Diferencia entre revisiones de «CROCO»
Sin resumen de edición |
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| Línea 168: | Línea 168: | ||
| 3. Always run in your '''salidas/''' folder never in <CODE>$HOME</CODE> | | 3. Always run in your '''salidas/''' folder never in <CODE>$HOME</CODE> | ||
|} | |} | ||
== Upwelling == | |||
Compilation of the upwelling test case in distributed memory (dmpar) with intel. | |||
<PRE> | |||
$ mkdir /share/CROCO/v210/intel/dmpar/ | |||
$ git clone --branch v2.1.0 https://gitlab.inria.fr/croco-ocean/croco.git croco | |||
$ cd croco | |||
$ CROCOsrc=/share/CROCO/v210/intel/dmpar/croco | |||
</PRE> | |||
= Example of use = | = Example of use = | ||
Revisión del 18:59 15 jul 2025
Web page of the instalation of the ocean model CROCO in CIMA's HPC 'hydra'
Installation
CIMA's HPC has a common folder where all the people has access. This is going to be the place where CROCO model will be installed.
The installation is going to be in the following INSTALLDIR=/share/CROCO folder.
Downloading the code (there is a GItlab repository, but by now, we are going to install closed releases)
$ wget https://gitlab.inria.fr/croco-ocean/croco/-/archive/v2.1.0/croco-v2.1.0.tar.gz
Creating the folder of the compilation (using intel compiler and shared memory dmpar) and where to deploy the code
$ mkdir $INSTALLDIR/v210 $ cd $INSTALLDIR/v210 $ mkdir -p intel/dmpar $ git clone --branch v2.1.0 https://gitlab.inria.fr/croco-ocean/croco.git croco-v2.1.0 Cloning into 'croco'... remote: Enumerating objects: 52646, done. remote: Counting objects: 100% (448/448), done. remote: Compressing objects: 100% (263/263), done. remote: Total 52646 (delta 268), reused 317 (delta 185), pack-reused 52198 (from 1) Receiving objects: 100% (52646/52646), 300.67 MiB | 4.59 MiB/s, done. Resolving deltas: 100% (40426/40426), done. Note: switching to '291e8cd11b2329ee171c7a02c52c9c481dda981e'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c <new-branch-name> Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false $ ls croco GRIF create_config.bash OBSTRUCTION README.md TEST_CASES BENCH MPI_NOLAND OCEAN requirements.txt XIOS CHANGELOG.md MUSTANG PISCES SCRIPTS
Go to compile, first we set-up the environment for intel compilation
$ source /opt/load-libs.sh 1 The following libraries, compiled with Intel 2021.4.0 compilers, were loaded: * MPICH 3.4.2 * NetCDF 4 * HDF5 1.10.5 * JASPER 2.0.33 To change it please logout and login again. To load this libraries from within a script add this line to script: source /opt/load-libs.sh 1 $ cd croco
We create an ASCII file with the specificities of the compilation with intel in hydra, name CROCO_hydra_intel.env (following the instructios from here tutorial 00)
#set environment variables for croco in HYDRA to be compiled with intel
source /opt/load-libs.sh 1
export CC=icc
export FC=ifort
export F90=ifort
export F77=ifort
export NETCDF=/opt/netcdf/netcdf-4/intel/2021.4.0
export PATH=$NETCDF/bin::${PATH}
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}::${NETCDF}/lib
Loading the compilation environment
$ source CROCO_hydra_intel.env
BASIN
The simplest installation would be the 'basin' configuration. We follow these instructions basin. Assuming that the source code resides in CROCOsrc=/share/CROCO/v210/intel/serie/croco
$ CROCOsrc=/share/CROCO/v210/intel/serie/croco
$ cd ${CROCOsrc}
$ mkdir -p CONFIGS/BASIN
cp OCEAN/cppdefs.h CONFIGS/BASIN
cp OCEAN/param.h CONFIGS/BASIN
cp OCEAN/jobcomp CONFIGS/BASIN
cd CONFIGS/BASIN
We need to edit the configuration files.
Editing the file with the configuration
$ cp cppdefs.h cppdefs.h_orig $ diff cppdefs.h cppdefs.h_orig 18c18 < #define BASIN /* Basin Example */ --- > #undef BASIN /* Basin Example */ 56c56 < #undef REGIONAL /* REGIONAL Applications */ --- > #define REGIONAL /* REGIONAL Applications */
Editing the file with the size of the domain and configuration of the parallel environment
$ cp param.h param.h_orig $ diff param.h param.h_orig
Editing the file with the compilation
$ cp jobcomp jobcomp_orig
$ diff jobcomp jobcomp_orig
34,35c34
< CROCOsrc=/share/CROCO/v210/intel/serie/croco
< SOURCE1=${CROCOsrc}/OCEAN
---
> SOURCE1=../croco/OCEAN
45c45
< FC=ifort
---
> FC=gfortran
And compile
$ ./jobcomp > jobcomp.log
If everything when fine, one should have:
$ tail -n 15 jobcomp.log
mv a.out croco
.,:looddddddd: ,;'
.cdddo;;oo'.... .ldd;
,ddddd, ;odoc.
.oddddo: .'';odoc
'dddddd;':, .;; .;;. :ccdo;
.oddddddddooooddoooddooodl.
.oddddddddddddddddddddddl;;
.,ldddddddddddddddddddoc:lolo'..
;ddc;::::::::::codo, .';:,
.ccc ,cc,
CROCO is OK
$ ls -l croco
-rwxrwxr-x 1 lluis.fita cima 1012160 Jul 15 15:11 croco
| IMPORTANT NOTES |
|---|
| 1. do not run the model in the same place where you compiled the source |
| 2. Always use a queue-system job to run simulations, never run without it |
3. Always run in your salidas/ folder never in $HOME
|
Upwelling
Compilation of the upwelling test case in distributed memory (dmpar) with intel.
$ mkdir /share/CROCO/v210/intel/dmpar/ $ git clone --branch v2.1.0 https://gitlab.inria.fr/croco-ocean/croco.git croco $ cd croco $ CROCOsrc=/share/CROCO/v210/intel/dmpar/croco
Example of use
How to run a basic example
$ cd $HOME/salidas $ mkdir CROCO $ cd CROCO $ mkdir tests $ cd tests/ $ cp /share/tools/workflows/direct/CROCO/hydra/launch_ideal_test_serie.pbs ./
Link the necessary files and editng them if needed:
$ ln -s $CROCOsrc/CONFIGS/BASIN/croco ./ $ cp $CROCOsrc/TEST_CASES/croco.in.Basin ./
And execute
$ qsub launch_ideal_test_serie.pbs 70619.hydra $ qstat Job ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- (...) 70619.hydra CROCO4L_ideal lluis.fita 0 R larga
Looking for the current step:
$ tail croco.out
2698 299.77778 8.942712777E-05-3.3148734E+00-3.3147840E+00 5.0400000E+16 0
2699 299.88889 8.942810068E-05-3.3148728E+00-3.3147833E+00 5.0400000E+16 0
2700 300.00000 8.942902900E-05-3.3148721E+00-3.3147827E+00 5.0400000E+16 0
WRT_HIS -- wrote history fields into time record = 31 / 31
2701 300.11111 8.942991352E-05-3.3148715E+00-3.3147820E+00 5.0400000E+16 0
2702 300.22222 8.943075502E-05-3.3148708E+00-3.3147814E+00 5.0400000E+16 0
2703 300.33333 8.943155431E-05-3.3148701E+00-3.3147807E+00 5.0400000E+16 0
2704 300.44444 8.943231222E-05-3.3148695E+00-3.3147800E+00 5.0400000E+16 0
2705 300.55556 8.943302959E-05-3.3148688E+00-3.3147794E+00 5.0400000E+16 0
2706 300.66667 8.943370728E-05-3.3148682E+00-3.3147787E+00 5.0400000E+16 0
Once finished:
$ qstat
Job ID Name User Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
(...)
70619.hydra CROCO4L_ideal lluis.fita 00:01:13 C larga
$ tail croco.out
3239 359.88889 9.041893005E-05-3.3144938E+00-3.3144033E+00 5.0400000E+16 0
3240 360.00000 9.041879739E-05-3.3144930E+00-3.3144026E+00 5.0400000E+16 0
WRT_HIS -- wrote history fields into time record = 37 / 37
MAIN - number of records written into history file(s): 37
number of records written into restart file(s): 0
MAIN: DONE
$ ls -lrt
total 15576
-rw-rw-r-- 1 lluis.fita cima 1412 Jul 15 15:40 launch_ideal_test_serie.pbs
lrwxrwxrwx 1 lluis.fita cima 55 Jul 15 15:44 croco -> /share/CROCO/v210/intel/dmpar/croco/CONFIGS/BASIN/croco
-rw-rw-r-- 1 lluis.fita cima 3361 Jul 15 15:46 croco.in.Basin
-rw------- 1 lluis.fita cima 3361 Jul 15 15:47 croco.in
-rw------- 1 lluis.fita cima 824 Jul 15 15:48 CROCO4L_ideal.o70619
-rw------- 1 lluis.fita cima 15653792 Jul 15 15:48 basin_his.nc
-rw------- 1 lluis.fita cima 274775 Jul 15 15:48 croco.out