Re: [AMBER] Probmlems compiling under macOS

From: Gustaf Olsson <>
Date: Sun, 10 Jan 2021 21:37:31 +0000

No non-standard macOS bison or yacc installed though brew.

extern OBJEKT oGetObject( char *sName );
static int yyerror( char *sStr );
static int yylex();
static int yyparse();


extern OBJEKT oGetObject( char *sName );
extern int yyparse();

So there are more then a few declarations missing in mine. I did download a fresh tarball and started from scratch.

Hmm, strange enough:

    find . -name "parser.y"

    ls -la /AmberTools/src/leap/src/leap/parser.y
    ls: /AmberTools/src/leap/src/leap/parser.y: No such file or directory

So the declaration comes from parser.y and this file, while being located, mysteriously does not exist.

Best regards

// Gustaf

Från: Gustaf Olsson <>
Skickat: den 10 januari 2021 18:24:07
Till: AMBER Mailing List
Ämne: Re: [AMBER] Probmlems compiling under macOS

Thank you David

I will look into this as soon as I have a few moments.

There has been nothing but strange behavior this time. Part of the issue no doubt relates to my use of homebrew instead of macports.

I was successful in compiling with clang/gfortran-9 serial, then the parallel compilation failed with some problem regarding open-mpi incompatibility. Strangely enough, after installing/uninstalling and doing a reboot, that error went away an I found myself with this new and interesting problem.

I will try to reboot my computer once or twice, check my cmake references one more time and try to also assign/define/export CC and FC as well, just to make sure and see what happens.

Just so I am not wasting time, gcc/gfortran 10 is not supported yet correct?

Is there anything else then CC/FC I make sure points to the right directory?

Best regards

// Gustaf

Från: David A Case <>
Skickat: den 10 januari 2021 14:46:50
Till: AMBER Mailing List
Ämne: Re: [AMBER] Probmlems compiling under macOS

On Sun, Jan 10, 2021, Gustaf Olsson wrote:
> /Users/xxx/amber20_src/build/AmberTools/src/leap/src/leap/ error: implicit declaration of function 'yyerror' is invalid in C99
> [-Werror,-Wimplicit-function-declaration]
> yyerror (YY_("memory exhausted"));

Have you installed some non-standard version of bison or yacc? I've never
done anything but use the programs in /usr/bin, and have not seen the error
you report, on either Catalina or Big Sur.

Look at your file, and search for "yyerror". You should see a line
like this:

static int yyerror( char *sStr );

In my code, it's at line 235, but I see the line cited above at line 1854,
not 1852, so our line numbers might be off.

The declaration of yyerror() comes from parser.y, at line 199.

You continue to find novel problems! :-) On Catalina, I use either XCode
11.3 -> Apple clang version 11.0.0 (clang-1100.0.33.16) or
gcc -> gcc-mp-9 (MacPorts gcc9 9.3.0_4) 9.3.0.

>I tried building with gcc-9 only though I received some error with
>memgen/memembed complaining about architecture and more.

Another problem that doesn't arise for me.

...not sure this is any help, unless it turns out to be a bison/yacc
problem. I'm attaching my (Catalina) version of, so you can make a

...good luck...dac

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Received on Sun Jan 10 2021 - 14:00:02 PST
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