Re: [AMBER-Developers] Requirement to build serial before building parallel

From: Jason Swails <>
Date: Tue, 9 Mar 2010 18:28:44 -0500

On Sat, Mar 6, 2010 at 3:23 PM, case <> wrote:
> On Sat, Mar 06, 2010, Ross Walker wrote:
>> That might be useful although right now the 'actual' limitation is that you
>> can't do:
>> make -f Makefile_at parallel
>> without AMBERHOME/exe/yacc
> I'll work on removing this dependency...not only does it (appear to) involve
> a piece of pnetcdf that we don't actually use, but according to Jason, the
> code doesn't even accept yacc.

As a follow-up to this (since I said I would try to verify my past
claims): I removed bison/byacc from my ubuntu machine, then checked
out a new version of Amber today. Serial installation/test went fine.
 Parallel install of ambertools yielded the same error for me as it
did when it was first introduced:

make[4]: Entering directory
cd ncgen && make
make[5]: Entering directory
-I./../../../src/lib -I. -I. -DNDEBUG main.c
-I./../../../src/lib -I. -I. -DNDEBUG load.c
flex ./ncgen.l; \
        mv lex.yy.c ncgenyy.c
yacc -d ./ncgen.y; \
        mv ncgentab.c; \
        mv ncgentab.h
yacc: e - line 10 of "./ncgen.y", syntax error
%expect 1
-I./../../../src/lib -I. -I. -DNDEBUG ncgentab.c
-I./../../../src/lib -I. -I. -DNDEBUG escapes.c
-I./../../../src/lib -I. -I. -DNDEBUG getfill.c
-I./../../../src/lib -I. -I. -DNDEBUG init.c
-I./../../../src/lib -I. -I. -DNDEBUG genlib.c
genlib.c(392): (col. 16) remark: LOOP WAS VECTORIZED.
genlib.c(578): (col. 5) remark: BLOCK WAS VECTORIZED.
genlib.c(781): (col. 16) remark: LOOP WAS VECTORIZED.
genlib.c(1153): (col. 5) remark: LOOP WAS VECTORIZED.
genlib.c(1090): (col. 5) remark: LOOP WAS VECTORIZED.
mpicc -o ncmpigen -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE main.o
load.o ncgentab.o escapes.o getfill.o init.o genlib.o
-L../../../src/lib -lpnetcdf
main.o: In function `main':
main.c:(.text+0x527): undefined reference to `yyin'
main.c:(.text+0x52c): undefined reference to `yyparse'
init.o: In function `init_netcdf':
init.c:(.text+0x2): undefined reference to `clearout'
make[5]: *** [ncmpigen] Error 1
make[5]: Leaving directory
make[4]: *** [ncmpigen] Error 2
make[4]: Leaving directory
make[3]: *** [all] Error 2
make[3]: Leaving directory
make[2]: *** [subdir_target] Error 1
make[2]: Leaving directory `/home/swails/newamber/03.09.10/amber11/src/pnetcdf'
make[1]: *** [src/lib/all] Error 2
make[1]: Leaving directory `/home/swails/newamber/03.09.10/amber11/src/pnetcdf'
make: *** [../pnetcdf/lib/libpnetcdf.a] Error 2

which yacc returns: /home/swails/newamber/03.09.10/amber11/bin/yacc

After re-installing bison from aptitude (so that there is a yacc in
/usr/bin), the compilation finishes successfully. My system uses
intel11 compilers with MKL.


> ...dac
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Tue Mar 09 2010 - 15:30:04 PST
Custom Search