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library:computing:xios_impi_troubles [2024/06/01 21:17]
84.88.52.107 old revision restored (2017/08/04 13:14) 		library:computing:xios_impi_troubles [2024/06/02 17:07] (current)
84.88.52.107 old revision restored (2017/08/04 14:29)
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 </code> </code>
  
-**Actions taken:** Operations had observed this error using NEMO standalone and NetCDF 4.4.4.1, so they installed NetCDF 4.4.0 version. We could not reproduce the failure they reported with NEMO and NetCDF 4.4.4.1 but we got the same error when running EC-Earth. So we also moved to NetCDF 4.4.0 and this error was not arising. However, we got other XIOS errors when writing outputs (commented in following issues) and we asked for the same version we were using at MN3 to be installed. When operations installed 4.2 version we surprisingly got again the same error.+**Actions taken:** BSC Ops had previously observed this error using NEMO standalone and NetCDF 4.4.4.1, so they installed NetCDF 4.4.0. We could not reproduce the failure that they had reported by running NEMO and NetCDF 4.4.4.1 but we got the same error when running EC-Earth. So we also moved to NetCDF 4.4.0 and this error was not arising. However, we got other XIOS errors with the output write (commented in following issues) and we asked for the same version we were using at MN3 to be installed. When operations installed 4.2 version we surprisingly got again the same error.
  
-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 used that gives parallel I/O support for classic NetCDF files), while NetCDF was supporting this features. Then operations compiled again NetCDF without linking P-NetCDF, and this error disappeared.+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, compiled with NetCDF with and without P-NetCDF support. Both executions were linked with NetCDF without P-NetCDF support at runtime. The result is that the NEMO compiled with P-NetCDF did not run, so something was wrong at the NEMO binary itself.+In order to know more about the source of this bug, we __compared the behavior of two NEMO executables__: one compiled with NetCDF and another one without P-NetCDF support. Both executions were linked with NetCDF without P-NetCDF support at runtime. The result is that the __NEMO compiled with P-NetCDF did not run__, no matter the library used at runtime were not using it. The conclusion was that something was wrong at the NEMO binary itself.
  
-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, but some of that differences were pointing to a XIOS header file called netcdf.hpp. This header is responsible to include some NetCDF function definitions, and its behavior depends on the environment (preprocessing macros). In order to know if this file is the responsible of the bug we would have to compile NetCDF ourselves in debugging mode (with -g flag).+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, but some of that differences were __pointing to a XIOS header file called netcdf.hpp__. This header is responsible to include some NetCDF function definitions, and its behavior depends on the environment (preprocessing macros). In order to know if this file is the responsible of the bug we would have to compile NetCDF ourselves in debugging mode (with -g flag).
  
 **Diagnosis:** What we know until now is that compiling NetCDF with P-NetCDF messes up the nc_open function so it cannot be used by NEMO. We are not sure if this problem is produced by NetCDF alone, or if netcdf.hpp header files included with XIOS 2.0 are doing the mess. As stated above, compiling NetCDF ourselves would be needed to know more about the problem. **Diagnosis:** What we know until now is that compiling NetCDF with P-NetCDF messes up the nc_open function so it cannot be used by NEMO. We are not sure if this problem is produced by NetCDF alone, or if netcdf.hpp header files included with XIOS 2.0 are doing the mess. As stated above, compiling NetCDF ourselves would be needed to know more about the problem.
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 [[https://github.com/Unidata/netcdf4-python/issues/170|https://github.com/Unidata/netcdf4-python/issues/170]] [[https://github.com/Unidata/netcdf4-python/issues/170|https://github.com/Unidata/netcdf4-python/issues/170]]
  
-==== Issue 2: ====+==== Issue 2: XIOS crashes when writing model output ====
  
 **Environment:** Auto-EC-Earth 3.2.2_develop_MN4 (EC-Earth 3.2 r4063-runtime-unification).  **Environment:** Auto-EC-Earth 3.2.2_develop_MN4 (EC-Earth 3.2 r4063-runtime-unification). 
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-**Actions taken:** A similar error was observed with NEMO standalone v3.6r6499. In that case, operations 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.+**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:** The problem is that an one point the buffer for data transfer is not 4-byte aligned, and the library assumes it is. This is a really low level problem and we do not completely understand the relation between this and reduce the congestion, but maybe in the future we can get more information.   
 + 
 +**Solution:** By the moment the solution used is to use enough number of XIOS servers (47 for SR).
  
 About Intel Communication Fabrics control: About Intel Communication Fabrics control:
  
 [[https://software.intel.com/en-us/node/528821]] [[https://software.intel.com/en-us/node/528821]]
 +
 +Ips_proto.c source code:
 +
 +[[https://github.com/01org/psm/blob/master/ptl_ips/ips_proto.c]]
 ==== Issue 4: ==== ==== Issue 4: ====
  
library/computing/xios_impi_troubles.txt · Last modified: 2024/06/02 17:07 by 84.88.52.107

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