[AMBER] reply： Amber12 compile with "intel" err.

From: javacfish <javacfish.yahoo.com.cn>
Date: Sun, 15 Apr 2012 03:57:36 +0800 (CST)

Hi all,

I had found the final answer, maybe the Modeller (http://salilab.org/modeller/) software conflict with amber Netcdf. When I comment the modeller path and library path, the compile err will not happen again.

I am not sure what is the exactly reason, but I had solved it.

javacfish 



________________________________
 
  
What version of the intel compiler are you using?

I've used Intel 11.1.069, 11.1.072, and 12.1.0 and I've never seen this
issue.

On Sat, Apr 14, 2012 at 10:48 AM, javacfish <javacfish.yahoo.com.cn> wrote:

> Dear all,
>
> I follow the steps to build amber 12 as below:
>
> 1. ./configure intel
>
> Then
> 2. make install
>
> the err happen:
>
>
> **************************************************************************************************************
> cd AmberTools/src && make install
> make[1]: Entering directory `/home/bai/soft/amber12/AmberTools/src'
> cd netcdf/src && make && make -j 1 install
> make[2]: Entering directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src'
> make  all-recursive
> make[3]: Entering directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src'
> Making all in f90
> make[4]: Entering directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src/f90'
> make[4]: Nothing to be done for `all'.
> make[4]: Leaving directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src/f90'
> Making all in fortran
> make[4]: Entering directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src/fortran'
> make  all-am
> make[5]: Entering directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src/fortran'
> depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
> if /bin/sh ../libtool --tag=CC --mode=compile icc -DHAVE_CONFIG_H -I. -I.
> -I.. -I.    -I../libsrc  -DNDEBUG  -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE  -MT fort-attio.lo -MD -MP -MF "$depbase.Tpo" -c -o
> fort-attio.lo fort-attio.c; \
> then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit
> 1; fi
>  icc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-attio.lo -MD -MP -MF
> .deps/fort-attio.Tpo -c fort-attio.c -o fort-attio.o
> ncfortran.h(26): catastrophic error: cannot open source file
> "NF_INT_IS_C_... not defined"
>  #  include "NF_INT_IS_C_... not defined"
>                                            ^
>
> compilation aborted for fort-attio.c (code 4)
> make[5]: *** [fort-attio.lo] Error 1
> make[5]: Leaving directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src/fortran'
> make[4]: *** [all] Error 2
> make[4]: Leaving directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src/fortran'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src'
> make[2]: *** [all] Error 2
> make[2]: Leaving directory
> `/home/bai/soft/amber12/AmberTools/src/netcdf/src'
> make[1]: *** [/home/bai/soft/amber12/include/netcdf.mod] Error 2
> make[1]: Leaving directory `/home/bai/soft/amber12/AmberTools/src'
> make: *** [install] Error 2
>
> *******************************************************************************************************
>
> So how do I solve this kind of problem?
>
> Thanks everyone~
>
> Javacfish~
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 14 2012 - 13:00:05 PDT
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