Calling MPI_Abort() from HOC

[CCohen]

Hello,
I'm wondering how to call MPI_Abort() from HOC, in the context of an MPI-run simulation on UNIX. The aim is to quit all hosts, including the master, without first receiving all returnable pc.working() calls. The following attempt, among others, did not work.
Charles

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system("MPI_Abort(MPI_COMM_WORLD, error_code)")

error_code = -1, 0, 1, etc.

[hines]

The internal wrapper for MPI_Abort is not exposed to the interpreter. You can do that with a mod file

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$ cat abrt.mod
NEURON {SUFFIX nothing}

VERBATIM
extern "C" { void nrnmpi_abort(int); }
ENDVERBATIM

PROCEDURE mpiabort(errcode) {
VERBATIM
  {
    nrnmpi_abort(int(_lerrcode));
  }
ENDVERBATIM
}

Then, after nrnivmodl

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$ nrniv
NEURON -- VERSION 9.0a-109-g1009732c7 master (1009732c7) 2023-11-27
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2022
See http://neuron.yale.edu/neuron/credits

loading membrane mechanisms from x86_64/.libs/libnrnmech.so
Additional mechanisms from files
 "abrt.mod"
oc>mpiabort(-3)
Aborted (core dumped)

[CCohen]

Thank you very much, Michael.

Unfortunately, abrt.mod did not compile on nrn 8.2.2, the last version available at the NSG WebPortal. Would a backward-compatible fix be possible? Details on the compilation error follow.

Best regards,
Charles


Relevant compilation error on 8.2.2 on OSX:

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NEURON -- VERSION 8.2.2 release/8.2 (93d41fafd) 2022-12-15
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2022
See http://neuron.yale.edu/neuron/credits

...

 -> Compiling abrt.c
abrt.c:150:8: error: expected identifier or '('
extern "C" { void nrnmpi_abort(int); }
       ^
abrt.c:156:5: warning: implicit declaration of function 'nrnmpi_abort' is
      invalid in C99 [-Wimplicit-function-declaration]
    nrnmpi_abort(int(_lerrcode));
    ^
abrt.c:156:18: error: expected expression
    nrnmpi_abort(int(_lerrcode));
                 ^
1 warning and 2 errors generated.
make: *** [abrt.o] Error 1
make: *** Waiting for unfinished jobs....

[hines]

Try

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NEURON {SUFFIX nothing}

VERBATIM
extern void nrnmpi_abort(int);        
ENDVERBATIM

PROCEDURE mpiabort(errcode) {
VERBATIM
  {
    nrnmpi_abort((int)_lerrcode);  
  }
ENDVERBATIM
}

[CCohen]

Hi Michael,

The last version of abrt.mod, above, now compiles on 8.2.2. However, it does not abort anything but rather generates a segmentation violation in a test as you had performed (see below).

Charles

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NEURON -- VERSION 8.2.2 release/8.2 (93d41fafd) 2022-12-15
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2022
See http://neuron.yale.edu/neuron/credits

	1 
	1 
	1 
	1 
	1 
	0 
	1 
loading membrane mechanisms from ./lib/arm64/.libs/libnrnmech.so
Additional mechanisms from files
 "abrt.mod"

oc>mpiabort(-1)
Segmentation violation
Backtrace:
	2   libsystem_platform.dylib            0x00007fff57ce6f5a : _sigtramp()+26
	3   ???                                 0x00007ffee43c6268 0x0 + 140732727583336
	4   libnrniv.dylib                      0x000000010b9bd99a : _Z8hoc_callv()+266
	5   libnrniv.dylib                      0x000000010b9ba0d4 : _Z11hoc_executeP4Inst()+100
	6   libnrniv.dylib                      0x000000010b9cc19d : _Z13hoc_moreinputv()+1197
	7   libnrniv.dylib                      0x000000010b9cbc85 : _Z9hoc_main1iPPKcS1_()+261
	8   libnrniv.dylib                      0x000000010b87af1b : _Z16ivocmain_sessioniPPKcS1_i()+7451
	9   nrniv                               0x000000010b83ced3 : main()+179
	10  libdyld.dylib                       0x00007fff579d8015 : start()+1
	11  ???                                 0x0000000000000004 0x0 + 4
/Applications/NEURON//bin/nrniv: Aborting.
 near line 1
 mpiabort(-1)
             ^
        mpiabort(-1)
oc>

[hines]

You didn't mention how you launched the program.
I'm guessing that you are running a NEURON version that dynamically loads mpi when you give it the -mpi arg. Otherwise the memory for nrnmpi_abort is NULL (hence the seg fault). Do you have a problem if you try

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mpiexec -n 1 nrniv -mpi -c 'mpiabort(-1)'