Re: namd 2.5 compilation error

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Mon Sep 29 2008 - 12:15:07 CDT

On Sun, Sep 28, 2008 at 11:27 AM, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Sat, 27 Sep 2008, Dong Xu wrote:
>
> DX> Hi,
> DX>
> DX> I was trying to compile namd 2.6 with myrinet mpich-gm and pgi
> DX> compiler. I managed to get charmm++ compile ok and passed megatest.
>
> trying to compile NAMD with PGI compilers is a "very bad idea(TM)".
> the PGI c++ compilers are very problematic. you'd be _much_ better
> off using GCC.

Hi Alex, the problem is that the system installed mpicc mpiCC mpirun
etc. are all compiled with pgi compilers. Would it work if I compile
namd using gcc? The gcc version is 2.95, I'm not sure if it's too
outdated?
>
> DX>
> DX> When I compile namd using Linux-i686-pgCC.arch, I got the following
> DX> error. Looks like there are some issues with tcl library libtcl8.3.a.
>
> it looks like the tcl library has been compiled with a gcc that
> was newer than the gcc that the pgi compiler runtime was compiled with.
> you need to recompiled the tcl library with your pgi or better yet
> compile NAMD with gcc/g++.

Yes, I also realized that I need to recompile tcol if non-gcc
compilers are used.

Thanks!

-DX

> DX>
> DX> Any help will be highly appreciated.
> DX>
> DX> -DX
> DX>
> DX> charmc> ----------- Module dependency search ------------
> DX> charmc> ----------- Module dependency search complete ------------
> DX> Adding registration for module NeighborLB
> DX> Adding registration for module commlib
> DX> charmc: Executing mpiCC -D__CHARMC__=1 -c moduleinit14691.C -o moduleinit14691.o
> DX> charmc: Executing mpiCC -L/home/dong/namd_lib/lib -L/home/dong/tcl/lib
> DX> -L/home/dong/namd_lib/lib -L/home/dong/fftm
> DX> C++ prelinker: executing: /usr/pgi/linux86/bin/pgCC
> DX> -I/home/dong/NAMD_2.6_Source/charm-5.9/mpi-linux/include -DCMC
> DX> "/usr/include/bits/in.h", line 69: warning: declaration of a member with the
> DX> same name as its class
> DX> char ip_opts[40]; /* Actually variable in size. */
> DX> ^
> DX>
> DX> C++ prelinker: executing: /usr/pgi/linux86/bin/pgCC
> DX> -I/home/dong/NAMD_2.6_Source/charm-5.9/mpi-linux/include -DCMC
> DX> "/usr/include/bits/in.h", line 69: warning: declaration of a member with the
> DX> same name as its class
> DX> char ip_opts[40]; /* Actually variable in size. */
> DX> ^
> DX>
> DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclUnixPipe.o): In function
> DX> `TclpCreateTempFile':
> DX> tclUnixPipe.o(.text+0xe2): the use of `tmpnam' is dangerous, better
> DX> use `mkstemp'
> DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclBinary.o): In function `.L174':
> DX> tclBinary.o(.text+0xa4f): undefined reference to `__ctype_b_loc'
> DX> tclBinary.o(.text+0xad2): undefined reference to `__ctype_b_loc'
> DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclBinary.o): In function `GetFormatSpec':
> DX> tclBinary.o(.text+0x1377): undefined reference to `__ctype_b_loc'
> DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclCmdAH.o): In function `Tcl_CaseObjCmd':
> DX> tclCmdAH.o(.text+0x16d): undefined reference to `__ctype_b_loc'
> DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclCmdAH.o): In function `Tcl_FormatObjCmd':
> DX> tclCmdAH.o(.text+0x233c): undefined reference to `__ctype_b_loc'
> DX> /home/dong/namd_lib/lib/libtcl8.3.a(tclCmdAH.o)(.text+0x2427): more
> DX> undefined references to `__ctype_b_loc' follow
> DX> Fatal Error by charmc in directory /home/dong/NAMD_2.6_Source/Linux-i686-pgCC
> DX> Command mpiCC -L/home/dong/namd_lib/lib -L/home/dong/tcl/lib
> DX> -L/home/dong/namd_lib/lib -L/home/dong/fftw/lib -2
> DX> charmc exiting...
> DX> rm -f moduleinit14691.C moduleinit14691.o
> DX> make: *** [namd2] Error 1
> 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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