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--- library:computing:xios_impi_troubles [2025/08/31 02:12]
84.88.52.107 old revision restored (2025/05/25 15:49)
+++ library:computing:xios_impi_troubles [2025/10/14 11:08] (current)
84.88.52.107 old revision restored (2025/10/05 10:52)
@@ Line 1: / Line 1: @@
-====== XIOS I/O server with Intel MPI ======
+====== NEMO-XIOS issues with Intel MPI ======
-===== XIOS @ MN3 =====
+===== NEMO-XIOS @ MN3 =====
 **Environment:** NEMO 3.6 stable, XIOS 1.0. This bug was documented using the following compilers and MPI libraries:
@@ Line 68: / Line 68: @@
-===== XIOS @ MN4 =====
+===== NEMO-XIOS @ MN4 =====
-==== Issue 1: ====
+==== Issue 1: NEMO fails to read input files ====
 **Environment:** Auto-EC-Earth 3.2.2_develop_MN4 (EC-Earth 3.2 r4063-runtime-unification).
@@ Line 126: / Line 126: @@
 </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 it 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. However, we got some other XIOS errors when writting outputs (commented in following issues). When operations installed 4.2 version we were seeing 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.
-**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__: 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).
+**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.
-**Solution:**
+**Solution:** Until we have more information the best solution is to use a NetCDF version that does not have P-NetCDF support (4.2 and 4.4.0 in MN4). In any case XIOS uses NC4, which is using HDF5 for parallel write.
 **More information:**
-This bug was reported in Unidata Github:
+This bug had already been reported in Unidata Github:
 [[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).
@@ Line 146: / Line 152: @@
   * NetCDF: 4.4.0
   * HDF5: 1.8.19
-  * Flags: -O3
+  * Flags: -O3 , with and without -fpe0
-**Problem:** XIOS2 breaks when writing output files.
+**Problem:** XIOS2 breaks when writing output files. As a result, output files are incomplete: they contain the headers for each one of the variables they are supposed to store, but only values for nav_lat, nav_lon, depthu and depthu_bounds are actually saved.
-__ocean.output__:
+__ocean.output__: ocean.output looks normal, the stop is just after writing the restarts.
+__log.err__:
 <code>
+forrtl: error (65): floating invalid
+Image              PC                Routine            Line        Source
+nemo.exe           0000000001B2B832  Unknown               Unknown  Unknown
+libpthread-2.22.s  00002B2472B71B10  Unknown               Unknown  Unknown
+nemo.exe           000000000189CE85  _ZN5blitz5ArrayId         182  fastiter.h
+nemo.exe           000000000189BDE9  _ZN5blitz5ArrayId          89  methods.cc
+nemo.exe           000000000189BA8C  _ZN4xios13COperat         175  operator_expr.hpp
+nemo.exe           000000000188A3BA  _ZN4xios27CFieldF          61  binary_arithmetic_filter.cpp
+nemo.exe           00000000018152E4  _ZN4xios7CFilter1          14  filter.cpp
+nemo.exe           0000000001563FBE  _ZN4xios9CInputPi          37  input_pin.cpp
+nemo.exe           000000000176284F  _ZN4xios10COutput          46  output_pin.cpp
+nemo.exe           0000000001762A48  _ZN4xios10COutput          35  output_pin.cpp
+nemo.exe           0000000001815364  _ZN4xios7CFilter1          16  filter.cpp
+nemo.exe           0000000001563FBE  _ZN4xios9CInputPi          37  input_pin.cpp
+nemo.exe           000000000176284F  _ZN4xios10COutput          46  output_pin.cpp
+nemo.exe           0000000001762A48  _ZN4xios10COutput          35  output_pin.cpp
+nemo.exe           0000000001815364  _ZN4xios7CFilter1          16  filter.cpp
+nemo.exe           0000000001563FBE  _ZN4xios9CInputPi          37  input_pin.cpp
+nemo.exe           000000000176284F  _ZN4xios10COutput          46  output_pin.cpp
+nemo.exe           0000000001762A48  _ZN4xios10COutput          35  output_pin.cpp
+nemo.exe           000000000178A260  _ZN4xios13CSource          32  source_filter.cpp
+nemo.exe           0000000001812DC7  _ZN4xios6CField7s          21  field_impl.hpp
+nemo.exe           00000000014B3586  cxios_write_data_         434  icdata.cpp
+nemo.exe           0000000000FFE0FD  idata_mp_xios_sen         552  idata.F90
+nemo.exe           0000000000738081  diawri_mp_dia_wri         252  diawri.f90
+nemo.exe           0000000000485B67  step_mp_stp_              284  step.f90
+nemo.exe           000000000043908B  nemogcm_mp_nemo_g         147  nemogcm.f90
+nemo.exe           0000000000438FDD  MAIN__                     18  nemo.f90
+nemo.exe           0000000000438F9E  Unknown               Unknown  Unknown
+libc-2.22.so       00002B247309B6E5  __libc_start_main     Unknown  Unknown
+nemo.exe           0000000000438EA9  Unknown               Unknown  Unknown
+,1      Final
+</code>
+**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, but this obviously has an effect on performance. At second instance we activated -O2 optimizations and the model runs, so this way performance loss is not that important as it would be running with -O0.
+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.
+**Diagnosis:** By now it is difficult to know the exact source of this problem. Further debugging will be required.
+**Solution:** Use -O2 flag (instead of -O2). But now it seems to work using NetCDF 4.2, -O3 & netcdf_par for XIOS2.
+==== Issue 3: MPI kills XIOS when writing model output ====
+**Environment:** Auto-EC-Earth 3.2.2_develop_MN4 (EC-Earth 3.2 r4063-runtime-unification).
+  * Compiler: Intel 2017.4
+  * MPI: Intel 2017.3.196
+  * NetCDF: 4.4.0 & 4.2 (after removed PNETCDF)
+  * HDF5: 1.8.19
+  * Flags: -O0
+**Problem:** The model crashes at one of the steps it is supposed to write an output file, getting what it seems it is an MPI problem. The step of the crash is not always the same, and it may write output files in previous timesteps.
+__ocean.output__: The ocean.output file presents no anomalies.
+__log.err__:
+<code>
+s11r1b56.58976Assertion failure at /nfs/site/home/phcvs2/gitrepo/ifs-all/Ofed_Delta/rpmbuild/BUILD/libpsm2-10.2.175/ptl_ips/ips_proto.c:1869: (scb->payload_size & 0x3) == 0
+forrtl: error (76): Abort trap signal
+Image              PC                Routine            Line        Source
+nemo.exe           00000000027A1F9A  Unknown               Unknown  Unknown
+libpthread-2.22.s  00002AD71847FB10  Unknown               Unknown  Unknown
+libc-2.22.so       00002AD7189BD8D7  gsignal               Unknown  Unknown
+libc-2.22.so       00002AD7189BECAA  abort                 Unknown  Unknown
+libpsm2.so.2.1     00002AD73FDD3E6E  Unknown               Unknown  Unknown
+libpsm2.so.2.1     00002AD73FDE7D59  Unknown               Unknown  Unknown
+libpsm2.so.2.1     00002AD73FDEA3F2  Unknown               Unknown  Unknown
+libpsm2.so.2.1     00002AD73FDE419D  Unknown               Unknown  Unknown
+libpsm2.so.2.1     00002AD73FDE10D3  Unknown               Unknown  Unknown
+libpsm2.so.2.1     00002AD73FDDF93B  Unknown               Unknown  Unknown
+libpsm2.so.2.1     00002AD73FDDABF0  psm2_mq_ipeek2        Unknown  Unknown
+libtmip_psm2.so.1  00002AD73FBBE2FE  Unknown               Unknown  Unknown
+libmpi.so.12.0     00002AD7174E05C1  Unknown               Unknown  Unknown
+libmpi.so.12.0     00002AD717364020  Unknown               Unknown  Unknown
+libmpi.so.12       00002AD7170E05F2  PMPIDI_CH3I_Progr     Unknown  Unknown
+libmpi.so.12       00002AD7174D1BFF  PMPI_Test             Unknown  Unknown
+nemo.exe           00000000022E5F14  _ZN4xios13CClient          79  buffer_client.cpp
+nemo.exe           00000000018A348B  _ZN4xios14CContex         201  context_client.cpp
+nemo.exe           000000000186A6E1  _ZN4xios8CContext         350  context.cpp
+nemo.exe           0000000001D262F1  cxios_write_data_         412  icdata.cpp
+nemo.exe           0000000001478A79  idata_mp_xios_sen         545  idata.F90
+nemo.exe           0000000000BF1463  iom_mp_iom_p2d_          1136  iom.f90
+nemo.exe           0000000000810534  diawri_mp_dia_wri         293  diawri.f90
+nemo.exe           00000000004A9EFC  step_mp_stp_              284  step.f90
+nemo.exe           000000000043A9E9  nemogcm_mp_nemo_g         147  nemogcm.f90
+nemo.exe           000000000043A7C6  MAIN__                     18  nemo.f90
+nemo.exe           000000000043A79E  Unknown               Unknown  Unknown
+libc-2.22.so       00002AD7189A96E5  __libc_start_main     Unknown  Unknown
+nemo.exe           000000000043A6A9  Unknown               Unknown  Unknown
 </code>
-**Actions taken:**
-**Diagnosis:**
+**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.
-**Solution:**
+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.
-==== Issue 3: ====
+**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 reducing the congestion (which is achieved by adding servers), but maybe in the future we can get more information.
-**Environment:**
+**Solution:** By the moment the solution used is to use enough number of XIOS servers (47 for SR).
-**Problem:**
+About Intel Communication Fabrics control:
-**Actions taken:**
+[[https://software.intel.com/en-us/node/528821]]
-**Diagnosis:**
+Ips_proto.c source code:
-**Solution:**
+[[https://github.com/01org/psm/blob/master/ptl_ips/ips_proto.c]]
+==== Issue 4: EC-Earth enters in a dead lock when using fabric (OFA network fabrics) module ====
-==== Issue 4: ====
+**Environment:** Auto-EC-Earth 3.2.2_develop_MN4 (EC-Earth 3.2 r4063-runtime-unification).
-**Environment:**
+  * Compiler: Intel 2017.4
+  * MPI: Intel 2017.3.196
+  * NetCDF: 4.4.0
+  * HDF5: 1.8.19
+  * Flags: -O0 & -O3
-**Problem:**
+**Problem:** When loading module fabric, created by Ops to solve Issue 2 on NEMO (assertion invalid), EC-Earth enters in a deadlock. Our NEMO benchmark was rather running, but MPI_Finalize was not working and jobs never finished until wallclock time limit was reached.
-**Actions taken:**
+**Actions taken:** We managed to solve the issues 1 to 3, so there is no need to solve this one by now. However, if we find the time we will debug this problem.
 **Diagnosis:**
-**Solution:**
+**Solution:** No solution yet, but model can work without fabric module.

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