AMBER Archive (2009)

Subject: Re: [AMBER] problems compiling ambertool

From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Mon Mar 16 2009 - 09:41:26 CDT

Hi,

Thanks now the nab/ compiles just fine but when area is fixed the next is
broken ;-) when I execute the command

make -f Makefile_at

the problem is then moved to nss/ which gives the following error
(cd nss && make install )
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o matgen matgen.o
libsym.a
Undefined first referenced
 symbol in file
__mt_WorkSharing_rtc_
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/libnab.a(sff.o)
__mt_int_reduc_
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/libnab.a(nblist.o)
__mt_get_next_chunk_invoke_mfunc_once_int_
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/libnab.a(sff.o)
omp_get_thread_num
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/libnab.a(sff.o)
__mt_barrier_rtc_
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/libnab.a(sff.o)
omp_get_num_threads
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/libnab.a(sff.o)
omp_get_max_threads
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/libnab.a(sff.o)
__mt_get_next_chunk_invoke_mfunc_once_uint_
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/f2c.a(open.o)
__mt_double_reduc_
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/libnab.a(sff.o)
__mt_MasterFunction_rtc_
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib/libnab.a(sff.o)
ld: fatal: Symbol referencing errors. No output written to matgen
cc failed!
*** Error code 1
make: Fatal error: Command failed for target `matgen'
Current working directory
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/src/nss
*** Error code 1
make: Fatal error: Command failed for target `install'

On Mon, Mar 16, 2009 at 3:27 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Mon, Mar 16, 2009, Per Jr. Greisen wrote:
>
> > cc -c -O -DSUN -DSYSV -DBINTRAJ -xopenmp=parallel -xautopar -DOPENMP
> -Dlex
> > sff.c
> > "lex.mm_options.c", line 75: non-constant initializer: op "NAME"
>
> Looks like you have to make the same change to lex.mm_options.c that you
> made to lex.dg_options.c.
>
> ...dac
>
>
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