[AMBER-Developers] Problem installing Amber12

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Wed, 10 Oct 2012 21:22:42 -0400

Hi all,

I am trying to install amber12 using pgi 11.5. I am first trying to install
serial and try to go parallel. Following is my config.log for the serial
installation.

Checking for updates...
AmberTools13 is up to date
Amber13 is up to date

Searching for python2... Found python2.7: /usr/local/bin/python2.7

Obtaining the PGI suite version:
      pgcc -V
The version is 12.6-0

Testing the pgcc compiler:
     pgcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK

Testing the pgf90 compiler:
     pgf90 -O1 -o testp testp.f
OK

Testing mixed C/Fortran compilation:
     pgcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
testp.c
     pgf90 -O1 -c -o testp.f.o testp.f
     pgcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
testp.f.o -pgf90libs
OK

Testing pointer size:
     pgcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
test_pointer_size.c
Detected 64 bit operating system.

Testing flex: OK

Configuring NetCDF (may be time-consuming)...

    NetCDF configure succeeded.

Checking for zlib: OK

Checking for libbz2: PGC-F-0206-Can't find include file bzlib.h (testp.c: 2)
PGC/x86-64 Linux 12.6-0: compilation aborted
./configure2: line 1884: ./testp: No such file or directory
Not found.

Configuring fftw-3.3 for mdgx (may be time-consuming)...

    fftw-3.3 configure succeeded.

The configuration file, config.h, was successfully created.

The next step is to type 'make install'

Cleaning the src directories. This may take a few moments.
Configure complete.

Then when I run make_install I get the following error (I have attached my
whole make_install.log file herewith).

"/wsu/usr/pgi/linux86-64_2.6/11.5/include/CC/stl/_function_base.h", line
76: error:
          no operator "<" matches these operands
            operand types are: const ClusterNode < const ClusterNode
    bool operator()(const _Tp& __x, const _Tp& __y) const { return __x <
__y; }
                                                                       ^
          detected during:
            instantiation of "bool std::less<_Tp>::operator()(const _Tp &,
                      const _Tp &) const [with _Tp=ClusterNode]" at line 165
                      of

"/wsu/usr/pgi/linux86-64_2.6/11.5/include/CC/stl/_list.c"
            instantiation of "void std::_S_merge(std::list<_Tp, _Alloc> &,
                      std::list<_Tp, _Alloc> &, _StrictWeakOrdering) [with
                      _Tp=ClusterNode, _Alloc=std::allocator<ClusterNode>,
                      _StrictWeakOrdering=std::less<ClusterNode>]" at line
191
                      of

"/wsu/usr/pgi/linux86-64_2.6/11.5/include/CC/stl/_list.c"
            instantiation of "void std::_S_sort(std::list<_Tp, _Alloc> &,
                      _StrictWeakOrdering) [with _Tp=ClusterNode,
                      _Alloc=std::allocator<ClusterNode>,
                      _StrictWeakOrdering=std::less<ClusterNode>]" at line
505
                      of

"/wsu/usr/pgi/linux86-64_2.6/11.5/include/CC/stl/_list.h"
            instantiation of "void std::list<_Tp, _Alloc>::sort() [with
                      _Tp=ClusterNode, _Alloc=std::allocator<ClusterNode>]"
at
                      line 58 of "ClusterList.cpp"

1 error detected in the compilation of "ClusterList.cpp".
make[3]: *** [ClusterList.o] Error 2
make[3]: Leaving directory
`/wsu/home/ej/ej02/ej0271/amber12/AmberTools/src/cpptraj/src'
make[2]: *** [install] Error 2
make[2]: Leaving directory
`/wsu/home/ej/ej02/ej0271/amber12/AmberTools/src/cpptraj'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/wsu/home/ej/ej02/ej0271/amber12/AmberTools/src'
make: *** [install] Error 2

Could anyone please give me suggestions to prevent this problem?

Thank you

Sajeewa Dewage


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Received on Wed Oct 10 2012 - 18:30:03 PDT
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