Re: namd 2.5 compilation error

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Sep 28 2008 - 13:27:38 CDT

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.

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++.

cheers,
   axel.

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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