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GTlab Module for embadding Python into GTlab
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HDF5 version mismatch leads to crash (renamed) #244

Open rainman110 opened 12 months ago

rainman110 commented 12 months ago

In GitLab by @haes_ja on Oct 23, 2023, 07:35

grafik grafik smarty-SMARTy-4.0.0.zip

A minimal example to reproduce:

rainman110 commented 12 months ago

Thanks @haes_ja . I can definitely reproduce it on my system. lets see, what causes the issue.

rainman110 commented 12 months ago

I could also reproduce it on linux and got an interesting error message:

The reason "could" be a HDF 5 library version mismatch

/home/sigg_ma/src/smarty-SMARTy-4.0.0/.eggs/scipy-1.11.3-py3.9-linux-x86_64.egg/scipy/__init__.py:132: UserWarning: A NumPy version >=1.21.6 and <1.28.0 is required for this version of SciPy (detected version 1.20.3)
  warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
/home/sigg_ma/miniforge3/envs/smarty/lib/python3.9/site-packages/h5py-3.10.0-py3.9-linux-x86_64.egg/h5py/__init__.py:36: UserWarning: h5py is running against HDF5 1.12.1 when it was built against 1.14.2, this may cause problems
  _warn(("h5py is running against HDF5 {0} when it was built against {1}, "
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.14.2, library is 1.12.1
        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:
-------------------
                   HDF5 Version: 1.12.1
                  Configured on: 2023-05-08
                  Configured by: Ninja
                    Host system: Linux-4.19.0-22-amd64
              Uname information: Linux
                       Byte sex: little-endian
             Installation point: /builds/gtlab-installer/deployment-tester/pkg-linux/01_third_party/hdf5/unstable/1-12-1/ThirdPartyLibraries/hdf5

Compiling Options:
------------------
                     Build Mode: Release
              Debugging Symbols: OFF
                        Asserts: OFF
                      Profiling: OFF
             Optimization Level: OFF

Linking Options:
----------------
                      Libraries: 
  Statically Linked Executables: OFF
                        LDFLAGS: 
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
                Extra libraries: m;dl
                       Archiver: /usr/bin/ar
                         Ranlib: /usr/bin/ranlib

Languages:
----------
                              C: YES
                     C Compiler: /usr/bin/cc 8.3.0
                       CPPFLAGS: 
                    H5_CPPFLAGS: 
                    AM_CPPFLAGS: 
                         CFLAGS:   -std=c99  -fstdarg-opt -fmessage-length=0
                      H5_CFLAGS: -Wall;-Wcast-qual;-Wconversion;-Wextra;-Wfloat-equal;-Wformat=2;-Winit-self;-Winvalid-pch;-Wmissing-include-dirs;-Wno-c++-compat;-Wno-format-nonliteral;-Wshadow;-Wundef;-Wwrite-strings;-pedantic;-Wbad-function-cast;-Wimplicit-function-declaration;-Wmissing-declarations;-Wmissing-prototypes;-Wnested-externs;-Wold-style-definition;-Wpacked;-Wpointer-sign;-Wpointer-to-int-cast;-Wredundant-decls;-Wstrict-prototypes;-Wswitch;-Wunused-function;-Wunused-variable;-Wunused-parameter;-Wcast-align;-Wunused-but-set-variable;-Wformat;-finline-functions;-Wno-aggregate-return;-Wno-inline;-Wno-missing-format-attribute;-Wno-missing-noreturn;-Wno-overlength-strings;-Wlarger-than=2560;-Wlogical-op;-Wframe-larger-than=16384;-Wpacked-bitfield-compat;-Wsync-nand;-Wstrict-overflow=5;-Wno-unsuffixed-float-constants;-Wdouble-promotion;-Wtrampolines;-Wstack-usage=8192;-Wmaybe-uninitialized;-Wno-jump-misses-init;-Wno-suggest-attribute=const;-Wno-suggest-attribute=noreturn;-Wno-suggest-attribute=pure;-Wno-suggest-attribute=format;-Warray-bounds=2;-Wc99-c11-compat;-Werror=incompatible-pointer-types;-Werror=shadow;-Wduplicated-cond;-Whsa;-Wnormalized;-Wnull-dereference;-Wunused-const-variable;-Walloca;-Walloc-zero;-Wduplicated-branches;-Wformat-overflow=2;-Wformat-truncation=1;-Wrestrict;-Wattribute-alias;-Wcast-align=strict;-Wshift-overflow=2;-Wno-suggest-attribute=cold;-Wno-suggest-attribute=malloc
                      AM_CFLAGS: 
               Shared C Library: YES
               Static C Library: NO

                        Fortran: OFF
               Fortran Compiler:  
                  Fortran Flags: 
               H5 Fortran Flags: 
               AM Fortran Flags: 
         Shared Fortran Library: YES
         Static Fortran Library: NO

                            C++: ON
                   C++ Compiler: /usr/bin/c++ 8.3.0
                      C++ Flags:     -fstdarg-opt -fmessage-length=0
                   H5 C++ Flags: -Wall;-Wcast-qual;-Wconversion;-Wctor-dtor-privacy;-Weffc++;-Wextra;-Wfloat-equal;-Wformat=2;-Winit-self;-Winvalid-pch;-Wmissing-include-dirs;-Wno-format-nonliteral;-Wnon-virtual-dtor;-Wold-style-cast;-Woverloaded-virtual;-Wreorder;-Wshadow;-Wsign-promo;-Wundef;-Wwrite-strings;-pedantic;-Wcast-align;-Wmissing-declarations;-Wpacked;-Wredundant-decls;-Wswitch;-Wunused-but-set-variable;-Wunused-function;-Wunused-variable;-Wunused-parameter;-Wno-aggregate-return;-Wno-inline;-Wno-missing-format-attribute;-Wno-missing-noreturn;-Wno-overlength-strings;-Wlarger-than=2560;-Wlogical-op;-Wframe-larger-than=16384;-Wpacked-bitfield-compat;-Wsync-nand;-Wstrict-overflow=5;-Wdouble-promotion;-Wtrampolines;-Wstack-usage=8192;-Wmaybe-uninitialized;-Wno-jump-misses-init;-Wno-suggest-attribute=const;-Wno-suggest-attribute=noreturn;-Wno-suggest-attribute=pure;-Wno-suggest-attribute=format;-Wdate-time;-Wopenmp-simd;-Wshadow;-Wduplicated-cond;-Whsa;-Wnormalized;-Wnull-dereference;-Wunused-const-variable;-Wattribute-alias;-Wcast-align=strict;-Wshift-overflow=2;-Wcast-function-type;-Wmaybe-uninitialized;-Wno-suggest-attribute=cold;-Wno-suggest-attribute=malloc
                   AM C++ Flags: 
             Shared C++ Library: YES
             Static C++ Library: NO

                            JAVA: OFF
                 JAVA Compiler:  

Features:
---------
                   Parallel HDF5: OFF
Parallel Filtered Dataset Writes: 
              Large Parallel I/O: 
              High-level library: OFF
                Build HDF5 Tests: OFF
                Build HDF5 Tools: OFF
                    Threadsafety: OFF (recursive RW locks: OFF) 
             Default API mapping: v112
  With deprecated public symbols: ON
          I/O filters (external):  DEFLATE
                             MPE: 
                      Direct VFD: 
                      Mirror VFD: 
              (Read-Only) S3 VFD: 
            (Read-Only) HDFS VFD: 
                         dmalloc: 
  Packages w/ extra debug output: 
                     API Tracing: OFF
            Using memory checker: OFF
 Memory allocation sanity checks: OFF
          Function Stack Tracing: OFF
                Use file locking: best-effort
       Strict File Format Checks: OFF
    Optimization Instrumentation: 
Bye...

GTlab:27957 terminated with signal 6 at PC=7fc51d3c77bb SP=7ffee9199910.  Backtrace:
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x10b)[0x7fc51d3c77bb]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x121)[0x7fc51d3b2535]
/home/sigg_ma/src/GTlab-DevTools_GitLab_MASTER/stable/2_0/bin/libhdf5.so.200(+0x53cd2)[0x7fc51f8b4cd2]
/home/sigg_ma/miniforge3/envs/smarty/lib/python3.9/site-packages/h5py-3.10.0-py3.9-linux-x86_64.egg/h5py/h5f.cpython-39-x86_64-linux-gnu.so(+0x7662)[0x7fc386012662]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(PyModule_ExecDef+0x72)[0x7fc50a07b6c2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x1ba628)[0x7fc50a07b628]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13cf81)[0x7fc509ffdf81]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x5405)[0x7fc509ff6e65]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0xd9)[0x7fc509ffeac9]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x4648)[0x7fc509ff60a8]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x684)[0x7fc509ff20e4]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3ea)[0x7fc509ff1e4a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3ea)[0x7fc509ff1e4a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13d308)[0x7fc509ffe308]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_CallMethodIdObjArgs+0x135)[0x7fc50a0091c5]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x78ff2)[0x7fc509f39ff2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x15039a)[0x7fc50a01139a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x14821d)[0x7fc50a00921d]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_Call+0x73)[0x7fc50a0085b3]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x5405)[0x7fc509ff6e65]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0xd9)[0x7fc509ffeac9]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3ea)[0x7fc509ff1e4a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0xd9)[0x7fc509ffeac9]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13d308)[0x7fc509ffe308]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_CallMethodIdObjArgs+0x135)[0x7fc50a0091c5]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x794a4)[0x7fc509f3a4a4]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x15039a)[0x7fc50a01139a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x14821d)[0x7fc50a00921d]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_Call+0x73)[0x7fc50a0085b3]
/home/sigg_ma/src/GTlab-DevTools_GitLab_MASTER/stable/2_0/bin/modules/libGTlabPython39.so(+0xb81af)[0x7fc508e7c1af]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_MakeTpCall+0x273)[0x7fc509ff9083]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x71828)[0x7fc509f32828]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalCodeWithName+0x4f)[0x7fc509ff09cf]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(PyEval_EvalCodeEx+0x3a)[0x7fc509ff097a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(PyEval_EvalCode+0x1c)[0x7fc50a078e4c]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x1bc684)[0x7fc50a07d684]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13e26a)[0x7fc509fff26a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x5405)[0x7fc509ff6e65]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0xd9)[0x7fc509ffeac9]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x4648)[0x7fc509ff60a8]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x684)[0x7fc509ff20e4]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3ea)[0x7fc509ff1e4a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3ea)[0x7fc509ff1e4a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13d308)[0x7fc509ffe308]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_CallMethodIdObjArgs+0x135)[0x7fc50a0091c5]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x78ff2)[0x7fc509f39ff2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x15039a)[0x7fc50a01139a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x14821d)[0x7fc50a00921d]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_Call+0x73)[0x7fc50a0085b3]
/home/sigg_ma/src/GTlab-DevTools_GitLab_MASTER/stable/2_0/bin/modules/libGTlabPython39.so(+0xb81af)[0x7fc508e7c1af]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_MakeTpCall+0x273)[0x7fc509ff9083]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x4581)[0x7fc509ff5fe1]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalCodeWithName+0x4f)[0x7fc509ff09cf]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(PyEval_EvalCodeEx+0x3a)[0x7fc509ff097a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(PyEval_EvalCode+0x1c)[0x7fc50a078e4c]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x1bc684)[0x7fc50a07d684]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13e26a)[0x7fc509fff26a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x5405)[0x7fc509ff6e65]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0xd9)[0x7fc509ffeac9]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x4648)[0x7fc509ff60a8]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x684)[0x7fc509ff20e4]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3ea)[0x7fc509ff1e4a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3ea)[0x7fc509ff1e4a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13d308)[0x7fc509ffe308]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_CallMethodIdObjArgs+0x135)[0x7fc50a0091c5]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x78ff2)[0x7fc509f39ff2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x15039a)[0x7fc50a01139a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x14821d)[0x7fc50a00921d]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_Call+0x73)[0x7fc50a0085b3]
/home/sigg_ma/src/GTlab-DevTools_GitLab_MASTER/stable/2_0/bin/modules/libGTlabPython39.so(+0xb81af)[0x7fc508e7c1af]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_MakeTpCall+0x273)[0x7fc509ff9083]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x71828)[0x7fc509f32828]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalCodeWithName+0x4f)[0x7fc509ff09cf]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(PyEval_EvalCodeEx+0x3a)[0x7fc509ff097a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(PyEval_EvalCode+0x1c)[0x7fc50a078e4c]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x1bc684)[0x7fc50a07d684]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13e26a)[0x7fc509fff26a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x5405)[0x7fc509ff6e65]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0xd9)[0x7fc509ffeac9]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x4648)[0x7fc509ff60a8]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x684)[0x7fc509ff20e4]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3ea)[0x7fc509ff1e4a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3ea)[0x7fc509ff1e4a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13ddc2)[0x7fc509ffedc2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13d308)[0x7fc509ffe308]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_CallMethodIdObjArgs+0x135)[0x7fc50a0091c5]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x78ff2)[0x7fc509f39ff2]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x15039a)[0x7fc50a01139a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x14821d)[0x7fc50a00921d]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_Call+0x73)[0x7fc50a0085b3]
/home/sigg_ma/src/GTlab-DevTools_GitLab_MASTER/stable/2_0/bin/modules/libGTlabPython39.so(+0xb81af)[0x7fc508e7c1af]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyObject_MakeTpCall+0x273)[0x7fc509ff9083]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x71828)[0x7fc509f32828]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalCodeWithName+0x4f)[0x7fc509ff09cf]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(PyEval_EvalCodeEx+0x3a)[0x7fc509ff097a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(PyEval_EvalCode+0x1c)[0x7fc50a078e4c]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x1bc684)[0x7fc50a07d684]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x13e26a)[0x7fc509fff26a]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x5405)[0x7fc509ff6e65]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(+0x12fd47)[0x7fc509ff0d47]
/home/sigg_ma/miniforge3/envs/smarty/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0xd9)[0x7fc509ffeac9]
rainman110 commented 12 months ago

Next step: I replaced GTlab's hdf version by the one provided by h5py and was successful:

GTlab> from smarty.sampling import doe
/home/sigg_ma/src/smarty-SMARTy-4.0.0/.eggs/scipy-1.11.3-py3.9-linux-x86_64.egg/scipy/__init__.py:132: UserWarning: A NumPy version >=1.21.6 and <1.28.0 is required for this version of SciPy (detected version 1.20.3)
  warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"

Next step will be, to downgrade h5py to be compatible with the one from gtlab. Otherwise, we could provide a gtlab core version with the newer hdf5 library.

rainman110 commented 12 months ago

Here's a workaround, to avoid crashing:

rainman110 commented 12 months ago

Note: The crash when running GTlab outside the smarty venv does not come from HDF5. Another library seems to cause the crash, i.e. a missing MPI or something else.

rainman110 commented 12 months ago

Indeed, something related to MPI seems to be the problem when running GTlab outside of the smarty venv:

 GTlab.exe 
   0.0.0.0 
   64f76175 
   impi.dll 
   2021.10.0.0 
   6490da00 
   c0000005 
   00000000000dac44 
   1df4 
   01da0596a473b386 
   C:\local\GTlab-DevTools_GitLab_MASTER\stable\2_0\bin\GTlab.exe 
   C:\local\miniforge3\envs\smarty\Library\bin\impi.dll 
   1d01eb70-81a3-42bb-8749-54620936db44
rainman110 commented 12 months ago

Running this import inside the GTlabConsole python command, gets:

Abort(1090959) on node 0 (rank 0 in comm 0): Fatal error in PMPI_Init_thread: Other MPI error, error stack:
MPIR_Init_thread(176)........:
MPID_Init(1548)..............:
MPIDI_OFI_mpi_init_hook(1554):
(unknown)(): Other MPI error
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1090959
:
system msg for write_line failure : No error
Abort(1090959) on node 0 (rank 0 in comm 0): Fatal error in PMPI_Init_thread: Other MPI error, error stack:
MPIR_Init_thread(176)........:
MPID_Init(1548)..............:
MPIDI_OFI_mpi_init_hook(1554):
(unknown)(): Other MPI error
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1090959
:
system msg for write_line failure : No error
rainman110 commented 12 months ago

Okay, this remaining issue is caused by the following import

from mpi4py import MPI
rainman110 commented 12 months ago

So... when entering a conda environment, conda executes all scripts in the directory C:\local\miniforge3\envs\smarty\etc\conda\activate.d .

If mpi4py is installed, there will be a script mpivars.activate.bat that is executed, which sets all required MPI variables.

If these aren't set, we'll get the error message above.

The question for the python module is, whether we can execute these script when loading the python module and wheather running these scripts will even make an effect or not. (note, these are batch scripts, calling them could potentially only set env-vars temporarily)

rainman110 commented 12 months ago

In Windows, setting set PATH=C:\local\miniforge3\envs\smarty\Library\bin\libfabric\utils;C:\local\miniforge3\envs\smarty\Library\bin\libfabric;%PATH% makes the import work also outside the smarty venv

rainman110 commented 12 months ago

We're mixing now up several issues now:

  1. Clashing of HDF5 libraries
  2. Correct initialization of virtual envs

I'll rename this one and create another issue for 2.

rainman110 commented 12 months ago

marked this issue as related to #242