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include MED 4.1.1 or libmed #12

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tomsail opened this issue Nov 17, 2023 · 7 comments
Open

include MED 4.1.1 or libmed #12

tomsail opened this issue Nov 17, 2023 · 7 comments

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@tomsail
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tomsail commented Nov 17, 2023

Here is an exttract of the systel.linux.cfg for compiling with MED librairies.

#
# MED info
#
flags_med: -DHAVE_MED
libs_med: -lm -lmed -lhdf5 -ldl -lstdc++ -lz
...
[gnu.dynamic]
brief: Scibian 10 dynamic build using GFortran 8.3.0 and Open MPI.
options: api
#
f2py_name: f2py3
pyd_fcompiler: gnu95
sfx_lib:    .so
#
obj_flags: -O2 -fPIC [fflags_gfo] [flags_mpi] [flags_mumps] [flags_gotm] [flags_aed] [flags_med]
lib_flags: -fPIC -shared [fflags_gfo]
#
exe_flags: -fPIC [fflags_gfo]
#
cmd_lib:    [fc] [lib_flags] -o <libname> <objs>
incs_all: 
libs_all: [libs_so_mumps] [libs_metis] [libs_aed] [libs_gotm] [libs_med]
cflags: -fPIC
#

2 different tentatives have been made :

  1. Trying with med-otm :
    The error I get is the following:

    - completed: .../telemac-mascaret/builds/gnu.dynamic/lib/libtelemac3d4api.so
    - completed: .../telemac-mascaret/builds/gnu.dynamic/lib/libartemis4api.so
/home/tomsail/miniconda3/conda-bld/opentelemac_1698950324172/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1698950324172/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libmed.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: error: ld returned 1 exit status

Which seems to be linked with the fact that I don't strictly use the same GNU compilers
Although I checked, doing mamba list for opentelemac:
libgfortran5 13.2.0 ha4646dd_2 conda-forge
and for med-otm:
libgfortran5 13.2.0 ha4646dd_2 conda-forge
The fix would be either:

  • pining the compiler (not really keen to do it)
  • installing MED in the build.sh when building telemac (not sure either, but still better than option 1)
  • using a fixed version from conda-forge (tried today 2023/11/17), but still fails : see below
  1. Trying with libmed :
    the error I get is the following :
    - completed: .../opentelemac/builds/gnu.dynamic/lib/libtelemac3d4api.so
    - completed: .../opentelemac/builds/gnu.dynamic/lib/libartemis4api.so
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfacre_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfdnfd_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mprnpr_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfdrvr_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhgnr_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mficom_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhcyr_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mprcre_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mficow_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhfnr_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfdcsi_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhcow_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mficor_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhmii_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfdrvw_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfanfg_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfanfa_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfafai_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhnme_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mprivw_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfdcre_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfdncn_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfdfin_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhgnw_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mficlo_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mprivr_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhfnw_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfinvr_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhnax_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfdfdi_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhcre_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhcor_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mprpri_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mfiope_'
/home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/tomsail/miniconda3/conda-bld/opentelemac_1700214085103/work/opentelemac/builds/gnu.dynamic/lib/libhermes4api.so: undefined reference to `mmhcyw_'
collect2: error: ld returned 1 exit status
@nicogodet
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Although I checked, doing mamba list for opentelemac:
libgfortran5 13.2.0 ha4646dd_2 conda-forge
and for med-otm:
libgfortran5 13.2.0 ha4646dd_2 conda-forge

Typo ? Same version

It might be the root cause indeed...

@tomsail
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tomsail commented Nov 17, 2023

indeed it is the same version. That's why I couldn't find the source of the problem

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in 1, it could be related to hdf5 package. On windows, I packed my own hdf5 and used it for med

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tomsail commented Nov 17, 2023

No it didn't. (Maybe I did something wrong there, because I would expect it to work)
I explained it in the other issue thread:

checking absolute name of <H5public.h>... checking for H5public.h... yes
//$BUILD_PREFIX/include/H5public.h
expr: non-integer argument
configure: error: 
This HDF5 version #define H5_VERS_MAJOR 1.#define H5_VERS_MINOR 14.#define H5_VERS_RELEASE 2 must not be used with med-fichier4.1.1.
The HDF5 library version used by med-fichier4.y.z MUST NOT be > 1.10 and have to be at least HDF5-1.10.2.
DO NOT TRY TO COMPILE med-fichier4.1.1 version with an HDF5 library which would generate an hdf5 file not compliant with HDF5-1.10.z library.
This would BREAK med-fichier compatibility between files with the same revision number !

If you want to reproduce : I implemented a hdf5 branch mirroring from their official repository.

Then there is another problem / limitation that I see with MED: it adds another constraint on the build i.e. HDF5 < 1.11
which is another obstacle to make the library cross-compatible with other libraries (like eccodes for instance).

This would be counter productive to pin hdf5 as I finally released the pin on numpy.

FIY: I am doing matrix builds on python/numpy/MPI using this script that I will eventually add in the repo:

# Define your matrices
python_versions=("3.8" "3.9" "3.10" "3.11" "3.12")
numpy_versions=("1.19" "1.20" "1.21" "1.22" "1.23" "1.24" "1.25" "1.26")
mpi_versions=("openmpi" "mpich")

# File to store the build results
results_file="build_results.txt"

# Loop over each configuration
for py in "${python_versions[@]}"; do
  for np in "${numpy_versions[@]}"; do
    for mpi in "${mpi_versions[@]}"; do
      echo "Building for Python $py, NumPy $np, and MPI $mpi"
      # Run conda build and check the result
      if conda build recipe --variants="{mpi: '$mpi', python: '$py', numpy: '$np'}" -c tomsail; then
        # If build succeeds
        echo "SUCCESS: Python $py, NumPy $np, MPI $mpi" >> "$results_file"
      else
        # If build fails
        echo "FAIL: Python $py, NumPy $np, MPI $mpi" >> "$results_file"
      fi
    done
  done
done

I will test on v8p4r0 and main. Expecting the builds on main to add much more versions of numpy. For more context, I started implementing TELEMAC in pyposeidon and couldn't get anywhere because of the pin on numpy.
I will report back to @sebourban and Boris on the forum as soon as I get the results for both of these branches

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nicogodet commented Nov 17, 2023 •
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I think we should start working on conda-forge integration with minimal build (full build, mpi, no med, no mumps, no aed, no gotm) on linux and macOS and progressively increase complexity by solving dependencies issues.

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Note that you can also generate a patch file to patch v8p4 release for hermes generation with numpy >=1.25

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tomsail commented Nov 17, 2023

I think we should start working on conda-forge integration with minimal build (full build, mpi, no med, no mumps, no aed, no gotm) on linux and macOS and progressively increase complexity by solving dependencies issues.

agreed. I still need to check their documentation to do it right. Or I let you you take the lead ? 😉 Once @brey has sorted the compilation on osx, we can create a minimal branch and start from there.

Note that you can also generate a patch file to patch v8p4 release for hermes generation with numpy >=1.25

I've never done it before, I'd be keen to more about this workaround.
Also I am creating a new issue on numpy / python versions, we should talk about this there.

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