AMBER Archive (2008)

Subject: AMBER: AMBER10 installation question

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Mon Nov 17 2008 - 21:20:14 CST

Dear all,

      I am trying to install AMBER10 and the corresponding ambertools. As in the INSTALLATION, the ambertools was installed successfully with the parameter: ./configure_at icc
But when moving to the second stage to install AMBER10 with the parameter: ./configure_amber ifort, the installation halted with the following error message:

-------
make[3]: Entering directory `/opt/amber10/src/netcdf/src/ncgen'
depbase=`echo main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -m32 -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -MT main.o -MD -MP -MF "$depbase.Tpo" -c -o main.o main.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
/bin/sh ../libtool --tag=CC --mode=link gcc -m32 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -L/opt/fftw/fftw3.1.2/lib -o ncgen main.o load.o ncgentab.o escapes.o getfill.o init.o genlib.o ../libsrc/libnetcdf.la
gcc -m32 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -o ncgen main.o load.o ncgentab.o escapes.o getfill.o init.o genlib.o -L/opt/fftw/fftw3.1.2/lib ../libsrc/.libs/libnetcdf.a
ncgentab.o(.text+0x5e8): In function `yyparse':
: undefined reference to `__intel_f2int'
ncgentab.o(.text+0x60c): In function `yyparse':
: undefined reference to `__intel_f2int'
ncgentab.o(.text+0x631): In function `yyparse':
: undefined reference to `__intel_f2int'
ncgentab.o(.text+0x655): In function `yyparse':
: undefined reference to `__intel_f2int'
ncgentab.o(.text+0x6e2): In function `yyparse':
: undefined reference to `__intel_f2int'
ncgentab.o(.text+0x706): more undefined references to `__intel_f2int' follow
ncgentab.o(.text+0xb88): In function `yyparse':
: undefined reference to `_intel_fast_memset'
ncgentab.o(.text+0x2552): In function `yylex':
: undefined reference to `__intel_f2int'
ncgentab.o(.text+0x2c66): In function `yy_get_next_buffer':
: undefined reference to `_intel_fast_memcpy'
ncgentab.o(.text+0x34c9): In function `yy_scan_bytes':
: undefined reference to `_intel_fast_memcpy'
ncgentab.o(.text+0x3690): In function `yy_scan_string':
: undefined reference to `_intel_fast_memcpy'
genlib.o(.text+0x2bfd): In function `cstrstr.':
: undefined reference to `_intel_fast_memcpy'
genlib.o(.text+0x3f19): In function `fstrstr.':
: undefined reference to `_intel_fast_memcpy'
collect2: ld returned 1 exit status
make[3]: *** [ncgen] Error 1
make[3]: Leaving directory `/opt/amber10/src/netcdf/src/ncgen'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/opt/amber10/src/netcdf/src'
make[1]: *** [netcdf.mod] Error 2
make[1]: Leaving directory `/opt/amber10/src/sander'
make: *** [serial] Error 2
-------------

Could someone please tell me how to fix this problem?
Any suggestion is greatly appreciated.

Thanks for the time.
Have a nice day.

-----
Jeffrey

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http://cn.mail.yahoo.com

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