touch forcing.wndewd.b forcing.wndnwd.b
if ( -z forcing.tauewd.a ) then
[1] 9327
endif
if ( -z forcing.tauewd.b ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/tauewd.a forcing.tauewd.a
[2] 9328
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/tauewd.b forcing.tauewd.b
if ( -z forcing.taunwd.a ) then
[3] 9329
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/taunwd.a forcing.taunwd.a
endif
if ( -z forcing.taunwd.b ) then
[4] 9330
endif
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/tauewd.a'if ( -z forcing.wndewd.a ) then
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/tauewd.b': No such file or directory: No such file or directory

[5] 9331
endif
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/taunwd.a'if ( -z forcing.wndewd.b ) then
[2]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/tauewd.b forcing.tauewd.b

: No such file or directory

[6] 9332
endif
[3]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/taunwd.a forcing.taunwd.a
[1]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/tauewd.a forcing.tauewd.a
if ( -z forcing.wndnwd.a ) then
[7] 9333
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndnwd.a forcing.wndnwd.a
if ( -z forcing.wndnwd.b ) then
[8] 9334
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndnwd.b forcing.wndnwd.b
if ( -z forcing.wndspd.a ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndewd.a forcing.wndewd.a
[9] 9335
endif
if ( -z forcing.wndspd.b ) then
[1] 9336
endif
if ( -z forcing.mslprs.a ) then
[2] 9337
endif
if ( -z forcing.mslprs.b ) then
[3] 9338
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/wndnwd.a'/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/wndewd.a'endif
if ( -z forcing.vapmix.a ) then

: No such file or directory
: No such file or directory

[10] 9339
[7]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndnwd.a forcing.wndnwd.a
[5]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndewd.a forcing.wndewd.a
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/mslprs.b forcing.mslprs.b
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/taunwd.b forcing.taunwd.b
if ( -z forcing.vapmix.b ) then
[5] 9340
endif
setenv AO
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/vapmix.a forcing.vapmix.a
if ( -z forcing.airtmp.a ) then
[7] 9341
endif
if ( -z forcing.airtmp.b ) then
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/wndnwd.b'[11] 9342
endif
setenv PO
: No such file or directoryif ( -z forcing.precip.a ) then

/bin/cp: [12] 9343
cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/taunwd.b'endif

: No such file or directory

if ( -z forcing.precip.b ) then
[13] 9344
[8]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndnwd.b forcing.wndnwd.b
[4]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/taunwd.b forcing.taunwd.b
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/mslprs.a forcing.mslprs.a
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndewd.b forcing.wndewd.b
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/airtmp.a forcing.airtmp.a
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/mslprs.b'endif
setenv FO
/bin/cp: /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/vapmix.b forcing.vapmix.b
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/wndewd.b': No such file or directory
if ( -z forcing.radflx.a ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndspd.b forcing.wndspd.b
[4] 9345
[6]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndewd.b forcing.wndewd.b
endif
if ( -z forcing.radflx.b ) then
[6] 9346
endif
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/vapmix.a'if ( -z forcing.shwflx.a ) then
[8] 9347
endif
if ( -z forcing.shwflx.b ) then
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/vapmix.b'[14] 9348
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndspd.a forcing.wndspd.a

: No such file or directory

endif
if ( -z forcing.surtmp.a ) then
cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/airtmp.a': No such file or directory[15] 9349

[5]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/vapmix.b forcing.vapmix.b
endif
[7]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/airtmp.a forcing.airtmp.a
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/shwflx.a forcing.shwflx.a
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/radflx.a forcing.radflx.a

: No such file or directory

if ( -z forcing.surtmp.b ) then
[3]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/mslprs.b forcing.mslprs.b

: No such file or directory

[3] 9350
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/airtmp.b forcing.airtmp.b
endif
[10]   Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/vapmix.a forcing.vapmix.a
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/wndspd.a'setenv FS ncep

: No such file or directory

if ( ncep !=  ) then
if ( -z forcing.seatmp.a ) then
[5] 9351
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/shwflx.b forcing.shwflx.b
[9]    Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndspd.a forcing.wndspd.a
endif
if ( -z forcing.seatmp.b ) then
[7] 9352
endif
endif
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/precip.a forcing.precip.a
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/mslprs.a': No such file or directory
/bin/cp: /bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/wndspd.b'/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/precip.b forcing.precip.b
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/surtmp.a forcing.surtmp.a
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/precip.a': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/airtmp.b'/bin/cp: : No such file or directory

: No such file or directory

/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/radflx.a': No such file or directorycannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/precip.b'/bin/cp: /bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/shwflx.a': No such file or directory
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/seatmp.b forcing.seatmp.b

: No such file or directory

cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/surtmp.a'/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/radflx.b forcing.radflx.b

: No such file or directory
C

cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/shwflx.b': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/radflx.b'/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/seatmp.b': No such file or directory

: No such file or directory

/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/surtmp.b forcing.surtmp.b
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/seatmp.a forcing.seatmp.a
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/surtmp.b': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/ncep/seatmp.a': No such file or directory
[7]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/seatmp.b forcing.seatmp.b
[5]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/seatmp.a forcing.seatmp.a
[3]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/surtmp.b forcing.surtmp.b
[15] + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/surtmp.a forcing.surtmp.a
[14] + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/shwflx.b forcing.shwflx.b
[8]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/shwflx.a forcing.shwflx.a
[6]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/radflx.b forcing.radflx.b
[4]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/radflx.a forcing.radflx.a
[13] + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/precip.b forcing.precip.b
[12] + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/precip.a forcing.precip.a
[11] + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/airtmp.b forcing.airtmp.b
[2]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/mslprs.a forcing.mslprs.a
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/ncep/wndspd.b forcing.wndspd.b

C --- time-invarent wind stress offset
C
setenv OFS

if ( !=  ) then
C
if ( 0103 !=  ) then
C
C --- annual heat flux offset, pre-positioned offlux files
C
setenv OFF
if ( !=  ) then
else
C
touch forcing.rivers.a
touch forcing.rivers.b
if ( -z forcing.rivers.a ) then
[1] 9363
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/rivers/rivers_07.a forcing.rivers.a
if ( -z forcing.rivers.b ) then
[2] 9364
endif
C
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/rivers/rivers_07.b forcing.rivers.b
/bin/cp: /bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/rivers/rivers_07.a'cannot stat '/home/HYCOM/hycom/PEGh0.02/force/rivers/rivers_07.b': No such file or directory

: No such file or directory

[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/rivers/rivers_07.b forcing.rivers.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/rivers/rivers_07.a forcing.rivers.a
touch forcing.chl.a
touch forcing.chl.b
if ( -z forcing.chl.a ) then
[1] 9368
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/seawifs/chl.a forcing.chl.a
if ( -z forcing.chl.b ) then
[2] 9369
endif
C
/bin/cp /home/HYCOM/hycom/PEGh0.02/force/seawifs/chl.b forcing.chl.b
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/seawifs/chl.b'/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/force/seawifs/chl.a': No such file or directory

: No such file or directory

[2]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/seawifs/chl.b forcing.chl.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/force/seawifs/chl.a forcing.chl.a
touch relax.rmu.a relax.saln.a relax.temp.a relax.intf.a
touch relax.rmu.b relax.saln.b relax.temp.b relax.intf.b
if ( -z relax.rmu.a ) then
if ( -z relax.rmu.b ) then
if ( -z relax.saln.a ) then
if ( -z relax.saln.b ) then
if ( -z relax.temp.a ) then
if ( -z relax.temp.b ) then
if ( -z relax.intf.a ) then
if ( -z relax.intf.b ) then
touch tbaric.a
touch tbaric.b
if ( -z tbaric.a ) then
[1] 9375
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/tbaric.a tbaric.a
if ( -z tbaric.b ) then
[2] 9376
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/tbaric.b tbaric.b
C
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/tbaric.a': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/tbaric.b': No such file or directory
[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/tbaric.b tbaric.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/tbaric.a tbaric.a
setenv XS
if ( !=  ) then
C
setenv XM 054
if ( 054 !=  ) then
touch relax.montg.a
if ( -z relax.montg.a ) then
[1] 9380
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/SSH/relax_montg_054_1994-1998.a relax.montg.a

touch relax.montg.b
if ( -z relax.montg.b ) then

[2] 9382
endif
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/SSH/relax_montg_054_1994-1998.b relax.montg.b
C
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/SSH/relax_montg_054_1994-1998.a': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/SSH/relax_montg_054_1994-1998.b': No such file or directory
[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/SSH/relax_montg_054_1994-1998.b  ...
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/SSH/relax_montg_054_1994-1998.a  ...
setenv XR _150_07
if ( _150_07 !=  ) then
touch relax.sssrmx.a
if ( -z relax.sssrmx.a ) then
[1] 9385
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/SSSRMX/sssrmx_150_07.a relax.sssrmx.a
touch relax.sssrmx.b
if ( -z relax.sssrmx.b ) then
[2] 9387
endif
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/SSSRMX/sssrmx_150_07.b relax.sssrmx.b
C
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/SSSRMX/sssrmx_150_07.a': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/SSSRMX/sssrmx_150_07.b': No such file or directory
[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/SSSRMX/sssrmx_150_07.b relax.sssrmx.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/SSSRMX/sssrmx_150_07.a relax.sssrmx.a
setenv XSE
if ( !=  ) then
C
touch cb.a
touch cb.b
if ( -z cb.a ) then
[1] 9392
endif
if ( -z cb.b ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/DRAG/cb_07_10mm.a cb.a
[2] 9393
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/DRAG/cb_07_10mm.b cb.b
touch cbar.a
touch cbar.b
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/DRAG/cb_07_10mm.a': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/DRAG/cb_07_10mm.b': No such file or directory
[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/DRAG/cb_07_10mm.b cb.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/DRAG/cb_07_10mm.a cb.a
if ( -z cbar.a ) then
[1] 9396
endif
if ( -z cbar.b ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/cbar.a cbar.a
[2] 9397
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/cbar.b cbar.b
touch iso.sigma.a
touch iso.sigma.b
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/cbar.a': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/cbar.b': No such file or directory
[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/cbar.b cbar.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/cbar.a cbar.a
if ( -z iso.sigma.a ) then
if ( -z iso.sigma.b ) then
C
touch iso.top.a
touch iso.top.b
if ( -z iso.top.a ) then
[1] 9403
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/iso_top.a iso.top.a
if ( -z iso.top.b ) then
[2] 9404
endif
C
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/iso_top.b iso.top.b
/bin/cp: /bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/iso_top.b'cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/iso_top.a': No such file or directory

: No such file or directory

[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/iso_top.b iso.top.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/iso_top.a iso.top.a
touch thkdf2.a
touch thkdf2.b
if ( -z thkdf2.a ) then
[1] 9408
endif
if ( -z thkdf2.b ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/thkdf2.a thkdf2.a
[2] 9409
endif
C
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/thkdf2.b thkdf2.b
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/thkdf2.a': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/thkdf2.b': No such file or directory
[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/thkdf2.b thkdf2.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/thkdf2.a thkdf2.a
touch thkdf4.a
touch thkdf4.b
if ( -z thkdf4.a ) then
[1] 9413
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/thkdf4.a thkdf4.a
if ( -z thkdf4.b ) then
[2] 9414
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/thkdf4.b thkdf4.b
C
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/thkdf4.b': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/thkdf4.a': No such file or directory
[2]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/thkdf4.b thkdf4.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/thkdf4.a thkdf4.a
touch veldf2.a
touch veldf2.b
if ( -z veldf2.a ) then
[1] 9418
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/veldf2.a veldf2.a
endif
if ( -z veldf2.b ) then
[2] 9419
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/veldf2.b veldf2.b
touch veldf4.a
touch veldf4.b
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/veldf2.a': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/veldf2.b': No such file or directory
[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/veldf2.b veldf2.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/veldf2.a veldf2.a
if ( -z veldf4.a ) then
[1] 9422
endif
if ( -z veldf4.b ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/veldf4.a veldf4.a
[2] 9423
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/veldf4.b veldf4.b
C
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/veldf4.b': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/010/veldf4.a': No such file or directory
[2]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/veldf4.b veldf4.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/010/veldf4.a veldf4.a
setenv TT
C
touch tidal.rh.a
touch tidal.rh.b
if ( -z tidal.rh.a ) then
[1] 9428
endif
if ( -z tidal.rh.b ) then
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/DRAG/tidal.rh.07.a tidal.rh.a
[2] 9429
endif
/bin/cp /home/HYCOM/hycom/PEGh0.02/relax/DRAG/tidal.rh.07.b tidal.rh.b
C
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/DRAG/tidal.rh.07.a': No such file or directory
/bin/cp: cannot stat '/home/HYCOM/hycom/PEGh0.02/relax/DRAG/tidal.rh.07.b': No such file or directory
[2]  - Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/DRAG/tidal.rh.07.b tidal.rh.b
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/relax/DRAG/tidal.rh.07.a tidal.rh.a
C --- restart input
C
touch restart_in.a restart_in.b restart_out.a restart_out.b restart_out1.a restart_out1.b
if ( -z restart_in.b ) then
setenv RI        0.00
else
if ( -z restart_out.b ) then
setenv RO        0.00
else
if ( -z restart_out1.b ) then
setenv R1        0.00
else
setenv LI `awk  '{printf("%11.2f\n", $1)}' limits`
awk {printf("%11.2f\n", $1)} limits
C
if ( `echo $LI | awk '{if ($1 <= 0.0) print 1; else print 0}'` ) then
awk {if ($1 <= 0.0) print 1; else print 0}
echo -0.00
C --- no restart needed

/bin/rm -f restart_in.a restart_in.b
/bin/rm -f restart_out.a restart_out.b
/bin/rm -f restart_out1.a restart_out1.b

else if ( `echo $LI $RI | awk '{if ($1-0.1 < $2 && $1+0.1 > $2) print 1; else print 0}'` ) then

if ( -e ./cice ) then

C
C --- model executable
C
if ( 96 == 0 && 1 == 0 ) then
if ( 96 == 0 ) then
if ( 1 == 0 ) then
setenv TYPE one

endif
if ( -e ./cice ) then

setenv HEXE hycom
endif
[1] 9445
C
/bin/cp /home/HYCOM/hycom/PEGh0.02/src_2.3.01_relo_one/hycom
/bin/cp: missing destination file operand after '/home/HYCOM/hycom/PEGh0.02/src_2.3.01_relo_one/hycom'
Try '/bin/cp --help' for more information.
[1]  + Exit 1                 /bin/cp /home/HYCOM/hycom/PEGh0.02/src_2.3.01_relo_one/hycom
C --- summary printout
C
touch summary_out
/bin/mv -f summary_out summary_old
C
C --- heat transport output
C
touch flxdp_out.a flxdp_out.b
/bin/mv -f flxdp_out.a flxdp_old.a
/bin/mv -f flxdp_out.b flxdp_old.b
C
touch ovrtn_out
/bin/mv -f ovrtn_out ovrtn_old
C
C --- clean up old archive files, typically from batch system rerun.
C
mkdir KEEP
mkdir: cannot create directory ‘KEEP’: File exists
touch archv.dummy.b
foreach f ( arch*.{a,b,txt} )
/bin/mv -f arche.dummy.a KEEP/arche.dummy.a
end
/bin/mv -f archm.dummy.a KEEP/archm.dummy.a
end
/bin/mv -f archv.dummy.a KEEP/archv.dummy.a
end
/bin/mv -f arche.dummy.b KEEP/arche.dummy.b
end
/bin/mv -f archm.dummy.b KEEP/archm.dummy.b
end
/bin/mv -f archv.dummy.b KEEP/archv.dummy.b
end
/bin/mv -f arche.dummy.txt KEEP/arche.dummy.txt
end
/bin/mv -f archm.dummy.txt KEEP/archm.dummy.txt
end
/bin/mv -f archv.dummy.txt KEEP/archv.dummy.txt
end
C
C --- Nesting input archive files.
C
if ( -e ./nest ) then
C
C --- let all file copies complete.
C
wait
C
C --- zero file length means no rivers.
C
if ( -z forcing.rivers.a ) then
/bin/rm -f forcing.rivers.a forcing.rivers.b
endif
C
C --- Just in time atmospheric forcing.
C
if ( 0 > = 1 ) then
wait
C
C --- Nesting input archive files for next segment.
C
setenv HEXE hycom
C
[1] 9491
chmod ug+x /home/HYCOM/hycom/PEGh0.02/src_2.3.01_relo_one/hycom
/bin/ls -laFq
total 2141148
drwxr-xr-x 15 root root      4096 Jun 26 03:33 ./
drwxr-xr-x  9 root root      4096 Jun 23 11:54 ../
drwxr-xr-x  4 root root      4096 Jun 22 19:22 archive/
-rw-r--r--  1 root root      1122 Jun 26 03:33 archs.input
-rw-r--r--  1 root root         0 Jun 26 03:33 archt.input
-rwxr--r--  1 root root     18993 Jun 26 03:33 blkdat.input*
-rw-r--r--  1 root root         0 Jun 26 03:33 cb.a
-rw-r--r--  1 root root         0 Jun 26 03:33 cbar.a
-rw-r--r--  1 root root         0 Jun 26 03:33 cbar.b
-rw-r--r--  1 root root         0 Jun 26 03:33 cb.b
-rw-r--r--  1 root root         0 Jun 25 19:54 cice.dummy.nc
-rw-r--r--  1 root root         0 Jun 25 19:54 core
-rw-r--r--  1 root root         0 Jun 26 03:33 flxdp_old.a
-rw-r--r--  1 root root         0 Jun 26 03:33 flxdp_old.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.airtmp.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.airtmp.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.chl.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.chl.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.mslprs.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.mslprs.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.precip.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.precip.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.radflx.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.radflx.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.seatmp.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.seatmp.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.shwflx.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.shwflx.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.surtmp.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.surtmp.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.tauewd.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.tauewd.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.taunwd.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.taunwd.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.vapmix.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.vapmix.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.wndewd.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.wndewd.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.wndnwd.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.wndnwd.b
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.wndspd.a
-rw-r--r--  1 root root         0 Jun 26 03:33 forcing.wndspd.b
-rw-r--r--  1 root root  58441728 Jun 26 03:33 iso.sigma.a
-rw-r--r--  1 root root      2173 Jun 26 03:33 iso.sigma.b
-rw-r--r--  1 root root         0 Jun 26 03:33 iso.top.a
-rw-r--r--  1 root root         0 Jun 26 03:33 iso.top.b
drwxr-xr-x  2 root root      4096 Jun 26 03:33 KEEP/
-rw-r--r--  1 root root         8 Jun 26 03:33 limits
drwxr-xr-x  3 root root      4096 Jun 22 18:54 meanstd/
drwxr-xr-x  2 root root      4096 Jun 22 19:22 movie/
-rw-r--r--  1 root root         0 Jun 26 03:33 ovrtn_old
-rw-r--r--  1 root root      4274 Jun 26 03:33 patch.input
drwxr-xr-x  3 root root      4096 Jun 22 19:22 plot/
-rw-r--r--  1 root root       103 Jun 26 03:33 ports.input
-rw-r--r--  1 root root         0 Jun 26 03:33 profile.input
-rw-r--r--  1 root root   1425408 Jun 26 03:33 regional.depth.a
-rw-r--r--  1 root root       440 Jun 26 03:33 regional.depth.b
-rw-r--r--  1 root root  27082752 Jun 26 03:33 regional.grid.a
-rw-r--r--  1 root root      1073 Jun 26 03:33 regional.grid.b
-rw-r--r--  1 root root 701300736 Jun 26 03:33 relax.intf.a
-rw-r--r--  1 root root     38284 Jun 26 03:33 relax.intf.b
-rw-r--r--  1 root root         0 Jun 26 03:33 relax.montg.a
-rw-r--r--  1 root root         0 Jun 26 03:33 relax.montg.b
-rw-r--r--  1 root root   1425408 Jun 26 03:33 relax.rmu.a
-rw-r--r--  1 root root       451 Jun 26 03:33 relax.rmu.b
-rw-r--r--  1 root root 701300736 Jun 26 03:33 relax.saln.a
-rw-r--r--  1 root root     38284 Jun 26 03:33 relax.saln.b
-rw-r--r--  1 root root         0 Jun 26 03:33 relax.sssrmx.a
-rw-r--r--  1 root root         0 Jun 26 03:33 relax.sssrmx.b
-rw-r--r--  1 root root 701300736 Jun 26 03:33 relax.temp.a
-rw-r--r--  1 root root     38284 Jun 26 03:33 relax.temp.b
-rw-r--r--  1 root root         0 Jun 26 03:33 summary_old
drwxr-xr-x  2 root root      4096 Jun 25 19:11 tare_103/
drwxr-xr-x  2 root root      4096 Jun 23 11:42 tare_103a/
drwxr-xr-x  2 root root      4096 Jun 22 18:54 tare_103b/
drwxr-xr-x  2 root root      4096 Jun 25 19:11 tarm_103/
drwxr-xr-x  2 root root      4096 Jun 23 11:42 tarm_103a/
drwxr-xr-x  2 root root      4096 Jun 25 19:54 tars_103/
drwxr-xr-x  2 root root      4096 Jun 23 11:42 tars_103a/
drwxr-xr-x  2 root root      4096 Jun 22 18:54 tars_103b/
-rw-r--r--  1 root root         0 Jun 26 03:33 tbaric.a
-rw-r--r--  1 root root         0 Jun 26 03:33 tbaric.b
-rw-r--r--  1 root root         0 Jun 26 03:33 thkdf2.a
-rw-r--r--  1 root root         0 Jun 26 03:33 thkdf2.b
-rw-r--r--  1 root root         0 Jun 26 03:33 thkdf4.a
-rw-r--r--  1 root root         0 Jun 26 03:33 thkdf4.b
-rw-r--r--  1 root root         0 Jun 26 03:33 tidal.rh.a
-rw-r--r--  1 root root         0 Jun 26 03:33 tidal.rh.b
-rw-r--r--  1 root root        42 Jun 26 03:33 tracer.input
-rw-r--r--  1 root root         0 Jun 26 03:33 veldf2.a
-rw-r--r--  1 root root         0 Jun 26 03:33 veldf2.b
-rw-r--r--  1 root root         0 Jun 26 03:33 veldf4.a
-rw-r--r--  1 root root         0 Jun 26 03:33 veldf4.b
[1]  + Done                   chmod ug+x /home/HYCOM/hycom/PEGh0.02/src_2.3.01_relo_one/hycom
C
if ( -e ./nest ) then
C
C --- Check to make sure restart file is there
C
if ( `echo $LI | awk '{print ($1 > 0.0)}'` && -z restart_in.a ) then
awk {print ($1 > 0.0)}
echo -0.00
C
if ( 96 == 0 ) then
C
C --- run the model, with MPI or SHMEM and perhaps also with OpenMP.
C
touch patch.input
if ( -z patch.input ) then
C
switch ( Linux )
C
C --- 96 MPI tasks and 1 THREADs, if compiled for OpenMP.
C
/bin/rm -f core
touch core
setenv OMP_NUM_THREADS 1
/usr/bin/mpirun -np 96 ./hycom
--------------------------------------------------------------------------
mpirun has detected an attempt to run as root.

Running as root is *strongly* discouraged as any mistake (e.g., in
defining TMPDIR) or bug can result in catastrophic damage to the OS
file system, leaving your system in an unusable state.

We strongly suggest that you run mpirun as a non-root user.

You can override this protection by adding the --allow-run-as-root option
to the cmd line or by setting two environment variables in the following way:
the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this
protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and
add one more layer of certainty that you want to do so.
We reiterate our advice against doing so - please proceed at your own risk.
--------------------------------------------------------------------------
breaksw
endif
C
touch PIPE_DEBUG
/bin/rm -f PIPE_DEBUG
C
C --- archive output in a separate tar directory
C
touch archv.dummy.a archv.dummy.b archv.dummy.txt
touch archm.dummy.a archm.dummy.b archm.dummy.txt
touch arche.dummy.a arche.dummy.b arche.dummy.txt
touch archs.dummy.a archs.dummy.b archs.dummy.txt
touch cice.dummy.nc
C
if ( -e ./SAVE ) then
C
foreach t ( s m e )
mkdir ./tars_103
mkdir: cannot create directory ‘./tars_103’: File exists
foreach f ( archs.*.a )
/bin/mv archs.dummy.a ./tars_103/010_archs.dummy.a
end
foreach f ( archs.*.b )
/bin/mv archs.dummy.b ./tars_103/010_archs.dummy.b
end
foreach f ( archs.*.txt )
/bin/mv archs.dummy.txt ./tars_103/010_archs.dummy.txt
end
date
Mon 26 Jun 2023 03:33:42 AM +0330

if ( -e ./cice ) then

C
if ( ! -z archt.input ) then
C
C --- add last day to next months tar directory, for actual day months only
C
pwd
/home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH
setenv DL `awk  '{printf("%15.2f\n", $2)}' limits`
awk {printf("%15.2f\n", $2)} limits
setenv DA `echo 3 1.0 1.0 $DL $DL | /home/HYCOM/hycom/ALL/bin/hycom_nest_dates | head -1`
/home/HYCOM/hycom/ALL/bin/hycom_nest_dates
echo 3 1.0 1.0 360.00 360.00
head -1
foreach t ( s e )
mkdir ./tars_103
mkdir: cannot create directory ‘./tars_103’: File exists
ln: No match.
end
mkdir ./tare_103
mkdir: cannot create directory ‘./tare_103’: File exists
ln: No match.
end
C
C --- build and run or submit the tar script
C
C
C --- heat transport statistics output
C
if ( -e flxdp_out.a ) then
if ( -e flxdp_out.b ) then
if ( -e ovrtn_out ) then
C
C --- restart output
C
if ( -e restart_out.a ) then
if ( -e restart_out.b ) then

endif
if ( -e ./cice ) then

C
if ( 0 > = 1 ) then
C
C --- wait for nesting .tar file.
C
if ( -e ./nest ) then
C
C --- HYCOM error stop is implied by the absence of a normal stop.
C
touch summary_out
tail -1 summary_out
tail -1 summary_out
grep -c ^normal stop
0
if ( `tail -1 summary_out | grep -c "^normal stop"` == 0 ) then
tail -1 summary_out
grep -c ^normal stop
cd /home/HYCOM/hycom/PEGh0.02/expt_01.0/
/bin/mv LIST LIST_BADRUN
echo BADRUN
endif
C
C --- submit postprocessing scripts
C
mkdir -p postproc
cd postproc
C
C --- 1 - meanstd
C
if ( 0 == 1 ) then
C
if ( 0 == 1 ) then
C
C --- 1b - basin-wide statistics from daily means
C
if ( 1 == 1 ) then
/bin/rm -f pp_statm_010_103.csh pp_statm_010_103.log
awk -f /home/HYCOM/hycom/PEGh0.02/postproc/postproc.awk y=103 p= ex=/home/HYCOM/hycom/PEGh0.02/expt_01.0 r=PEGh0.02 x=01.0 /home/HYCOM/hycom/PEGh0.02/postproc/pp_statm.csh
csh pp_statm_010_103.csh
set time = 1
date
Mon 26 Jun 2023 03:33:42 AM +0330
C
setenv X 01.0
setenv R PEGh0.02
setenv EX /home/HYCOM/hycom/PEGh0.02/expt_01.0
source /home/HYCOM/hycom/PEGh0.02/expt_01.0/EXPT.src
setenv OS `uname`
uname
setenv R PEGh0.02
setenv V 2.3.01
setenv T 07
setenv K 41
setenv E 010
setenv X 01.0
setenv P /home/HYCOM/hycom/PEGh0.02/expt_01.0
setenv D /home/HYCOM/hycom/PEGh0.02/expt_01.0
setenv S /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH
setenv DS /home/HYCOM/hycom/PEGh0.02
setenv N cfsr_peg
setenv W /home/HYCOM/hycom/DATA/CFSR_PEG
setenv MAKE_FORCE 0
setenv NOMP 0
setenv NMPI 7
setenv restart off
setenv ARCHIVE 1
setenv QSUBMIT csh
setenv mnsqa 0
setenv mnsqe 0
setenv statm 1
setenv plots 1
setenv transp 0
setenv data2d 0
setenv netcdf 1
setenv Y 103
setenv YRFLAG `grep yrflag ${D}/blkdat.input | awk '{print $1}'`
grep yrflag /home/HYCOM/hycom/PEGh0.02/expt_01.0/blkdat.input
awk {print $1}
if ( 1 == 3 ) then
setenv YZ `echo ${Y} | awk '{printf("%04d", $1)}'`
awk {printf("%04d", $1)}
echo 103
endif
setenv P
setenv SM /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../tarm_103
setenv H /home/HYCOM/hycom/PEGh0.02/archive
if ( ! -d /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../tarm_103 ) mkdir -p /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../tarm_103
cd /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../tarm_103
/bin/rm -f 010_statm_103.csh 010_statm_103.log
awk -f /home/HYCOM/hycom/PEGh0.02/archive/statm.awk y=103 p= ex=/home/HYCOM/hycom/PEGh0.02/expt_01.0 r=PEGh0.02 x=01.0 /home/HYCOM/hycom/PEGh0.02/archive/999_statm.csh
wait
echo FINISHED Creating HYCOM statms
FINISHED Creating HYCOM statms
date
Mon 26 Jun 2023 03:33:42 AM +0330
endif
C
C --- 2 - plots
C
if ( 1 == 1 ) then
/bin/rm -f pp_plot_010_103.csh pp_plot_010_103.log
awk -f /home/HYCOM/hycom/PEGh0.02/postproc/postproc.awk y=103 p= ex=/home/HYCOM/hycom/PEGh0.02/expt_01.0 r=PEGh0.02 x=01.0 /home/HYCOM/hycom/PEGh0.02/postproc/pp_plot.csh
csh pp_plot_010_103.csh
set time = 1
C
setenv X 01.0
setenv R PEGh0.02
setenv EX /home/HYCOM/hycom/PEGh0.02/expt_01.0
source /home/HYCOM/hycom/PEGh0.02/expt_01.0/EXPT.src
setenv OS `uname`
uname
setenv R PEGh0.02
setenv V 2.3.01
setenv T 07
setenv K 41
setenv E 010
setenv X 01.0
setenv P /home/HYCOM/hycom/PEGh0.02/expt_01.0
setenv D /home/HYCOM/hycom/PEGh0.02/expt_01.0
setenv S /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH
setenv DS /home/HYCOM/hycom/PEGh0.02
setenv N cfsr_peg
setenv W /home/HYCOM/hycom/DATA/CFSR_PEG
setenv MAKE_FORCE 0
setenv NOMP 0
setenv NMPI 7
setenv restart off
setenv ARCHIVE 1
setenv QSUBMIT csh
setenv mnsqa 0
setenv mnsqe 0
setenv statm 1
setenv plots 1
setenv transp 0
setenv data2d 0
setenv netcdf 1
setenv SRC /home/HYCOM/hycom/ALL
setenv BINRUN
switch ( Linux )
setenv Y 103
setenv IDM `grep idm ${D}/blkdat.input | awk '{print $1}'`
grep idm /home/HYCOM/hycom/PEGh0.02/expt_01.0/blkdat.input
awk {print $1}
setenv JDM `grep jdm ${D}/blkdat.input | awk '{print $1}'`
grep jdm /home/HYCOM/hycom/PEGh0.02/expt_01.0/blkdat.input
awk {print $1}
setenv YRFLAG `grep yrflag ${D}/blkdat.input | awk '{print $1}'`
grep yrflag /home/HYCOM/hycom/PEGh0.02/expt_01.0/blkdat.input
awk {print $1}
if ( 1 == 3 ) then
setenv YY `echo ${Y}  | awk '{printf("%04d", $1)}'`
echo 103
awk {printf("%04d", $1)}
endif
setenv YX `echo ${YY} | awk '{printf("%04d", $1+1)}'`
awk {printf("%04d", $1+1)}
echo 0103
setenv P
setenv M /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../movie
setenv TMP /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../plot/0103
setenv F /home/HYCOM/hycom/PEGh0.02/plot/010/movie
if ( ! -d /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH ) mkdir -p /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH
if ( ! -d /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../movie ) mkdir -p /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../movie
if ( ! -d /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../plot/0103 ) mkdir -p /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../plot/0103
cd /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../plot/0103
/bin/rm -f regional.depth.a regional.depth.b regional.grid.a regional.grid.b regional.mask.a src
ln -sf /home/HYCOM/hycom/PEGh0.02/topo/depth_PEGh0.02_07.a regional.depth.a
ln -sf /home/HYCOM/hycom/PEGh0.02/topo/depth_PEGh0.02_07.b regional.depth.b
ln -sf /home/HYCOM/hycom/PEGh0.02/topo/regional.grid.a regional.grid.a
ln -sf /home/HYCOM/hycom/PEGh0.02/topo/regional.grid.b regional.grid.b
ln -sf /home/HYCOM/hycom/PEGh0.02/topo/regional.mask.a regional.mask.a
ln -sf /home/HYCOM/hycom/ALL/plot/src src
ln -sf /home/HYCOM/hycom/PEGh0.02/plot/010/movie/lonlat_arctic.txt .
ln -sf /home/HYCOM/hycom/PEGh0.02/plot/010/movie/lonlat_antarc.txt .
/bin/rm -f LIST FILE
/bin/touch LIST
foreach f ( /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../tarm_103/010_archm.0103_???_12.b /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../tarm_103/010_archm.0104_???_12.b )
foreach: No match.
endif
C
C --- 3 - sample transports
C
if ( 0 == 1 ) then
C
C --- 4 - data2d extraction, moorings, ice creation and plotting
C
if ( 0 == 1 ) then
C
C --- 5 - to netCDF
C
if ( 1 == 1 ) then
/bin/rm -f pp_netcdf_010_103.csh pp_netcdf_010_103.log
awk -f /home/HYCOM/hycom/PEGh0.02/postproc/postproc.awk y=103 p= ex=/home/HYCOM/hycom/PEGh0.02/expt_01.0 r=PEGh0.02 x=01.0 /home/HYCOM/hycom/PEGh0.02/postproc/pp_netcdf.csh
csh pp_netcdf_010_103.csh
set time = 1
date
Mon 26 Jun 2023 03:33:43 AM +0330
C
setenv X 01.0
setenv R PEGh0.02
setenv EX /home/HYCOM/hycom/PEGh0.02/expt_01.0
source /home/HYCOM/hycom/PEGh0.02/expt_01.0/EXPT.src
setenv OS `uname`
uname
setenv R PEGh0.02
setenv V 2.3.01
setenv T 07
setenv K 41
setenv E 010
setenv X 01.0
setenv P /home/HYCOM/hycom/PEGh0.02/expt_01.0
setenv D /home/HYCOM/hycom/PEGh0.02/expt_01.0
setenv S /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH
setenv DS /home/HYCOM/hycom/PEGh0.02
setenv N cfsr_peg
setenv W /home/HYCOM/hycom/DATA/CFSR_PEG
setenv MAKE_FORCE 0
setenv NOMP 0
setenv NMPI 7
setenv restart off
setenv ARCHIVE 1
setenv QSUBMIT csh
setenv mnsqa 0
setenv mnsqe 0
setenv statm 1
setenv plots 1
setenv transp 0
setenv data2d 0
setenv netcdf 1
setenv SRC /home/HYCOM/hycom/ALL
setenv BINRUN
switch ( Linux )
setenv YFLAG `grep yrflag ${D}/blkdat.input | awk '{print $1}'`
grep yrflag /home/HYCOM/hycom/PEGh0.02/expt_01.0/blkdat.input
awk {print $1}
setenv Y 103
if ( 1 == 3 ) then
setenv YZ `echo ${Y} | awk '{printf("%04d", $1)}'`
echo 103
awk {printf("%04d", $1)}
endif
setenv P
setenv A /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../archive
setenv ATMP /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../archive/ncdf_0103
setenv C /home/HYCOM/hycom/PEGh0.02/archive
if ( ! -d /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../archive ) mkdir -p /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../archive
if ( ! -d /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../archive/ncdf_0103 ) mkdir -p /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../archive/ncdf_0103
foreach f ( /home/HYCOM/hycom/PEGh0.02/expt_01.0/data/SCRATCH/../tarm_103/010_archm.0103_???_12.b )
foreach: No match.
endif
C
C --- wait for tar bundles to complete
C
wait
C
C --- END OF MODEL RUN SCRIPT
C
root@mostafa-G41D3C:/home/HYCOM/hycom/PEGh0.02/expt_01.0#

[Alan Wallcraft]

There is an error invoking MPI:

C
C --- 96 MPI tasks and 1 THREADs, if compiled for OpenMP.
C
/bin/rm -f core
touch core
setenv OMP_NUM_THREADS 1
/usr/bin/mpirun -np 96 ./hycom
--------------------------------------------------------------------------
mpirun has detected an attempt to run as root.

So HYCOM was never run.

Alan.

[_ solgi]

Dear Alan,

Thank you for your help. How can I solve this error? Do I need to unroot or do I need to make a script change for MPI?

Is it possible to explain more? Thank you.

With regards,

Solgi

[Alan Wallcraft]

Unroot.

Alan.