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Fix MATLAB bindings for MacOS #3950

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merged 2 commits into from
Dec 1, 2023
Merged

Fix MATLAB bindings for MacOS #3950

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8c06009
Fix MATLAB bindings for MacOS - updated bindings/Matlab/Makefile, add…
tomgade09 Nov 30, 2023
e9b7c0c
Update adiosopenc.c to use adios2_init_serial regardless of MPI use.
tomgade09 Dec 1, 2023
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2 changes: 1 addition & 1 deletion bindings/C/adios2/c/adios2_c_adios.h
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Expand Up @@ -46,7 +46,7 @@ adios2_adios *adios2_init_config_mpi(const char *config_file, MPI_Comm comm);

#else
#define adios2_init() adios2_init_serial()
#define adios2_init_config(config_file) adios2_init_config_seria(config_file)
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Ouch. We may need to push this into the release branch too.

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Seems like no one uses the non-MPI version 🤣

#define adios2_init_config(config_file) adios2_init_config_serial(config_file)
#endif

/**
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10 changes: 10 additions & 0 deletions bindings/Matlab/Makefile
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Expand Up @@ -18,6 +18,16 @@ MEXLIBS="LDFLAGS=${ADIOS_LIBS}"
ADIOS_INC=-I${ADIOS_DIR}/include
ADIOS_LIBS=`${ADIOS_DIR}/bin/adios2-config --c-libs`

### MacOS - example using homebrew installed ADIOS2 and Xcode 15 clang
### 1) Install homebrew (https://brew.sh/) and Xcode (App Store)
### 2) brew install adios2
### OR
### 2) Compile Adios2 from scratch and update ADIOS_DIR below to match install directory
#ADIOS_DIR=/opt/homebrew/opt/adios2
#ADIOS_INC=-I${ADIOS_DIR}/include
#ADIOS_LIBS=-Wl,-rpath,${ADIOS_DIR}/lib -shared -L${ADIOS_DIR}/lib -ladios2_c -ladios2_core
#MEXLIBS="LDFLAGS=${ADIOS_LIBS}"


MEXOPTS=-largeArrayDims -DDEBUG CFLAGS="-g -std=c99 -fPIC -O0"
default:
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4 changes: 4 additions & 0 deletions bindings/Matlab/adiosopenc.c
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Expand Up @@ -140,7 +140,11 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])

/********************************************************/
/* Open ADIOS file now and get variables and attributes */
#if ADIOS2_USE_MPI
adiosobj = adios2_init(false);
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Should this call be passing the MPI communicator into ADIOS?

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@tomgade09 tomgade09 Nov 30, 2023 •
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Honestly, I don't think so, but this is where my knowledge of ADIOS breaks down a bit....

The previous version of this line in adiosopenc.c passed false, so I imagine that it's ok. Even in the event the library uses MPI, passing an MPI communicator would require creating one (which would then require finalizing / destroying after use), which is I assume why the original author just passed false. But the makefile links against the non-MPI version of ADIOS (which is what I used to do my testing), so I'm not sure how this would behave if linked against the MPI version.

Do:

adios2_inquire_all_variables(&adios_vars, &nvars, group);
adios2_inquire_all_attributes(&adios_attrs, &nattrs, group);

or any of the other adios2 functions in adiosreadc.c or adiosclosec.c use MPI for anything? If so, maybe the best bet is to have a preprocessor assert that ADIOS2_USE_MPI is not defined (or just undefine it). It doesn't make sense in the context of MATLAB to use MPI anyway...I know this can be done, but probably isn't common.

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We never used MPI in Matlab, and apparently false has been a value compilers could live with.

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I guess explicitly calling adios2_adios *adios2_init_serial(void); would be the clean solution

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I guess explicitly calling adios2_adios *adios2_init_serial(void); would be the clean solution

Probably so. There's some other stuff in the bindings that could use to be cleaned up (unreferenced mpi_comm_dummy variable, etc.). I was going to try to get Matlab installed for myself so I could at least try things before merging.

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@tomgade09 tomgade09 Dec 1, 2023 •
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I guess explicitly calling adios2_adios *adios2_init_serial(void); would be the clean solution

Done.

#else
adiosobj = adios2_init();
#endif
group = adios2_declare_io(adiosobj, "matlabiogroup"); // name is arbitrary
fp = adios2_open(group, fname, adios2_mode_read);
if (fp == NULL)
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