Hi Jason,
Thank you for your kind suggestions.
>
> These are architecture issues arising from the new 64-bit support in snow
> leopard. Look at the config.h and config_amber.h and remove all instances
> of "-m32" or "-march=i686" or i386, or anything else that looks like it
> could be implying a 32-bit architecture (since uname -m returns i386 for Mac
> OS X 10.6 unless you boot into the 64-bit kernel).
I took -m32 out from config.h and make proceeded, before I get another error..
------------------------------------------------------------------------------------------------------------
[isa5-dhcp-96-220:~/apps/amber10/src] kenske% make -f Makefile_at
=======================================
================MANY LINES============
=======================================
gcc -c -DBINTRAJ -o clusterLib.o clusterLib.c
gcc -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.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 /Users/kenske/apps/amber10/lib/libpdb.a /Users/kenske/apps/amber10/lib/libsym.a /Users/kenske/apps/amber10/lib/arpack.a /Users/kenske/apps/amber10/lib/lapack.a /Users/kenske/apps/amber10/lib/blas.a /Users/kenske/apps/amber10/lib/f2c.a ../netcdf/lib/libnetcdf.a -lm
ld: warning: in ../netcdf/lib/libnetcdf.a, file was built for unsupported file format which is not the architecture being linked (x86_64)
Undefined symbols:
"_nc_enddef", referenced from:
_ptrajOutputCoordinates in ptraj.o
"_nc_open", referenced from:
_checkCoordinates in ptraj.o
_ptrajPreprocessInputCoordinates in ptraj.o
=========================================================
================MANY LINES for undefined symbols============
=========================================================
"_nc_put_vara_text", referenced from:
_ptrajOutputCoordinates in ptraj.o
_ptrajOutputCoordinates in ptraj.o
_ptrajOutputCoordinates in ptraj.o
"_nc_put_vara_double", referenced from:
_ptrajOutputCoordinates in ptraj.o
_ptrajOutputCoordinates in ptraj.o
"_nc_set_fill", referenced from:
_ptrajOutputCoordinates in ptraj.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [rdparm] Error 1
make: *** [install] Error 2
------------------------------------------------------------------------------------------------------------
> Amber10/AmberTools 1.2 procedure is quite a bit different from Amber11 and
> AmberTools 1.4. However, AmberTools 1.4 is a free (open source) download
> from ambermd.org, so I would recommend downloading that version of
> AmberTools. The seg-fault you're seeing above is from AmberTools 1.2, and I
> think that may have been fixed in the most recent version (1.4). Try
> installing AmberTools 1.4 and seeing if that error goes away when you test
> that installation.
AmberTools1.4 extract into amber11 directory and I was not sure how to merge it with AMBER10,
and was suggested to use AmberTools1.2... Maybe I should just get AMBER11...
Kensuke Nakamura
Nara Institute of Science and Technology
Graduate School of Information Science
8916-5 Takayama, Ikoma, Nara 630-0101
JAPAN
TEL: +81-743-72-5257 (Fax:5258)
E-mail: kensuke-nm.is.naist.jp
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Received on Thu May 20 2010 - 19:00:03 PDT
