AMBER Archive (2009)

Subject: Re: [AMBER] problems compiling ambertool

From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Mon Mar 16 2009 - 17:35:38 CDT

Hi,

I have now tried to compile the serial version on the my SUN cluster but the
problems persist and it seems that the error is the same using the openmp
option as posted earlier

(cd nss && make install )
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c symop.nab
"symop.c", line 219: warning: argument #2 is incompatible with prototype:
        prototype: pointer to double :
"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/include/nabcode.h", line 187
        argument : pointer to array[3] of double
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c matop.c
"matop.c", line 34: warning: old-style declaration or incorrect type for:
MAT_sprint
"matop.c", line 73: warning: implicit function declaration: isspace
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c tss.c
"tss.c", line 1308: warning: implicit function declaration: MAT_tetra
"tss.c", line 1310: warning: implicit function declaration: MAT_cube
"tss.c", line 1312: warning: implicit function declaration: MAT_octa
"tss.c", line 1318: warning: implicit function declaration: MAT_ico
"tss.c", line 1320: warning: implicit function declaration: MAT_dihedral
"tss.c", line 1418: warning: implicit function declaration: MAT_helix
"tss.c", line 1470: warning: implicit function declaration: MAT_orient
"tss.c", line 1553: warning: implicit function declaration: MAT_concat
ar rv libsym.a symop.o matop.o tss.o
a - symop.o
a - matop.o
a - tss.o
ar: creating libsym.a
ranlib libsym.a
cp -p libsym.a /xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c matextract.nab
"matextract.c", line 31: warning: old-style declaration or incorrect type
for: main
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o matextract
matextract.o libsym.a
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c matgen.nab
"matgen.c", line 371: warning: old-style declaration or incorrect type for:
main
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o matgen matgen.o
libsym.a
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c matmerge.nab
"matmerge.c", line 54: warning: old-style declaration or incorrect type for:
main
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o matmerge
matmerge.o libsym.a
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c matmul.nab
"matmul.c", line 44: warning: old-style declaration or incorrect type for:
main
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o matmul matmul.o
libsym.a
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c transform.nab
"transform.c", line 49: warning: old-style declaration or incorrect type
for: main
"transform.c", line 76: warning: argument #3 is incompatible with prototype:
        prototype: pointer to double :
"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/include/nabcode.h", line 205
        argument : pointer to array[3] of double
"transform.c", line 79: warning: argument #3 is incompatible with prototype:
        prototype: pointer to double :
"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/include/nabcode.h", line 200
        argument : pointer to array[3] of double
"transform.c", line 115: warning: argument #2 is incompatible with
prototype:
        prototype: pointer to double :
"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/include/nabcode.h", line 218
        argument : pointer to array[3] of double
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o transform
transform.o libsym.a
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c tss_init.nab
"tss_init.c", line 18: warning: old-style declaration or incorrect type for:
main
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o tss_init
tss_init.o libsym.a
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c tss_main.nab
"tss_main.c", line 218: warning: old-style declaration or incorrect type
for: main
"tss_main.c", line 300: warning: argument #3 is incompatible with prototype:
        prototype: pointer to double :
"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/include/nabcode.h", line 205
        argument : pointer to array[3] of double
"tss_main.c", line 301: warning: argument #2 is incompatible with prototype:
        prototype: pointer to double :
"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/include/nabcode.h", line 218
        argument : pointer to array[3] of double
"tss_main.c", line 302: warning: argument #3 is incompatible with prototype:
        prototype: pointer to double :
"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/include/nabcode.h", line 200
        argument : pointer to array[3] of double
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o tss_main
tss_main.o libsym.a
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -c tss_next.nab
"tss_next.c", line 41: warning: old-style declaration or incorrect type for:
main
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o tss_next
tss_next.o libsym.a
cp -p matextract matgen matmerge matmul \
        transform tss_init tss_main \
        tss_next /xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin
cp -p libsym.a /xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib
(cd antechamber && make install )
cc -DSYSV -DBINTRAJ -c
-DDATDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/dat"'
-DBINDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin"' am1bcc.c
cc am1bcc.o -lm -o am1bcc
cc -DSYSV -DBINTRAJ -c
-DDATDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/dat"'
-DBINDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin"' acdoctor.c
cc acdoctor.o -lm -o acdoctor
cc -DSYSV -DBINTRAJ -c
-DDATDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/dat"'
-DBINDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin"'
antechamber.c
cc antechamber.o -lm -o antechamber
cc -DSYSV -DBINTRAJ -c
-DDATDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/dat"'
-DBINDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin"' atomtype.c
cc atomtype.o -lm -o atomtype
cc -DSYSV -DBINTRAJ -c
-DDATDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/dat"'
-DBINDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin"' bondtype.c
cc -DSYSV -DBINTRAJ -c
-DDATDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/dat"'
-DBINDIR='"/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin"'
ncsu-penalties.c
"ncsu-penalties.c", line 148: warning: statement not reached
cc ncsu-penalties.o bondtype.o -o bondtype
Undefined first referenced
 symbol in file
fabs bondtype.o
ld: fatal: Symbol referencing errors. No output written to bondtype
*** Error code 1
make: Fatal error: Command failed for target `bondtype'
Current working directory
/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/src/antechamber
*** Error code 1
make: Fatal error: Command failed for target `install'

I don't know what the the root of this is

On Mon, Mar 16, 2009 at 4:12 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Mon, Mar 16, 2009, Per Jr. Greisen wrote:
> >
> > /xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin/nab -o matgen matgen.o
> > libsym.a
> > Undefined first referenced
> > symbol in file
> > __mt_WorkSharing_rtc_
>
> Looks like you have asked for some sort of parallel configuration(?).
> Try a completely vanilla, serial, compile first.
>
> ...dac
>
>
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