Hannes:
You may try to add stl library include search path.
pgCC -I/usr/local/pgi/linux86-64/5.2/include/ -o bondtype.o bondtype.C
On 10/24/05, Hannes Barsch <hbarsch.physik.uni-bielefeld.de> wrote:
>
> Dear AMBER community!
>
> On a newly installed Opteron system I am not able to compile AMBER 8 using
> the Portland Group compilers. I use the same settings as in a former
> install - the only differences are the version of PGI (now 5.2.4, before
> 5.2.2) and the Rocks-OS version (now 4.0.0 (based on CentOS 4.0), before
> 3.2.0 (based on RHEL 3.0)). I also included Bob Duke's configuration
> updates
> for PMEMD now, but the compilation error occurs already earlier at the
> compilation of bondtype.C in the antechamber module:
>
> pgcc -O2 atomtype.o -lm -o atomtype
> pgCC -c -o bondtype.o bondtype.C
> "/usr/local/pgi/linux86-64/5.2/include/CC/stl/_bvector.h", line 86:
> error:
> identifier "__CHAR_BIT__" is undefined
> if (_M_offset++ == __WORD_BIT - 1) {
> ^
>
> "/usr/local/pgi/linux86-64/5.2/include/CC/stl/_bvector.h", line 94:
> error:
> identifier "__CHAR_BIT__" is undefined
> _M_offset = __WORD_BIT - 1;
> ^
>
> "/usr/local/pgi/linux86-64/5.2/include/CC/stl/_bvector.h", line 106:
> error:
> identifier "__CHAR_BIT__" is undefined
> _M_p += __n / __WORD_BIT;
> ^
>
> "/usr/local/pgi/linux86-64/5.2/include/CC/stl/_bvector.h", line 116:
> error:
> identifier "__CHAR_BIT__" is undefined
> return __WORD_BIT * (_M_p - __x._M_p) + _M_offset - __x._M_offset;
> ^
>
> 4 errors detected in the compilation of "bondtype.C".
> make[1]: *** [bondtype.o] Error 2
> make[1]: Leaving directory
> `/usr/src/redhat/BUILD/amber-8/src/antechamber'
> make: *** [serial] Error 2
> error: Bad exit status from /var/tmp/rpm-tmp.72495 (%build)
>
> The /usr/local/pgi/linux86-64/5.2/include/CC/stl/_bvector.h does not
> differ
> from the header file of the older PGI installation.
>
> Has anyone compiled amber with this combination of HW / OS / compilers and
> realized similar compile errors? Does anybody know why this error might
> happen? If so, please give me a hint!
> Thanks for your help! Regards,
>
> Hannes Barsch
>
>
>
> ____________________________________________________________________________
> _
>
> The RPM spec file looks like this:
>
> Summary: AMBER 8
> Name: amber
> Version: 8
> Release: 0
> Copyright: University of California
> Group: Sciences/Chemistry
> Source0: %{name}-%{version}.tar.gz # amber 8 source from CD
> Source1: %{name}-%{version}.pmemd.tar.gz # new configuration files from
> http://amber.scripps.edu/pmemd-mar05.html
> Source2: %{name}-%{version}.local.tar.gz # configuration files for
> opterons/PGI from http://www.pgroup.com/resources/amber/amber8_pgi52.htm
> Patch0: %{name}-%{version}.patch0 # amber bugfixes from
> http://amber.scripps.edu/bugfixes/8.0/bugfix.all
> Patch1: %{name}-%{version}.patch1 # PGI fixes adopted from
> http://www.pgroup.com/resources/amber/amber8_pgi52.htm
> URL: http://amber.scripps.edu
> Packager: Hannes Barsch, University of Bielefeld
> AutoReq: no
> Requires: /bin/csh, /bin/sh, /bin/sh, /bin/sh, /usr/bin/perl,
> libICE.so.6()(64bit), libSM.so.6()(64bit), libX11.so.6()(64bit),
> libXext.so.6()(64bit), libXt.so.6()(64bit), libc.so.6()(64bit),
> libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3)(64bit),
> libgm.so.0()(64bit), libm.so.6()(64bit), libm.so.6(GLIBC_2.2.5)(64bit),
> libpthread.so.0()(64bit), libpthread.so.0(GLIBC_2.2.5)(64bit), perl(CPin),
> perl(Carp), perl(Data::Dumper), perl(Getopt::Long), perl(IO::File),
> perl(lib), perl(strict), rpmlib(CompressedFileNames)<= 3.0.4-1,
> rpmlib(PayloadFilesHavePrefix) <= 4.0-1
>
>
> %description
> Amber refers to two things: a set of molecular mechanical force fields
> for the simulation of biomolecules (which are in the public domain, and
> are
> used in a variety of simulation programs); and a package of molecular
> simulation programs which includes source code and demos.
>
> %prep
> %setup -q
> %setup -qDTb 1
> %setup -qDTb 2
> %patch -P 0
> %patch -P 1
>
> %build
> PATH=/usr/local/pgi/linux86-64/5.2/bin:$PATH
> export PGI=/usr/local/pgi
> export AMBERHOME=$RPM_BUILD_DIR/%{name}-%{version}
> export GM_LIBDIR=/opt/gm/lib
> cd $AMBERHOME/src
> ./configure -nopar -opteron -acml -lapack pgf90
> make -e YACC="/usr/bin/bison -y" X11LIBDIR="lib64" serial
> cd pmemd
> ./new_configure linux_opteron pgf90 nopar
> make install
> cd $AMBERHOME/exe
> mv pmemd pmemd.serial
> mv sander sander.serial
> mv sander.LES sander.LES.serial
>
> cd $AMBERHOME/src
> ./configure -mpich -opteron -acml -lapack pgf90
> make -e YACC="/usr/bin/bison -y" X11LIBDIR="lib64" parallel
> cd pmemd
> ./new_configure linux_opteron pgf90 mpich
> make install
>
> [...]
>
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Received on Mon Oct 24 2005 - 16:53:01 PDT
