Debug Mode

Run several tests in debug mode is a necessary step before committing your updates on the master branch.

COMPILE

To compile the GCM or 1-D model, enter this command line:

 ./makelmdz_fcm -arch your_arch -parallel mpi -d 64x48x32 -p mars gcm_or_testphys1d -j 8 -debug

You can add or remove debug flag manually in the file trunk/LMDZ.COMMON/arch.fcm at the line %DEBUG_FFLAGS. Make sure you are using correct flags regarding your compiler, and the debug mode performs no optimization (e.g: -O0 with mpif90).

Methodology: 1 + 1 = 2

This methodology is very useful when:

• the simulation crashes with no obvious reason
• crash is not replicable at different duration simulations (e.g: 1 simulation of 60 days = OK, 3*20 days = crashed!)

The procedure of the methodology is quite simple, modify the file called 'run_month1'

• 1 run: 1 day and 1 day

  num_now = 1
  num_end = 2
  ....
  case $true_num in
  1) sed/9999/1/ ....
  2) sed/9999/1/ ....
  

  At the end of the runs, you have done 2 days (tips: mv startfi2.nc startfi2_1j.nc)

• 1 run: 2 days (mv startfi1.nc startfi1_2j.nc)

  num_now = 1
  num_end = 1
  ....
  case $true_num in
  1) sed/9999/2/ ....
  

  At the end of the runs, you have done 2 days in a single row (tips: mv startfi1.nc startfi1_2j.nc)

Then, do the difference between startfi1_2j.nc and startfi2_1j.nc. The command ncdiff is very useful to deal with netcdf file (from nco package):

ncdiff startfi1_2j.nc startfi2_1j.nc diff_startfi.nc

Then, look at which variable is not equals to zero.

ncdump diff_startfi.nc > diff_startfi.txt

Vi diff_stratfi.txt

Tips

You can do this check quickly by using the GCM variable 'ndynstep' in run.def file, this variable means the number of dynamical steps you want to perform during the simulation. Be sure to set this variable equals to iphysiq to perform at least one physical call. For example, with iphysiq = 10, you can do : 10 + 10 = 20 dynamical steps, corresponding to 1 call to physiq_mod + 1 call to physiq_mod = 2 calls to physiq_mod.

Methodology: 1 = 1

Same as 1 + 1 = 2, except you perform runs with 1 day with 1 CPU, and 1 day with 24 CPUs! Very useful when you have memory issues.

USING GDB FOR DEBUG

If you have a really vicious bug in your code, you may want to use the gdb tool. Here is some advice to use it, but it is not exhaustive, so please complete this info as it pleases you. You can also find more details in the ​GDB documentation

To use gdb, go in your simulation repository (where your have all your .def and start files, and your gcm executable gcm_exec.e), and source your arch.env from your trunk/LMDZ.COMMON to have the required librairies to run the model. Then, run the command

 gdb gcm_exec.e

It opens a gdb session. You can now run the model and interact with it while it runs. For instance, you can create break points, which stop the run at a given point. You can then look at some variables via the print command, then continue the run. Here is an example below :

 (gdb) break aeropacity_mod.f:183
 (gdb) run
Starting program:...
.....
.....
Breakpoint 1, aeropacity_mod::aeropacity (ngrid=3010, nlayer=54, nq=11, zday=0.0041666666666666666, pplay=..., pplev=..., ls=3.723693225921032e-05, pq=..., pt=..., 
    tauscaling=..., dust_rad_adjust=..., irtoviscoef=..., tau_pref_scenario=..., tau_pref_gcm=..., tau=..., taucloudtes=..., aerosol=..., dsodust=..., reffrad=..., 
    qrefvis3d=..., qrefir3d=..., omegarefir3d=..., totstormfract=..., clearatm=4294967295, dsords=..., dsotop=..., alpha_hmons=..., nohmons=4294967295, clearsky=.FALSE., 
    totcloudfrac=...)
    at /scratch/cnt0027/lmd1167/abierjon/simurefs_topflows_GCM6/trunk_r2577/LMDZ.COMMON/libo/X64_OCCIGEN_64x48x54_phymars_para.e/.config/ppsrc/phys/aeropacity_mod.f:183
183	      tau(1:ngrid,1:naerkind)=0
Missing separate debuginfos, use: debuginfo-install glibc-2.17-324.el7_9.x86_64 libgcc-4.8.5-44.el7.x86_64 numactl-devel-2.0.12-5.el7.x86_64 zlib-1.2.7-19.el7_9.x86_64
(gdb) break aeropacity_mod.f:266
Breakpoint 2 at 0x13e792a: file /scratch/cnt0027/lmd1167/abierjon/simurefs_topflows_GCM6/trunk_r2577/LMDZ.COMMON/libo/X64_OCCIGEN_64x48x54_phymars_para.e/.config/ppsrc/phys/aeropacity_mod.f, line 266.
(gdb) continue
Continuing.
.....
.....