Re: namd 2.5 compilation error

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Sep 29 2008 - 14:45:44 CDT

On Mon, 29 Sep 2008, Dong Xu wrote:

DX> I think I will try it. The hurdle is the cluster uses myrinet and thus
DX> mpich-gm library. I have icc/ifort installed in my home dir. Not sure
DX> how difficult to compile mpich-gm with the intel compilers. Any
DX> recommendations?

you don't _have_ to compile MPICH-gm. as i was mentioning before,
you can just as easily compile OpenMPI (just add --with-gm=/path/to/gm
to configure). i've done both and in general found using OpenMPI
the most convenient. unlike MPICH, OpenMPI can be compiled with the
"native" gcc/g++/gfortran compilers and can be made to use other
compilers via environment variables.

the fact that your base operating system is quite outdated will
be a problem for any compiler and requires a careful eye towards
each compilation. i hope the machine is worth the effort...

cheers,
   axel.

DX>
DX> Dong
DX>
DX> >
DX> > DX> namd using gcc? The gcc version is 2.95, I'm not sure if it's too
DX> > DX> outdated?
DX> >
DX> > gcc 2.95 is some unofficial redhat version and generally discouraged
DX> > to be used for anything, not to mention _very_ old.
DX> > when trying to compile software on such old installations, one always
DX> > has to consider whether it is actually worth the effort. usually, the
DX> > hardware is slow as well...
DX> >
DX> > DX> > DX>
DX> > DX> > DX> When I compile namd using Linux-i686-pgCC.arch, I got the following
DX> > DX> > DX> error. Looks like there are some issues with tcl library libtcl8.3.a.
DX> > DX> >
DX> > DX> > it looks like the tcl library has been compiled with a gcc that
DX> > DX> > was newer than the gcc that the pgi compiler runtime was compiled with.
DX> > DX> > you need to recompiled the tcl library with your pgi or better yet
DX> > DX> > compile NAMD with gcc/g++.
DX> > DX>
DX> > DX> Yes, I also realized that I need to recompile tcol if non-gcc
DX> > DX> compilers are used.
DX> >
DX> > no, it is not about non-gcc compilers. it is about the version of
DX> > libc and particularly the header files that go with it that have
DX> > to match. PGI's c/c++ compilers used to be very outdated.
DX> >
DX> > cheers,
DX> > axel.
DX> >
DX> > DX>
DX> > DX> Thanks!
DX> > DX>
DX> > DX> -DX
DX> > DX>
DX> > DX> > DX>
DX> > DX> > DX> Any help will be highly appreciated.
DX> > DX> > DX>
DX> > DX> > DX> -DX
DX> > DX> > DX>
DX> > DX> > DX> charmc> ----------- Module dependency search ------------
DX> > DX> > DX> charmc> ----------- Module dependency search complete ------------
DX> > DX> > DX> Adding registration for module NeighborLB
DX> > DX> > DX> Adding registration for module commlib
DX> > DX> > DX> charmc: Executing mpiCC -D__CHARMC__=1 -c moduleinit14691.C -o moduleinit14691.o
DX> > DX> > DX> charmc: Executing mpiCC -L/home/dong/namd_lib/lib -L/home/dong/tcl/lib
DX> > DX> > DX> -L/home/dong/namd_lib/lib -L/home/dong/fftm
DX> > DX> > DX> C++ prelinker: executing: /usr/pgi/linux86/bin/pgCC
DX> > DX> > DX> -I/home/dong/NAMD_2.6_Source/charm-5.9/mpi-linux/include -DCMC
DX> > DX> > DX> "/usr/include/bits/in.h", line 69: warning: declaration of a member with the
DX> > DX> > DX> same name as its class
DX> > DX> > DX> char ip_opts[40]; /* Actually variable in size. */
DX> > DX> > DX> ^
DX> > DX> > DX>
DX> > DX> > DX> C++ prelinker: executing: /usr/pgi/linux86/bin/pgCC
DX> > DX> > DX> -I/home/dong/NAMD_2.6_Source/charm-5.9/mpi-linux/include -DCMC
DX> > DX> > DX> "/usr/include/bits/in.h", line 69: warning: declaration of a member with the
DX> > DX> > DX> same name as its class
DX> > DX> > DX> char ip_opts[40]; /* Actually variable in size. */
DX> > DX> > DX> ^
DX> > DX> > DX>
DX> > DX> > DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclUnixPipe.o): In function
DX> > DX> > DX> `TclpCreateTempFile':
DX> > DX> > DX> tclUnixPipe.o(.text+0xe2): the use of `tmpnam' is dangerous, better
DX> > DX> > DX> use `mkstemp'
DX> > DX> > DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclBinary.o): In function `.L174':
DX> > DX> > DX> tclBinary.o(.text+0xa4f): undefined reference to `__ctype_b_loc'
DX> > DX> > DX> tclBinary.o(.text+0xad2): undefined reference to `__ctype_b_loc'
DX> > DX> > DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclBinary.o): In function `GetFormatSpec':
DX> > DX> > DX> tclBinary.o(.text+0x1377): undefined reference to `__ctype_b_loc'
DX> > DX> > DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclCmdAH.o): In function `Tcl_CaseObjCmd':
DX> > DX> > DX> tclCmdAH.o(.text+0x16d): undefined reference to `__ctype_b_loc'
DX> > DX> > DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclCmdAH.o): In function `Tcl_FormatObjCmd':
DX> > DX> > DX> tclCmdAH.o(.text+0x233c): undefined reference to `__ctype_b_loc'
DX> > DX> > DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x2427): more
DX> > DX> > DX> undefined references to `__ctype_b_loc' follow
DX> > DX> > DX> Fatal Error by charmc in directory /home/dong/NAMD_2.6_Source/Linux-i686-pgCC
DX> > DX> > DX> Command mpiCC -L/home/dong/namd_lib/lib -L/home/dong/tcl/lib
DX> > DX> > DX> -L/home/dong/namd_lib/lib -L/home/dong/fftw/lib -2
DX> > DX> > DX> charmc exiting...
DX> > DX> > DX> rm -f moduleinit14691.C moduleinit14691.o
DX> > DX> > DX> make: *** [namd2] Error 1
DX> > DX> > DX>
DX> > DX> >
DX> > DX> > --
DX> > DX> > =======================================================================
DX> > DX> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
DX> > DX> > Center for Molecular Modeling -- University of Pennsylvania
DX> > DX> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
DX> > DX> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
DX> > DX> > =======================================================================
DX> > DX> > If you make something idiot-proof, the universe creates a better idiot.
DX> > DX> >
DX> > DX>
DX> >
DX> > --
DX> > =======================================================================
DX> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
DX> > Center for Molecular Modeling -- University of Pennsylvania
DX> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
DX> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
DX> > =======================================================================
DX> > If you make something idiot-proof, the universe creates a better idiot.
DX> >
DX>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

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