Mark pointed this issue out earlier today. This seems to be happening
because icc can't find the fortran routines it needs. Adding a -L flag with
the fortran compiler library directory, something like:
icc -o ptraj main.o rdparm.o dispatch.o help.o utility.o second.o io.o
trajectory.o netcdf_ptraj.o parallel_ptraj.al.o ptraj.o actions.o analyze.o
thermo.o pubfft.o cluster.o clusterLib.o* -L/opt/intel/fce/10.1.015/lib* ...
in the FLIBS variable seems to do the trick. Its strange because even when
you have the correct library directory in LD_LIBRARY PATH it still won't
find it unless it is explicitly listed with -L. I'm not sure why this
happened in the first place or what the best way to correct this in the
Makefile/configure script is, but its a recent development.
-Dan
On Thu, Mar 4, 2010 at 4:12 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> ifort -V
> Intel(R) Fortran Compiler for applications running on Intel(R) 64, Version
> 10.1 Build 20080801 Package ID: l_fc_p_10.1.018
>
> icc -V
> Intel(R) C Compiler for applications running on Intel(R) 64, Version 10.1
> Build 20080801 Package ID: l_cc_p_10.1.018
>
> ./configure intel
> make -f Makefile_at -j8
>
> Crashes at ptraj with:
>
> icc -o ptraj main.o rdparm.o dispatch.o help.o utility.o second.o io.o
> trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o rms.o
> display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o
> thermo.o pubfft.o cluster.o clusterLib.o
> /home/rcw/cvs_checkouts/amber11/lib/libpdb.a
> /home/rcw/cvs_checkouts/amber11/lib/arpack.a
> -L/opt/intel/mkl/10.1.1.019//lib/em64t -Wl,--start-group
> /opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_intel_lp64.a
> /opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_sequential.a
> /opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_core.a<http://10.1.1.019//lib/em64t/libmkl_intel_lp64.a%0A/opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_sequential.a%0A/opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_core.a>-Wl,--end-group -lpthread
> -lifport -lifcore -lsvml ../netcdf/lib/libnetcdf.a -lm
> thermo.o(.text+0x475): In function `thermo_':
> : undefined reference to `for_write_seq_fmt'
> thermo.o(.text+0x4c0): In function `thermo_':
> ...
> ...
> ...
>
> Probably missing a bunch of libraries here.
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> 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 Thu Mar 04 2010 - 13:30:05 PST
