**From:** Axel Kohlmeyer (*akohlmey_at_cmm.chem.upenn.edu*)

**Date:** Mon Sep 29 2008 - 14:45:44 CDT

**Next message:**David Tanner: "Re: Cyclopeptide: connectivity between the first and last residues"**Previous message:**Dong Xu: "Re: namd 2.5 compilation error"**In reply to:**Dong Xu: "Re: namd 2.5 compilation error"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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 outdated?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.

**Next message:**David Tanner: "Re: Cyclopeptide: connectivity between the first and last residues"**Previous message:**Dong Xu: "Re: namd 2.5 compilation error"**In reply to:**Dong Xu: "Re: namd 2.5 compilation error"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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