AMBER Archive (2008)

Subject: Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64)

From: wl2290_at_columbia.edu
Date: Tue Dec 30 2008 - 11:54:58 CST

Dear Dr. Case and All,

I have been trying to "make parallel" of amber 10 on my linux
computer. I got the compiling message:
cpp -traditional -I/opt/amber10/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI constants.f > _constants.f
/opt/amber10/bin/mpif77 -c -O3 -fno-range-check -fno-second-underscore
-ffree-form -o constants.o _constants.f
f771: error: unrecognized option `-fno-range-check'
make[1]: *** [constants.o] Error 1

I have set PATH to f771, mpif77 and mpirun, and LD_LIBRARY_PATH to libg2c:

set PATH = ( $PATH
/guam.raid.home/sbgrid/programs/i386-linux/mpich/2-1.0.3/bin /usr/bin
/bin /usr/X11R6/bin /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5 )

setenv LD_LIBRARY_PATH
/guam.raid.home/sbgrid/programs/i386-linux/mpich/2-1.0.3/lib:/usr/lib:/usr/lib64:/usr/X11R6/lib64:/usr/X11R6/lib

More information on my computer:
g77 -v
Reading specs from /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/specs
Configured with: ../configure --enable-threads=posix --prefix=/usr
--with-local-prefix=/usr/local --infodir=/usr/share/info
--mandir=/usr/share/man --enable-languages=c,f77 --disable-checking
--libdir=/usr/lib64 --disable-libgcj --with-slibdir=/lib64
--with-system-zlib --enable-shared --enable-__cxa_atexit
x86_64-suse-linux
Thread model: posix
gcc version 3.3.5 20050117 (prerelease) (SUSE Linux)

I was hoping you could help me.

Thanks!

Wen

Quoting "David A. Case" <case_at_biomaps.rutgers.edu>:

> On Mon, Dec 22, 2008, wl2290_at_columbia.edu wrote:
>>
>> ./configure_amber -static gfortran -> successful
>
> Great...I'm glad things are working. At the worst, it looks like in
> some circumstances you have problems compiling elsize:
>
>> g++ -c -DBINTRAJ -I../netcdf/include -o elsize.o elsize.cc
>> make[1]: Leaving directory `/opt/amber10/src/etc'
>
> Above it looks like it worked. Then in the next attachment:
>
>> ...
>> ...
>
> It's not easy to see what command is being executed for the following
> types of errors.
>
>> /usr/include/c++/4.1.2/bits/ios_base.h: In member function ???void
>> std::ios_base::_Callback_list::_M_add_reference()???:
>> make[1]: *** [elsize.o] Error 1
>
> But, in this run, elsize was not correctly made.
>
> Good news, however: (1) The first time it worked, so use that; (2)
> elsize is very rarely used anyway, so it's likely you will never miss
> it.
>
> For Amber11, we have rewritten elsize as a C program which is a lot more
> portable. [It's not the language per se, but it is true (in my
> experience) that C++ can be abused to give code that is both
> compiler-dependent and which gives compiler errors in other environments
> that are very hard to track down.]
>
> ...dac
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