AMBER Archive (2008)

Subject: Re: AMBER: Amber10 installation error

From: juyong Lee (drfaust23_at_gmail.com)
Date: Thu May 01 2008 - 23:52:10 CDT

Dear, Ross

Thanks for you immediate response.
And I'm sorry for my ambiguous question. The first error message occurred
when I tried to
complie AmberTools with icc(ver 8.1)
I generated config.h by ./configure_at icc command and It was successful.
However when I tried make -f Makefile_at install , It showed the following
error logs.......

====================
../../freelib/boost/format/internals.hpp: In method `void
boost::io::detail::stream_format_state<Ch,
Tr>::apply_on (basic_ios<Ch, Tr> &, locale_t *) const [with Ch = char, Tr =
string_char_traits<char>]':
../../freelib/boost/format/feed_args.hpp:134: instantiated from
`boost::io::detail::put (T, const boost::io::detail::format_item<Ch, Tr,
Alloc> &, typename boost::basic_format<Ch, Tr, Alloc>::string_type &,
typename boost::basic_format<Ch, Tr, Alloc>::internal_streambuf_t &,
locale_t *) [with Ch = char, Tr = string_char_traits<char>, Alloc =
__default_alloc_template<true, 0>, T = double &]'
../../freelib/boost/format/internals_fwd.hpp:242: instantiated from
`boost::io::detail::distribute (boost::basic_format<Ch, Tr, Alloc> &, T)
[with Ch = char, Tr = string_char_traits<char>, Alloc =
__default_alloc_template<true, 0>, T = double &]'
../../freelib/boost/format/internals_fwd.hpp:251: instantiated from
`boost::io::detail::feed (boost::basic_format<Ch, Tr, Alloc> &, T) [with Ch
= char, Tr = string_char_traits<char>, Alloc =
__default_alloc_template<true, 0>, T = double &]'
../../freelib/boost/format/format_class.hpp:68: instantiated from
`boost::basic_format<Ch, Tr, Alloc>::operator% (T &) [with T = double, Ch =
char, Tr = string_char_traits<char>, Alloc = __default_alloc_template<true,
0>]'
/usr/include/g++-3/iostream.h:106: instantiated from here
../../freelib/boost/format/internals.hpp:106: warning: unused parameter
`locale_t *loc_default'
make[3]: *** [numvec.o] Error 1
===================================

In addtion, now I'm asking system manager to upgrade gcc to newer version,
also.

In summary, I can't compile AmberTools using icc because it make a compile
time error.
About gcc, I realized that problem with -m32 option is caused by obsolescent
version and I asked administrator to fix it. :)

So, my question is what seems to be the problem of compiling amber10 using
icc :) ?

Thanks in advance,
Juyong

2008/5/2 Ross Walker <ross_at_rosswalker.co.uk>:

> Hi Juyong,
>
>
>
> Your compilers are very old – especially gcc-2.96. You need to update your
> compilers. Ideally you want at least gcc-3.4. If it is difficult to get the
> cluster software upgraded then you could try compiling statically on your
> local machine and then copying thing over – I think this should work, at
> least for amber tools.
>
>
>
> All the best
>
> Ross
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *juyong Lee
> *Sent:* Thursday, May 01, 2008 7:28 PM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: Amber10 installation error
>
>
>
>
> Dear, amber developers
>
> Hi, I'm trying to install amber10 in the linux cluster.
> Though I succeded in installing single CPU version amber10 in my desktop,
> I encounted following error message while compiling AmberTools in the
> cluster.
>
> ======================================
> /usr/include/g++-3/iostream.h:106: instantiated from here
> ../../freelib/boost/format/internals.hpp:106: warning: unused parameter
> `locale_t *loc_default'
> ======================================
>
> Another problem is that ./configure_at -mpi gcc command also occurs the
> error.
> It says that -m32 option is not valid.
>
> Could you give me a hint for these problems?
> I couldn't find the thread about this kind of the problems. :)
>
> Specification of the cluster is as following :
> OS : Linux lg03 2.4.20-28.7smp #1 SMP Thu Dec 18 11:18:31 EST 2003 i686
> unknown
> ifort version : Version 8.1
> gcc version 2.96
> cpu : xeon 2.8GHz
>
> --
> Lee, Juyong
> Lab of Computational biology
> Ph.D. Candidate, Department of chemistry
> Seoul National University, Seoul, Korea.
>
>
> 

-- 
Lee, Juyong
Lab of Computational biology
Ph.D. Candidate, Department of chemistry
Seoul National University, Seoul, Korea.
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