#1962 closed Task (fixed)
HPC-07(2017WP) Write restart file using XIOS
| Reported by: | andmirek | Owned by: | andmirek |
|---|---|---|---|
| Priority: | high | Milestone: | 2018 release-4.0 |
| Component: | OCE | Version: | trunk |
| Severity: | major | Keywords: | OPA v4.0 |
| Cc: |
Description
Context
Implementation of XIOS restart write interface in trunk (see ticket #1882 for version 3.6)
Proposal
Write an interface to use XIOS to write restart file (core variables only,the ones written to numror)
Commit History (30)
| Changeset | Author | Time | ChangeLog |
|---|---|---|---|
| 9536 | andmirek | 2018-05-01T13:37:48+02:00 | #1953 and #1962 stop immediately if XIOS restart read/write functionality is used without key_iomput |
| 9535 | andmirek | 2018-05-01T13:22:33+02:00 | #1953 and #1962 disable XIOS related calls when key_iomput is not set |
| 9405 | andmirek | 2018-03-15T17:29:06+01:00 | |
| 9367 | mathiot | 2018-02-28T17:23:20+01:00 | Add restart read/write via XIOS capability (#1953 and #1962 and twiki: 2017WP/Met_Office-1_Mirek_XIOSread). WARNING: need to upgrade XIOS to r1296 to compile |
| 8990 | andmirek | 2017-12-12T15:56:38+01:00 | |
| 8858 | andmirek | 2017-11-30T15:50:38+01:00 | |
| 8857 | andmirek | 2017-11-30T15:24:15+01:00 | #1953 and #1962 handle together setting XIOS restart read and write flags |
| 8836 | andmirek | 2017-11-28T15:45:20+01:00 | |
| 8821 | andmirek | 2017-11-27T14:46:12+01:00 | |
| 8816 | andmirek | 2017-11-27T12:01:56+01:00 | |
| 8812 | andmirek | 2017-11-24T17:34:50+01:00 | |
| 8802 | andmirek | 2017-11-23T17:48:06+01:00 | |
| 8801 | andmirek | 2017-11-23T16:52:17+01:00 | |
| 8800 | andmirek | 2017-11-23T16:48:37+01:00 | |
| 8799 | andmirek | 2017-11-23T16:45:20+01:00 | |
| 8793 | andmirek | 2017-11-23T13:02:23+01:00 | #1953 and #1962 change lxios_read to lrxios to be consistent with write branch |
| 8792 | andmirek | 2017-11-23T12:29:39+01:00 | |
| 8786 | andmirek | 2017-11-22T14:39:57+01:00 | |
| 8785 | andmirek | 2017-11-22T13:34:53+01:00 | #1953 and #1962 change in subroutine name and way temperature first level is read |
| 8774 | andmirek | 2017-11-21T17:54:04+01:00 | |
| 8770 | andmirek | 2017-11-21T17:21:22+01:00 | #1953 and #1962 merged (and some modifications) with write branch |
| 8763 | andmirek | 2017-11-21T11:28:18+01:00 | #1962 correct name of XIOS write context |
| 8760 | andmirek | 2017-11-21T10:44:53+01:00 | #1962 bug fix |
| 8759 | andmirek | 2017-11-21T09:57:42+01:00 | |
| 8662 | andmirek | 2017-10-26T13:15:54+02:00 | #1962 change variable names to follow NEMO coding convention |
| 8661 | andmirek | 2017-10-26T12:06:21+02:00 | #1962 put back tabs, spaces and lines removed when implementiong XIOS write functionality |
| 8644 | andmirek | 2017-10-20T10:04:07+02:00 | ticket #1962 xios write functionality works |
| 8630 | andmirek | 2017-10-17T14:31:49+02:00 | #1962 merge with branches/UKMO/dev_r7573_xios_write (doesn't woork) |
| 8622 | andmirek | 2017-10-12T18:38:26+02:00 | ticket #1962 - write restart file with XIOS |
| 8620 | andmirek | 2017-10-12T16:18:23+02:00 | ticket #1962 - write restart file with XIOS |
Change History (18)
comment:1 Changed 6 years ago by andmirek
- Milestone set to 2017 WP
- Owner set to andmirek
- Status changed from new to assigned
comment:2 Changed 6 years ago by andmirek
comment:3 Changed 6 years ago by andmirek
To enable write functionality nn_wxios must be set to value larger than 0 (namelist namrun). nn_wxios = 0 - uses NEMO interface to write restart; nn_write = 1 - XIOS writes restart to a single file; nn_write = 2 - XIOS writes restart to a multiple files (one per server).
No changes in iodef.xml are required, all definitions are in NEMO.
For AGRIF configuration setting for AGRIF is ignored and NEMO value is used.
comment:4 Changed 6 years ago by clevy
- Type changed from Enhancement to Task
comment:5 Changed 6 years ago by andmirek
- Type changed from Task to Enhancement
comments by Tim Graham:
1)) The purpose of writing restart files via XIOS. I guess the main purpose is preparation for being able to read them with XIOS but I think it’s important to clarify this. You could also comment on the advantage of being able to write to a single restart file instead of having to rebuild it first.
On a HPC system writing multiple files at the same time may impact I/O performance. This situation may happen during writing restart file. In NEMO all processors write the restart file at the end of the simulation at the same time. With XIOS number of files written at the same time may be significantly reduced; either to the number of XIOS servers or to a single file if necessary. Because writing to multiple files may be faster than to a single file rebuild of the restart will still be necessary when performance is major concern (and there is a need to use single file restart, for instance when change in processors decomposition is needed). Rebuild may be easier and fasted when there are only few sub-domains to rebuild. In this ticket only data written to numror is considered. NEMO restart file is the biggest file and for high resolution configuration (ORCA12) the rebuild is time consuming process, especially when netcdf4 is used.
2) Is it necessary to have the lxios argument to iom_rstput. Why not just check the variable locally withing the iom_rstput subroutine instead of passing it as an argument every time.
iom_rstput is a general subroutine and not all output (files) have to be written by XIOS. I think the implementation with argument is more general.
3) The NEMO coding conventions state that the variables should be l_xios and l_wxios (assuming that they are logicals). If they are integers then they should start with n (i.e. n_xios).
done in r8662
4) There are a lot of places where it looks like lines of code have changed but it is just spaces have been replaced by tabs (or vice versa). This is a pain at the merge party so it would be good to try to revert these changes if possible.
done in r8661
comment:6 Changed 6 years ago by andmirek
- Type changed from Enhancement to Task
comment:7 Changed 6 years ago by andmirek
Results from tests performed to evaluate XIOS write functionality for Met Office GO6 configuration, for 2 model resolutions: ORCA25 and ORCA12. NEMO 3.6 was used for tests. Runs were for 1 day.
NEMO - default NEMO functionality for reading single file restart
XIOS - XIOS read interface for reading single file restart
For XIOS data was written to ONE file and MULTIPLE files
Results: eORCA12:
Execution time [s] | Execution time [s] | |
|---|---|---|
CPU (decomposition) | XIOS ONE/MULTIPLE (36 servers) | NEMO |
1602 (50x50) | 1513/1195 | 1119 |
2262 (60x60) | 1556/1185 | 1066 |
3027 (70x70) | 1871/1644 | 1062 |
Results: eORCA25:
Execution time [s] | Execution time [s] | |
|---|---|---|
CPU (decomposition) | XIOS ONE/MULTIPLE (6 servers) | NEMO |
120 (10x12) | 645/613 | 560 |
440 (20x24) | 308/396 | 246 |
1440 (40x36) | 284/260 | 173 |
comment:8 Changed 5 years ago by andmirek
In 8990:
comment:9 Changed 5 years ago by mathiot
- Milestone changed from 2017 WP to 2018 release-4.0
comment:10 Changed 5 years ago by nicolasmartin
- Summary changed from Write restart file using XIOS to Met_Office-1(2017WP) Write restart file using XIOS
Modification of summary for standardisation
comment:11 Changed 5 years ago by clevy
- Summary changed from Met_Office-1(2017WP) Write restart file using XIOS to HPC-07(2017WP) Write restart file using XIOS
comment:12 Changed 5 years ago by mathiot
In 9367:
comment:13 Changed 5 years ago by mathiot
- Resolution set to fixed
- Status changed from assigned to closed
comment:14 Changed 5 years ago by andmirek
In 9405:
comment:15 Changed 5 years ago by andmirek
In 9535:
comment:16 Changed 5 years ago by andmirek
In 9536:
comment:17 Changed 5 years ago by andmirek
- wp_comment set to In the trunk. Currently tested in MO GO8 (eORCA25) configuration.
comment:18 Changed 16 months ago by nemo
- Keywords OPA v4.0 added
Branch dev_r8600_xios_write: http://forge.ipsl.jussieu.fr/nemo/log/branches/2017/dev_r8600_xios_write created.