practical_guide.md

### Example on MareNostrum 4

```r
library(startR)

repos <- paste0('/esarchive/exp/ecmwf/system5_m1/6hourly/',
                '$var$-longitudeS1latitudeS1all/$var$_$sdate$.nc')
# Slower alternative, using files with a less efficient NetCDF 
# compression configuration
#repos <- '/esarchive/exp/ecmwf/system5_m1/6hourly/$var$/$var$_$sdate$.nc'

data <- Start(dat = repos,
              var = 'tas',
              sdate = indices(1),
              ensemble = 'all',
              time = 'all',
              latitude = indices(1:40),
              longitude = indices(1:40),
              retrieve = FALSE)
lons <- attr(data, 'Variables')$common$longitude
lats <- attr(data, 'Variables')$common$latitude

fun <- function(x) apply(x + 1, 2, mean)
step <- Step(fun, c('ensemble', 'time'), c('time'))
wf <- AddStep(data, step)

res <- Compute(wf,
               chunks = list(latitude = 2,
                             longitude = 2),
               threads_load = 1,
               threads_compute = 2,
               cluster = list(queue_host = 'mn2.bsc.es',
                              queue_type = 'slurm',
                              data_dir = '/gpfs/projects/bsc32/share/startR_data_repos/',
                              temp_dir = '/gpfs/scratch/pr1efe00/pr1efe03/startR_tests/',
                              r_module = 'R/3.4.0',
                              cores_per_job = 2,
                              job_wallclock = '00:10:00',
                              max_jobs = 4,
                              extra_queue_params = list('#SBATCH --qos=prace'),
                              bidirectional = FALSE,
                              polling_period = 10,
                              special_setup = 'marenostrum4'
                             ),
               ecflow_suite_dir = '/home/Earth/nmanuben/test_remove/',
               ecflow_server = NULL,
               silent = FALSE,
               debug = FALSE,
               wait = TRUE)
```

### Example on CTE-Power using GPUs

### Seasonal forecast verification example on cca

```r
crps <- function(x, y) {
  mean(SpecsVerification::EnsCrps(x, y, R.new = Inf))
}

library(startR)

repos <- '/perm/ms/spesiccf/c3ah/qa4seas/data/seasonal/g1x1/ecmf-system4/msmm/atmos/seas/tprate/12/ecmf-system4_msmm_atmos_seas_sfc_$date$_tprate_g1x1_init12.nc'

data <- Start(dat = repos,
              var = 'tprate',
              date = 'all',
              time = 'all',
              number = 'all',
              latitude = 'all',
              longitude = 'all',
              return_vars = list(time = 'date'))

dates <- attr(data, 'Variables')$common$time

repos <- '/perm/ms/spesiccf/c3ah/qa4seas/data/ecmf-ei_msmm_atmos_seas_sfc_19910101-20161201_t2m_g1x1_init02.nc'

obs <- Start(dat = repos,
             var = 't2m',
             time = values(dates),
             latitude = 'all',
             longitude = 'all',
             split_multiselected_dims = TRUE)

s <- Step(crps, target_dims = list(c('date', 'number'), c('date')),
                output_dims = NULL)
wf <- AddStep(list(data, obs), s)

r <- Compute(wf,
             chunks = list(latitude = 10,
                           longitude = 3),
             cluster = list(queue_host = 'cca',
                            queue_type = 'pbs',
                            max_jobs = 10,
                            init_commands = list('module load ecflow'),
                            r_module = 'R/3.3.1',
                            extra_queue_params = list('#PBS -l EC_billing_account=spesiccf')),
             ecflow_output_dir = '/perm/ms/spesiccf/c3ah/startR_test/',
             is_ecflow_output_dir_shared = FALSE
            )
```

## 7. Compute() cluster templates

### Nord3-v2

```r
cluster = list(queue_host = 'nord4.bsc.es',
               queue_type = 'slurm',
               temp_dir = '/gpfs/scratch/bsc32/bsc32734/startR_hpc/',
               cores_per_job = 2,
               job_wallclock = '01:00:00',
               max_jobs = 4,
               bidirectional = FALSE,
               polling_period = 10
               )
```

### Nord3 (deprecated)

```r
cluster = list(queue_host = 'nord1.bsc.es',
               queue_type = 'lsf',
               data_dir = '/gpfs/projects/bsc32/share/startR_data_repos/',
               temp_dir = '/gpfs/scratch/bsc32/bsc32473/startR_hpc/',
               init_commands = list('module load intel/16.0.1'),
               cores_per_job = 2,
               job_wallclock = '00:10',
               max_jobs = 4,
               extra_queue_params = list('#BSUB -q bsc_es'),
               bidirectional = FALSE,
               polling_period = 10
              )
```

### CTE-Power9

```r
cluster = list(queue_host = 'p9login1.bsc.es',
               queue_type = 'slurm',
               temp_dir = '/gpfs/scratch/bsc32/bsc32473/startR_hpc/',
               cores_per_job = 4,
               job_wallclock = '00:10:00',
               max_jobs = 4,
               bidirectional = FALSE,
               polling_period = 10
              )
```

### BSC ES fat nodes (deprecated)

```r
cluster = list(queue_host = 'bsceslogin01.bsc.es',
               queue_type = 'slurm',
               cores_per_job = 2,
               job_wallclock = '00:10:00',
               max_jobs = 4,
               bidirectional = TRUE
              )
```

### Marenostrum 4

```r
cluster = list(queue_host = 'mn2.bsc.es',
               queue_type = 'slurm',
               data_dir = '/gpfs/projects/bsc32/share/startR_data_repos/',
               temp_dir = '/gpfs/scratch/pr1efe00/pr1efe03/startR_hpc/',
               r_module = 'R/3.4.0',
               cores_per_job = 2,
               job_wallclock = '00:10:00',
               max_jobs = 4,
               extra_queue_params = list('#SBATCH --qos=prace'),
               bidirectional = FALSE,
               polling_period = 10,
               special_setup = 'marenostrum4'
              )
```

### MinoTauro

```r
cluster = list(queue_host = 'mt1.bsc.es',
               queue_type = 'slurm',
               data_dir = '/gpfs/projects/bsc32/share/startR_data_repos/',
               temp_dir = '/gpfs/scratch/bsc32/bsc32473/startR_hpc/',
               r_module = 'R/3.3.3',
               cores_per_job = 2,
               job_wallclock = '00:10:00',
               max_jobs = 4,
               extra_queue_params = list('#SBATCH --qos=bsc_es'),
               bidirectional = FALSE,
               polling_period = 10,
               special_setup = 'marenostrum4'
              )
```

### ECMWF ecgate (workstation) + cca/ccb (HPC)

```r
cluster = list(queue_host = 'cca',
               queue_type = 'pbs',
               max_jobs = 10,
               init_commands = list('module load ecflow'),
               r_module = 'R/3.3.1',
               extra_queue_params = list('#PBS -l EC_billing_account=spesiccf')
              )
```