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library:computing:xios_impi_troubles [2017/08/03 11:26] 84.88.184.232 [Issue 4:] |
library:computing:xios_impi_troubles [2024/06/24 18:04] 84.88.52.107 old revision restored (2024/06/02 17:07) |
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===== NEMO-XIOS @ MN4 ===== | ===== NEMO-XIOS @ MN4 ===== | ||
- | ==== Issue 1: ==== | + | ==== Issue 1: NEMO fails to read input files ==== |
**Environment: | **Environment: | ||
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</ | </ | ||
- | **Actions taken: | + | **Actions taken: |
- | **Diagnosis: | + | After looking for differences between NetCDF 4.4.0 and NetCDF 4.2 configurations (using nc-config & nf-config commands), we found out that while NetCDF 4.4.0 was compiled with no support for nc4 nor P-NetCDF (a library that gives parallel I/O support for classic NetCDF files), NetCDF 4.2 was installed with support for these features. We commented this to Ops and they installed __NetCDF without linking to P-NetCDF__, and this seemed to fix the problem. |
+ | |||
+ | In order to know more about the source of this bug, we __compared the behavior of two NEMO executables__: | ||
+ | |||
+ | We did a __comparison of the functions included in both binaries__ through the nm command, and we found that __they were identical__. Then we did a __more in deep comparison of both binaries__ with objdump and we found out little differences, | ||
+ | |||
+ | **Diagnosis: | ||
- | **Solution: | + | **Solution: |
**More information: | **More information: | ||
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[[https:// | [[https:// | ||
- | ==== Issue 2: ==== | + | ==== Issue 2: XIOS crashes when writing model output |
**Environment: | **Environment: | ||
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* Compiler: Intel 2017.4 | * Compiler: Intel 2017.4 | ||
* MPI: Intel 2017.3.196 | * MPI: Intel 2017.3.196 | ||
- | * NetCDF: 4.4.0 | + | * NetCDF: 4.4.0 & 4.2 (after removed PNETCDF) |
* HDF5: 1.8.19 | * HDF5: 1.8.19 | ||
* Flags: -O0 | * Flags: -O0 | ||
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- | **Actions taken:** A similar error was observed with NEMO standalone v3.6r6499. In that case, operations | + | **Actions taken:** A similar error was observed with NEMO standalone v3.6r6499. In that case, Ops told us to use the //fabric// module, which selects //ofi// as internode fabrics, similarly to the solution used in MN3 (see above). Using this module solved the problem for NEMO standalone, although it had the collateral effect that jobs were never ending. In coupled EC-Earth this module produced a dead lock, commented below. |
- | **Diagnosis: | + | We tried an alternative solution, which was to increment the number of XIOS servers in order to reduce the number of messages sent to the same process and by the moment it seems that it is effective. |
- | **Solution: | + | **Diagnosis: |
+ | |||
+ | **Solution: | ||
About Intel Communication Fabrics control: | About Intel Communication Fabrics control: | ||
[[https:// | [[https:// | ||
+ | |||
+ | Ips_proto.c source code: | ||
+ | |||
+ | [[https:// | ||
==== Issue 4: ==== | ==== Issue 4: ==== | ||