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Frequently Asked Questions

Frequently (and not so frequently) Asked Questions

1. FAQ : Setting up and performing a simulation

1.1. How do I overwrite an existing simulation?

If you want to relaunch a simulation from the beginning you need to delete everything created previously. All the output files must be deleted because they cannot be overwritten. Do the following:

  1. Delete the run.card file in your experiment directory.
  2. Delete all output directories:
  1. Launch the job.

TIP: If you have already done a simulation before you could find all output paths in the Script_output* file. Delete it before starting a new simulation.

1.2. How do I continue or restart a simulation?

See here.

1.3. How do I setup a new experiment?

See here.

1.4. How can I start from another simulation?

See here.

1.5. How do I create the LMDZ histins.nc file?

You have several options. The easiest one is to change the output frequency of one of the existing files. For instance, you can change the output frequency of the histhf.nc file to instantaneous without changing the file name. To do so, keep HF in WriteFrequency in config.card: 

[ATM]
#
WriteFrequency="1M 1D HF"

Change the 3rd column of the phys_out_filetimesteps parameter in PARAM/output.def_OutLevel. OutLevel is chosen in lmdz.card and by default OutLevel=low. Specify 1800.s in PARAM/output.def_low if you want the output to be saved every 30 minutes: 

phys_out_filetimesteps = 1.mth,  1.day,  1800.s,  0.125day, 0.125day, 1800.s

You can also change phys_out_filelevels in the 3rd column.

2. FAQ : Running the model

2.1. How do I read the Script_Output file?

During each job execution, a corresponding Script_Output file is created.
Important : If your simulation stops you can look for the keyword "IGCM_debug_CallStack" in this file. This word will be preceded by a line giving more details on the problem that occurred.

See can be found here for more details.

2.2. The LMDZ parallelism and the Bands files

See here.

2.3. How do I define the number of MPI jobs and the number of OpenMP threads?

If you run your model in MPI mode only (without OpenMP) the number of MPI processes is defined in config.card by the JobNumProcTot parameter: 

#-- Total Number of Processors
JobNumProcTot=32

If you run your model in hybrid mode (MPI-OpenMP), the number of MPI processes and the number of OpenMP threads are set in config.card in the section "Executable". You still need to precise the CPU total number in JobNumProcTot parameter by summing all components processes.

For instance, for LMDZ : 16 MPI processes and 2 OpenMP threads (ATM compenent needs 2OMP x 16MPI = 32CPU). 

ATM= (gcm.e, lmdz.x, 16MPI, 2OMP)

Notice that the job header differs from the one for openMP.

2.4. Why does the run.card file contain the keyword Fatal?

The keyword Fatal indicates that something went wrong in your simulation. Below is a list of the most common reasons:

See the corresponding chapter about monitoring and debug for further information.

2.5. How do I use a different version of libIGCM?

libIGCM is constantly being updated. We recommend to choose the latest tag of libIGCM. Here is what to do:

In case you need version XXX of the trunk of libIGCM, change the "svn checkout" line into: 

svn checkout -r XXX http://forge.ipsl.jussieu.fr/libigcm/svn/trunk/libIGCM libIGCM

If AA_job has been modified, you must :

2.6. How do I restart a simulation to recover missing output files?

UPDATE - ON CURIE (4/18/2016 ACo) / TO BE DONE ON ADA (idea : change $STOREDIR by ergon or ada workdir)

This method shows how to rerun a complete simulation period in a different directory (REDO instead of DEVT/PROD).

Example : To rerun v3.historicalAnt1 to recompute a whole year (e.g. 1964) you must :

2.7. How can I change the atmosphere horizontal resolutions using the same LMDZOR libIGCM configuration ?

To do this you have to make some changes in your files. 

(cd ../../modeles/LMDZ; ./makelmdz_fcm -cpp ORCHIDEE_NOOPENMP -d $(RESOL_LMDZ) -cosp true -v true -parallel mpi -arch $(FCM_ARCH) ce0l ; cp bin/ce0l_$(RESOL_LMDZ)_phylmd_para_orch.e ../../bin/create_etat0_limit.e_$(RESOL_LMDZ) ; )
(cd ../../modeles/LMDZ; ./makelmdz_fcm -cpp ORCHIDEE_NOOPENMP -d $(RESOL_LMDZ) -cosp true -v true -mem -parallel mpi -arch $(FCM_ARCH) gcm ; cp bin/gcm_$(RESOL_LMDZ)_phylmd_para_mem_orch.e ../../bin/gcm.e_$(RESOL_LMDZ) ; )

[ -f ${SUBMIT_DIR}/../.resol ] && RESOL=$(head -1 ${SUBMIT_DIR}/../.resol)

become

[ -f ${SUBMIT_DIR}/../.resol_myresolution ] && RESOL=$(head -1 ${SUBMIT_DIR}/../.resol_myresolution)

[ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) || RESOL_ATM_3D=96x95x19

by

[ -f ${SUBMIT_DIR}/../.resol_myresolution ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol_myresolution) || RESOL_ATM_3D=96x95x19

Now you can create as many experiment as you have compiled your model. 

cd modipsl/config/LMDZOR/
cp EXPERIMENT/LMDZOR/clim/config.card . 
etc...



3. FAQ : Special configurations

3.1. How do I create the initial conditions for LMDZOR?

For a few configurations such as LMDZOR and LMDZREPR, you must create initial and boundary conditions in advance. This is not necessary for coupled configurations such as IPSLCM5_v5.

For more information, see this chapter.

3.2. How do I deactivate STOMATE in IPSLCM5 or in LMDZOR?

The IPSLCM5 model has not been evaluated for these cases.

Here is how to do it.

3.3. How do I perform a nudged run?

Atmospherical nudging
This paragraph describes how to perform a nudged run for configurations that include LMDZ. To do so, you have to:

For example: 

[BoundaryFiles]
List= ....\
      (/ccc/work/cont003/subipsl/subipsl/ECMWF96x95/AN${year}/u_ecmwf_${year}${month}.nc, u.nc)\
      (/ccc/work/cont003/subipsl/subipsl/ECMWF96x95/AN${year}/v_ecmwf_${year}${month}.nc, v.nc)\

Oceanic nudging
To force the oceanic model in salinity or SST you could find the procedure in ​NEMO official documentation (section 7.12.3: Surface restoring to observed SST and/or SSS)

Notice that NEMO uses the salinity nudging, by default, when it's used in oceanic forced configurations.

3.4. How do I run simulations with specific versions of compiler and/or libraries on CURIE at the TGCC ? (modules)

For various reasons you may want to run simulations with different versions of compiler or libraries (mainly netCDF).

The first thing is to keep a dedicated installation of modipsl for this specific setup since you will have to modify the libIGCM associated with the simulations.

Keep in mind that you need the modules of the libraries you want to use to be properly loaded at both:

Compile time

You can create a script shell that unloads the modules of the default configuration and loads the modules you want to use. Here is an example of the file modules.sh to use intel/12 and netCDF3.6.3: (the order in which you unload and load the modules is important) 

#!/bin/bash

#set -vx

# unload modules
module unload nco    #/4.1.0
module unload netcdf #/4.2_hdf5_parallel
module unload hdf5   #/1.8.9_parallel
module unload intel

# load modules
module load intel/12.1.9.293
module load netcdf/3.6.3
module load hdf5/1.8.8
module load nco/4.1.0

You have to make sure the modules you want to be used by your code are loaded before each compilation of your configuration. Use module list to view the currently loaded modules. If necessary source module.sh before compiling.

Runtime

The proper modules have to be loaded for the dynamic linking to your libraries to succeed.

You can source modules.sh before submitting (ccc_msub), however this is not very convenient.

A better way is to modify libIGCM_sys_curie.ksh in your libIGCM installation ((...)/modipsl/libIGCM/libIGCM_sys/ directory).

Locate the part where the environment tools are set in this file and add module unload and load commands: 

#====================================================
# Set environment tools (ferret, nco, cdo)
#====================================================
if [ X${TaskType} = Xcomputing ] ; then
  . /ccc/cont003/home/dsm/p86ipsl/.atlas_env_netcdf4_curie_ksh > /dev/null 2>&1
# to run with netcdf 3.6.3 ie compilation done before 17/2/2014
# uncomment 2 lines :
#  module unload netcdf
#  module load netcdf/3.6.3
  # set the proper modules
  module unload nco
  module unload netcdf
  module unload hdf5
  module unload intel
  module load intel/12.1.9.293
  module load netcdf/3.6.3_p1
  module load hdf5/1.8.8
  module load nco/4.1.0
  #set the proper modules end
  export PATH=${PATH}:/ccc/cont003/home/dsm/p86ipsl/AddNoise/src_X64_CURIE/bin
  export PATH=${PATH}:/ccc/cont003/home/dsm/p86ipsl/AddPerturbation/src_X64_CURIE/bin
else
  . /ccc/cont003/home/dsm/p86ipsl/.atlas_env_netcdf4_curie_ksh > /dev/null 2>&1
  PCMDI_MP=/ccc/work/cont003/dsm/p86ipsl/PCMDI-MP
fi

This way you can launch experiments on CURIE without having to source your module.sh file.

Keep in mind that the code has to be compiled with the same modules that the ones that are loaded by libIGCM at runtime.

In case of module mismatch you will have a runtime error stating a library was not found.

3.5. How to have min and max value exchanged through OASIS?

To add min max sum values of one field exchanged through OASIS, one has to add verbose mode (LOGPRT 1) , to add 2 operations (4 instead of 2 operations, CHECKIN CHECKOUT) and to describe them (INT=1 added for CHECKIN and for CHECKOUT). Then you will find information in output text file.

Example :

3.6. How to output exchanged fields by OASIS?

To have output of exchanged fields by OASIS, one have to set 3 parameters :

Then you will obtain 2 types of files :

On 2017/05/10 improvment still to be done to have the calendar of the simulation and the right number of values.

4. FAQ : Post processing

4.1. Where are post processing jobs run?

libIGCM allows you to perform post processing jobs on the same machine as the main job. You can also start post processing jobs on other machines dedicated particularly to post processing. It is not done anymore.

Currently used machines:

Center Computing machine Post processing
CCRT Titane Titane, queue mono
TGCC Curie Curie, thin node, -q standard
IDRIS Ada Ada (ongoing)

4.2. How do I check that the post processing jobs were successful?

See here.

4.3. How do I read/retrieve/use files on esgf/thredds?

More information on Monitoring can be found here: DocFsimu

4.4. How do I add a variable to the Time Series?

See this section.

4.5. How do I superimpose monitoring plots (intermonitoring)?

​Audio
Short link :

To select simulations from two centers or for two different logins, you must go back to step 1 and click on append directories to add new simulations.

4.6. What is the Monitoring?

See chapter Simulation and post-processing, section Postprocessing with libIGCM here

4.7. How do I add a plot to the monitoring?

The answer to this question is here.

4.8. How do I calculate seasonal means over 100 years?

In order to compute a seasonal mean over 100 years, check that all decades are on the file server (SE_checker). Then run the job create_multi_se on the post processing machine.

Note that an atlas for these 100 years will also be created. See the example for the 100-year atlas for piControlMR1 here : ​SE 2000 2099

  1. If not done yet, create a specific post processing directory. See the chapter on how to run or restart post processing jobs for details.
  2. Copy create_se.job, SE_checker.job and create_multi_se.job
  3. Check/change the following variables in create_se.job: 
    libIGCM=${libIGCM:=.../POST_CMIP5/libIGCM_v1_10/modipsl/libIGCM}
  4. Check that all decades exist.
  5. Check/change the variables in SE_checker.job: 
    libIGCM=${libIGCM:=.../POST_CMIP5/libIGCM_v1_10/modipsl/libIGCM} 
SpaceName=${SpaceName:=PROD}
ExperimentName=${ExperimentName:=piControl}
JobName=${JobName:=piControlMR1}
CARD_DIR=${CARD_DIR:=${CURRENT_DIR}}
  6. Start the ./SE_checker.job in interactive mode. All needed jobs create_se.job will be started. For example: 
     ./SE_Checker.job

====================================================
Where do we run ? cesium21
Linux cesium21 2.6.18-194.11.4.el5 #1 SMP Tue Sep 21 05:04:09 EDT 2010 x86_64
====================================================

sys source cesium Intel X-64 lib.

--Debug1--> DefineVariableFromOption : config_UserChoices
--------------Debug3--> config_UserChoices_JobName=piControlMR1
--------------Debug3--> config_UserChoices_CalendarType=noleap
--------------Debug3--> config_UserChoices_DateBegin=1800-01-01
--------------Debug3--> config_UserChoices_DateEnd=2099-12-31

--Debug1--> DateBegin/End for SE : 1800_1809
--Debug1--> ATM
--Debug1--> SRF
--Debug1--> SBG
--Debug1--> OCE
--Debug1--> ICE
--Debug1--> MBG
--Debug1--> CPL
...
--Debug1--> DateBegin/End for SE : 2030_2039
--Debug1--> ATM
--Debug1--> 2 file(s) missing for ATM :
--Debug1--> piControlMR1_SE_2030_2039_1M_histmth.nc
--Debug1--> piControlMR1_SE_2030_2039_1M_histmthNMC.nc
--Debug1--> SRF
--Debug1--> 1 file(s) missing for SRF :
--Debug1--> piControlMR1_SE_2030_2039_1M_sechiba_history.nc
--Debug1--> SBG
--Debug1--> 2 file(s) missing for SBG :
--Debug1--> piControlMR1_SE_2030_2039_1M_stomate_history.nc
--Debug1--> piControlMR1_SE_2030_2039_1M_stomate_ipcc_history.nc
--Debug1--> OCE
--Debug1--> 4 file(s) missing for OCE :
--Debug1--> piControlMR1_SE_2030_2039_1M_grid_T.nc
--Debug1--> piControlMR1_SE_2030_2039_1M_grid_U.nc
--Debug1--> piControlMR1_SE_2030_2039_1M_grid_V.nc
--Debug1--> piControlMR1_SE_2030_2039_1M_grid_W.nc
--Debug1--> ICE
--Debug1--> 1 file(s) missing for ICE :
--Debug1--> piControlMR1_SE_2030_2039_1M_icemod.nc
--Debug1--> MBG
--Debug1--> 3 file(s) missing for MBG :
--Debug1--> piControlMR1_SE_2030_2039_1M_ptrc_T.nc
--Debug1--> piControlMR1_SE_2030_2039_1M_diad_T.nc
--Debug1--> piControlMR1_SE_2030_2039_1M_dbio_T.nc
--Debug1--> CPL
--Debug1--> 2 file(s) missing for CPL :
--Debug1--> piControlMR1_SE_2030_2039_1M_cpl_atm.nc
--Debug1--> piControlMR1_SE_2030_2039_1M_cpl_oce.nc
--------Debug2--> Submit create_se  for period 2030-2039
IGCM_sys_MkdirWork : .../POST_CMIP5/piControl/piControlMR1/OutScript
IGCM_sys_QsubPost : create_se
Submitted Batch Session 179472
...
  7. Wait for the create_se jobs to be completed
  8. Copy create_multi_se.job
  9. Check/change the variables : 
    libIGCM=${libIGCM:=.../POST_CMIP5/libIGCM_v1_10/modipsl/libIGCM}
  10. If needed, adjust the number of decades in config.card: default=50Y (i.e. 50 years). Add the following line to the POST section, i.e. at the end after the keyword [POST] 
    MultiSeasonalFrequency=100Y
  11. Run the create_multi_se.job job:ccc_msub create_multi_se.job
  12. The years used for the calculations are those between DateEnd (set in config.card in the local directory) and DateEnd - MultiSeasonalFrequency.

The mean values are stored in the "Analyse" directories of each model component in the subdirectory SE_100Y (e.g. ATM/Analyse/SE_100Y).

5. FAQ : Unix tricks

5.1. How to delete a group of files using the find command?

We recommend to also read the find manual.

Examples :

5.2. Allowing read-access to everybody

The chmod -R ugo+rX * command gives access to everybody to all files and subdirectories in the current directory.

6. FAQ : Miscellaneous

6.1. How do I use TimeSeries_Checker.job to create files on $STORE when the output files are on DMNFS?

6.1.1. Example for the rcp45 simulation

cd modipsl
mv libIGCM libIGCM.old
svn checkout http://forge.ipsl.jussieu.fr/libigcm/svn/tags/libIGCM_v1_12 libIGCM
modipsl/ins_job

TimeSeries_Checker.job révision 658

line 169
#R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${config_Ensemble_EnsembleName}/${config_Ensemble_EnsembleDate}/${FreeName}

R_SAVE=${CCCSTOREDIR}/IGCM_OUT/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${FreeName}

create_ts.job révision 316

line 300
#DIRECTORY=${R_SAVE}/${comp}/Analyse/${TS_Dir}
DIRECTORY=${CCCSTOREDIR}/IGCM_OUT/IPSLCM5A/PROD/rcp45/v3.rcp45.strat/${comp}/Analyse/${TS_Dir}

line 768
#eval IGCM_sys_Put_Out ${file_out} \${R_OUT_${comp}}/Analyse/${TS_Dir}/${file_out}
IGCM_sys_Put_Out ${file_out} ${CCCSTOREDIR}/IGCM_OUT/IPSLCM5A/PROD/rcp45/v3.rcp45.strat/${comp}/Analyse/${TS_Dir}/${file_out}

line 780
#eval IGCM_sys_Put_Out ${file_out_YE} \${R_OUT_${comp}}/Analyse/TS_MO_YE/${file_out_YE}
IGCM_sys_Put_Out ${file_out_YE} ${CCCSTOREDIR}/IGCM_OUT/IPSLCM5A/PROD/rcp45/v3.rcp45.strat/${comp}/Analyse/TS_MO_YE/${file_out_YE}

6.2. How do I restart one simulation month which ran on $DMFDIR when the outputs are stored on $STORE?

Example: the past1000 simulation 

login on titane: ssh titane.ccc.cea.fr

1455-12 to be reran on STORE, original on dmnfs
1477-12 to be reran on STORE, original on dmnfs
1517-11 to be reran on STORE, original on dmnfs

cd $DMFDIR/IGCM_OUT/IPSLCM5A/TEST/PD_TEST

dmget LMCMP5/???/Restart/*14551130* LMCMP5/???/Restart/*14771130* LMCMP5/???/Restart/*15171030* LMCMP5/OCE/Output/LMCMP5_mesh_mask.nc LMCMP5/ATM/Debug/LMCMP5_Bands_96x95x39_26prc.dat_*

tar cvf $SCRATCHDIR/IGCM_OUT/IPSLCM5A/TEST/PD_TEST/RESTART.REDO.past1000.tar LMCMP5/???/Restart/*14551130* LMCMP5/???/Restart/*14771130* LMCMP5/???/Restart/*15171030* LMCMP5/OCE/Output/LMCMP5_mesh_mask.nc LMCMP5/ATM/Debug/LMCMP5_Bands_96x95x39_26prc.dat_*

cd $SCRATCHDIR/IGCM_OUT/IPSLCM5A/TEST/PD_TEST

tar xvf RESTART.REDO.past1000.tar

cd /work/cont003/p25khod/IPSLCM5A/modipsl/config/IPSLCM5A/LMCMP5_newlibIGCM.REDO

==> edit run.card

==> PackFrequency=NONE in config.card

==> qsub

#========================================================================
#D-- Post -
[Post]
#D- Do we rebuild parallel output, this flag determines
#D- frequency of rebuild submission (use NONE for DRYRUN=3)
RebuildFrequency=1Y
#D- Do we rebuild parallel output from archive (use NONE to use SCRATCHDIR as buffer)
RebuildFromArchive=NONE
# Pas de PACK
PackFrequency=NONE
#D- If you want to produce time series, this flag determines
#D- frequency of post-processing submission (NONE if you don't want)
TimeSeriesFrequency=NONE
#D- If you want to produce seasonal average, this flag determines
#D- the period of this average (NONE if you don't want)
SeasonalFrequency=NONE
#D- Offset for seasonal average first start dates ; same unit as SeasonalFrequency
#D- Useful if you do not want to consider the first X simulation's years
SeasonalFrequencyOffset=0

6.3. How do I copy a model installation directory instead of downloading from the forge (or move a directory)?

Copy or move the target installation: 

cp -r OldInstall NewInstall
  or
mv OldInstall NewInstall

Regenerate the makefiles to account for the new path: 

cd NewInstall/modipsl/util
./ins_make

Recompile if you've done modifications in the source code: 

cd NewInstall/modipsl/config/[YourConfig]
gmake clean
gmake [target]

Update your libIGCM installation:

Prepare a new experiment as usual and launch ins_job to generate the .job files in your libIGCM directory and your experiment directory.
Depending on your libIGCM version you will have to launch NewInstall/modipsl/libIGCM/ins_job or NewInstall/modipsl/util/ins_job for older versions.

Check that the .job files are properly generated in NewInstall/modipsl/libIGCM/ and you are set.

6.4. I need to compile IPSL model in debug mode. How to do that?

You have to modify Makefile to add debug option for each component :

(cd ../../modeles/ORCHIDEE/ ; ./makeorchidee_fcm -debug -parallel mpi_omp -arch $(FCM_ARCH) -j 8 -xios2)

(cd ../../modeles/LMDZ ; ./makelmdz_fcm -d $(RESOL_LMDZ) -mem -debug ...

cd ../../modeles/XIOS; ./make_xios --arch $(FCM_ARCH) --debug

and in SOURCES/NEMO/arch-X64_CURIE.fcm add traceback :

%FCFLAGS -i4 -r8 -O3 -traceback -fp-model precise 

gmake clean
gmake