Hi everyone,
it looks like the .o file that has *_pca* subroutines is absent from
the linker command line; most probably a typo in the Makefile [case
likely matters for file names, but everything can be expected].
HTH,
Volodymyr
On Mon, Jun 20, 2011 at 6:59 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi All,
>
> Can anyone build sander from the git tree successfully right now?
>
> cd $AMBERHOME/AmberTools/src/
> ./configure gnu
> make install
> cd ../../src
> make install
>
> ...
> ...
> ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o
> ncsu-cftree.o ncsu-colvar.o ncsu-colvar-math.o ncsu-colvar-type.o
> ncsu-colvar-utils.o ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-COM_ANGLE.o
> ncsu-cv-COM_DISTANCE.o ncsu-cv-COM_TORSION.o ncsu-cv-COS_OF_DIHEDRAL.o
> ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o ncsu-cv-LCOD.o ncsu-cv-MULTI_RMSD.o
> ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o ncsu-cv-R_OF_GYRATION.o
> ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o ncsu-pmd-hooks.o ncsu-rmsd.o
> ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-smd-hooks.o ncsu-umbrella.o
> ncsu-utils.o ncsu-value.o mt19937.o \
> /home/rcw/amber11_patch/amber/lib/libFpbsa.a
> /home/rcw/amber11_patch/amber/lib/arpack.a -Wl,--start-group
> /opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_intel_lp64.a
> /opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_sequential.a
> /opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_core.a -Wl,--end-group
> -lpthread ../../AmberTools/src/lib/nxtsec.o \
> ../../AmberTools/src/lib/sys.a
> /home/rcw/amber11_patch/amber/lib/libnetcdf.a
> ncsu-colvar.o: In function `__ncsu_colvar__colvar_print':
> _ncsu-colvar.f:(.text+0xb06): undefined reference to
> `__ncsu_cv_pca__print_details'
> ncsu-colvar.o: In function `__ncsu_colvar__colvar_cleanup':
> _ncsu-colvar.f:(.text+0xbe1): undefined reference to
> `__ncsu_cv_pca__colvar_cleanup'
> ncsu-colvar.o: In function `__ncsu_colvar__colvar_mdread':
> _ncsu-colvar.f:(.text+0x10b5): undefined reference to
> `__ncsu_read_pca__read_refcrd'
> _ncsu-colvar.f:(.text+0x12a8): undefined reference to
> `__ncsu_read_pca__read_evec'
> _ncsu-colvar.f:(.text+0x1497): undefined reference to
> `__ncsu_read_pca__read_avgcrd'
> _ncsu-colvar.f:(.text+0x175f): undefined reference to
> `__ncsu_read_pca__read_index'
> ncsu-colvar.o: In function `__ncsu_colvar__colvar_value':
> _ncsu-colvar.f:(.text+0x129): undefined reference to
> `__ncsu_cv_pca__colvar_value'
> ncsu-colvar.o: In function `__ncsu_colvar__colvar_force':
> _ncsu-colvar.f:(.text+0x19b): undefined reference to
> `__ncsu_cv_pca__colvar_force'
> ncsu-colvar.o: In function `__ncsu_colvar__colvar_bootstrap':
> _ncsu-colvar.f:(.text+0x244b): undefined reference to
> `__ncsu_cv_pca__colvar_bootstrap'
> collect2: ld returned 1 exit status
> make[1]: *** [sander] Error 1
> make[1]: Leaving directory `/home/rcw/amber11_patch/amber/src/sander'
> make: *** [serial] Error 2
>
> Comments?
>
> ncsu_cv_PCA is present (does case matter here?).
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
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Received on Mon Jun 20 2011 - 20:00:03 PDT
