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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 [2017/08/07 15:52] 84.88.184.232 [Issue 4: EC-Earth enters in a dead lock when using fabric (OFA network fabrics) module] |
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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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- | **Actions taken:** Given that the error is a floating invalid we disabled the -fpe0 flag, but we still were having the same problem. Then we disabled compiler optimizations (use -O0) and the problem disappeared, | + | **Actions taken:** Given that the error is a floating invalid we disabled the -fpe0 flag, but we still were having the same problem. Then we disabled compiler optimizations (use -O0) and the problem disappeared, |
- | **Diagnosis:** | + | Update: Using the new NetCDF 4.2 installed by Ops and key netcdf_par for XIOS2 the model can run using O3. We have to investigate further this issue. |
- | **Solution:** Disabling compiler optimizations (activate -O0). | + | **Diagnosis:** By now it is difficult to know the exact source of this problem. Further debugging will be required. |
- | ==== Issue 3: ==== | + | **Solution: |
+ | |||
+ | ==== Issue 3: MPI kills XIOS 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 | ||
- | **Problem: | + | **Problem: |
__ocean.output__: | __ocean.output__: | ||
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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:// | ||
- | ==== Issue 4: ==== | + | |
+ | Ips_proto.c source code: | ||
+ | |||
+ | [[https:// | ||
+ | ==== Issue 4: EC-Earth enters in a dead lock when using fabric (OFA network fabrics) module | ||
**Environment: | **Environment: | ||
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* Flags: -O0 & -O3 | * Flags: -O0 & -O3 | ||
- | **Problem: | + | **Problem: |
- | **Actions taken:** | + | **Actions taken: |
**Diagnosis: | **Diagnosis: | ||
- | **Solution: | + | **Solution: |